Fully human DNA binding monoclonal antibodies

Abstract

The present invention includes antibodies and antigen-binding fragments thereof that specifically bind a double-stranded deoxyribonucleic acid (DNA) strand. Polynucleotides encoding an antibody or an antigen-binding fragment, vectors, and host cells that comprise a polynucleotide and pharmaceutical compositions are also included in this invention. Also described herein are methods of using the presently disclosed antibodies, antigen-binding fragments, polynucleotides, vectors, host cells, and compositions to diagnose, prevent or treat a DNA virus infection.

Description

FULLY HUMAN DNA BINDING MONOCLONAL ANTIBODIESCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a non-provisional patent application of and claims priority to U.S. provisional patent application serial number 63 / 601,444 filed on November 22, 2023, the contents of which are incorporated by reference in its entirety.TECHNICAL FIELD OF THE INVENTION

[0002] The present invention relates in general to the field of full length, fully human monoclonal antibodies, and more particularly, to human monoclonal antibodies to DNA.STATEMENT OF FEDERALLY FUNDED RESEARCH

[0003] This invention was made with government support under N01AI50026 awarded by the National Institutes of Health. The government has certain rights in the invention.INCORPORATION-BY-REFERENCE OF MATERIALS FILED ON COMPACT DISC

[0004] The present application includes a Sequence Listing that has been submitted electronically in .XML format and is hereby incorporated by reference in its entirety. Said .XML copy, created on November 20, 2024, is named “OMRF 1040. XML” and is 148,190 bytes in size. The sequence listing contained in this .XML file is part of the specification and is hereby incorporated by reference herein in its entirety.BACKGROUND OF THE INVENTION

[0005] Without limiting the scope of the invention, its background is described in connection with broadly specific full-length, fully human monoclonal antibodies against DNA.

[0006] One such antibody is taught in U.S. Patent No. 9,701,740, issued to Hansen, et al, and entitled, “Cell-penetrating anti-DNA antibodies and uses thereof inhibit DNA repair”. These inventors are said to teach antibodies that penetrate cell nuclei and inhibit DNA repair or interfere with DNA metabolism and are provided for treatment of cancer (both directly and by sensitizing cancer cells to DNA-damaging treatments) or inhibiting or preventing viral infection, proliferation, or metabolism. The antibodies are used in a method that involves treating cells with a composition containing cellpenetrating anti-DNA antibodies or derivatives thereof, alone or in combination with treatment that induces DNA damage such as DNA-damaging chemotherapy or radiation. The impact of the cell-penetrating anti-DNA antibodies or derivatives thereof is potentiated in cancer cells that are deficient in DNA repair, and the cell-penetrating anti-DNA antibodies or derivatives thereof are synthetically lethal to cancer cells with DNA repair deficiencies.

[0007] Despite these advances, a need remains for novel anti-DNA antibodies.SUMMARY OF THE INVENTION

[0008] As embodied and broadly described herein, an aspect of the present disclosure relates to an antibody (Ab), an antigen (Ag)-binding fragment, a single chain, a bivalent, or a multivalent antibody capable of binding to a double- stranded deoxyribonucleic acid (DNA) strand comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively. In one aspect, the Ab or fragment thereof is a human Ab or a human Ag-binding fragment. In another aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39. In another aspect, at least one of: the Ab, Ab fragment, single chain, bivalent, or multivalent antibody neutralizes a DNA virus infection: (i) in an in vitro model of infection; (ii) in an in vivo animal model of infection; (iii) in a human; or (iv) any combination of (i)-(iii); or further comprising a second agent as a fusion protein, or conjugated to the Ab, Ab fragment, single chain, bivalent, or multivalent antibody. In another aspect, the Ab or fragment thereof comprises a monoclonal Ab, a single chain Ab, a Fab, a Fab’, an F(ab’)2, an Fv, an scFv, or a scFab. In another aspect, the Ab, single chain, bivalent, or multivalent antibody is an IgGl, IgG2, IgG3, IgG4, IgAl, IgA2, IgM, IgE, or IgD isotype. In another aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a hybridoma or engineered cell comprising a polynucleotide encoding the Ab, binding fragment, single chain, bivalent, or multivalent antibody described hereinabove. In another aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a nucleic acid moleculeencoding the Ab or fragment. In another aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a vector comprising the nucleic acid molecule. In another aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a host cell comprising the vector. In another aspect, the antibody is prepared by a method comprising: obtaining the host cell; culturing the host cell in a medium under conditions permitting expression of the Ab, binding fragment, single chain, bivalent, or multivalent antibody encoded by the vector; and purifying the Ab, binding fragment, single chain, bivalent, or multivalent antibody thereof from the cultured cell or a medium thereof. In another aspect, the antibody further comprises a pharmaceutically acceptable carrier or excipient. In another aspect, the antibody further comprises a second therapeutic agent, wherein the second therapeutic agent is selected from the group consisting of: an antiinflammatory agent, or an anti-viral agent.

[0009] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of treating a mammalian or human subject infected with a DNA virus or preventing infection of the DNA virus in a subject at risk of infection with the DNA virus comprising administering to a subject in need thereof a therapeutically effective amount of a Ab, binding fragment, single chain, bivalent, or multivalent antibody specific to DNA and having antibody comprises the amino acid sequences of the following three VH CDRs: SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33; and comprises the amino acid sequences of the following three VL CDRs SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38. In one aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody capable of binding to DNA comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively. In another aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39.

[0010] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of detecting DNA in a mammalian or human subject comprising the steps of: (a) contacting a sample from the subject suspected of having DNA; and (b) detecting binding of a Ab, binding fragment, single chain, bivalent, or multivalent antibody to DNA in the sample, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody is capable of binding to DNA comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively. In another aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39. sample is selected from a nasopharyngeal swab, a nares swab, saliva, urine, tears, cerebrospinal fluid, amniotic fluid, serum, plasma, whole blood, bronchopulmonary lavage, vaginal sampling and a rectal / stool sampling obtained from the subject. In another aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39. Ab, binding fragment, single chain, bivalent, or multivalent antibody is conjugated to at least one of: a nanoparticle, a liposome, or a detectable label, and wherein the detectable label comprises a radioactive tag, a fluorescent tag, a biological, or an enzymatic tag.

[0011] As embodied and broadly described herein, an aspect of the present disclosure relates to a kit for the detection of DNA in a subject comprising: (a) an Ab, binding fragment, single chain, bivalent, or multivalent antibody capable of binding to the DNA, (b) a suitable container, and (c) an immunodetection reagent, wherein the Ab or Ag-binding fragment capable of binding to the DNAcomprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively. In one aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39. at least one of: the Ab, binding fragment, single chain, bivalent, or multivalent antibody are affixed to a support selected from one or more beads, a dipstick, a filter, a membrane, a plate, a chip, or a column matrix; the immunodetection reagent comprises at least a second Ab that binds an immunocomplex formed when the Ab, binding fragment, single chain, bivalent, or multivalent antibody binds DNA; the kit further comprises DNA for use as a standard; or wherein at least one of the Ab, binding fragment, single chain, bivalent, or multivalent antibody, or the immunodetection reagent are linked to a detectable label, and the detectable label comprises a radioactive tag, a fluorescent tag, a biological, or an enzymatic tag.

[0012] As embodied and broadly described herein, an aspect of the present disclosure relates to an isolated nucleic acid molecule, a group of isolated nucleic acid molecules, or a vector encoding an antibody, binding fragment, single-chain, bivalent, or multivalent antibody comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively; a VH sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO.: 5, 15, 25, or 35; and a VL sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO.: 10, 20, 30, or 40; or the single-chain, bivalent, or multivalent antibody encoding nucleic acid sequence that comprises: a VH sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 99%, or 100% identity to SEQ ID NO.: 5, 15, 25, or 35; and a VLsequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 99%, or 100% identity to SEQ ID NO.: 10, 20, 30, or 40.

[0013] As embodied and broadly described herein, an aspect of the present disclosure relates to an isolated host cell comprising the nucleic acid molecule, the group of isolated nucleic acid molecules, or the vector disclosed herein.BRIEF DESCRIPTION OF THE DRAWINGS

[0014] For a more complete understanding of the features and advantages of the present invention, reference is now made to the detailed description of the invention along with the accompanying figures and in which:

[0015] FIG. 1 is a graph that shows the DNA binding of the anti-DNA antibodies of the present invention, (1) blank, (2) Positive Control, (3) Antibody 1, (4) Antibody 2, (5) Antibody 3, and (6) Antibody 4.DETAILED DESCRIPTION OF THE INVENTION

[0016] While the making and using of various embodiments of the present invention are discussed in detail below, it should be appreciated that the present invention provides many applicable inventive concepts that can be embodied in a wide variety of specific contexts. The specific embodiments discussed herein are merely illustrative of specific ways to make and use the invention and do not delimit the scope of the invention.

[0017] To facilitate the understanding of this invention, a number of terms are defined below. Terms defined herein have meanings as commonly understood by a person of ordinary skill in the areas relevant to the present invention. Terms such as “a”, “an” and “the” are not intended to refer to only a singular entity, but include the general class of which a specific example may be used for illustration. The terminology herein is used to describe specific embodiments of the invention, but their usage does not delimit the invention, except as outlined in the claims.

[0018] The present invention relates to novel monoclonal antibodies (Mabs) that bind to doublestranded deoxyribonucleic acid (DNA) strands. The present invention provides such Mabs and Ab fragments thereof, which are useful for detection or prevention and / or treatment of DNA viruses. The present invention also provides a pharmaceutical composition comprising the novel Mabs or Ab fragments thereof. In addition, the present invention provides a kit and method for detecting DNAand a method for preventing or treating DNA viruses, using the novel Mabs or Ab fragments thereof as described herein.

[0019] As used herein, the term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally, occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, y-carboxyglutamate, and O-phosphoserine. Amino acid analogs refer to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a-carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.

[0020] As used herein, “antibody” or “antigen-binding fragment” refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen (Ag) binding portion that immunospecifically binds a glycoprotein. As such, the term antibody (Ab) encompasses not only whole Ab molecules, but also Ab fragments as well as variants (including derivatives) of Abs and Ab fragments. In natural Abs, two heavy chains are linked to each other by disulfide bonds and each heavy chain is linked to a light chain by a disulfide bond. There are two types of light chain, lambda (1) and kappa (k). Five main heavy chain classes (or isotypes) determine the functional activity of an Ab molecule: IgM, IgD, IgG, IgA and IgE. Each chain contains distinct sequence domains. Modified versions of each of these classes and isotypes are readily discernable to the skilled artisan in view of the instant disclosure and, accordingly, are within the scope of the instant disclosure. All immunoglobulin classes are clearly within the scope of the present disclosure, the following discussion will generally be directed to the IgG class of immunoglobulin molecules. With regard to IgG, a standard immunoglobulin molecule comprises two identical light chain polypeptides of molecular weight approximately 23,000 Daltons, and two identical heavy chain polypeptides of molecular weight 53,000-70,000.

[0021] The light chain includes two domains, a variable domain (VL) and a constant domain (CL). The heavy chain includes four domains, a variable domain (VH) and three constant domains (CHI,CH2 and CH3, collectively referred to as CH). The variable regions of both light (VL) and heavy (VH) chains determine binding recognition and specificity to the Ag. The light and heavy chains of an Ab each have three complementarity determining regions (CDRs), designated LCDR1, LCDR2, LCDR3 and HCDR1, HCDR2, HCDR3, respectively. An Ag-binding site, therefore, includes six CDRs, comprising the CDR set from each of a heavy and a light chain variable region. Framework Regions (FRs) refer to amino acid sequences interposed between CDRs.

[0022] Non-limiting examples of antigen-binding fragments include: (i) Fab fragments; (ii) F(ab')2 fragments; (iii) Fd fragments; (iv) Fv fragments; (v) single-chain Fv (scFv) molecules; (vi) dAb fragments; and (vii) minimal recognition units consisting of the amino acid residues that mimic the hypervariable region of an antibody (e.g., an isolated complementarity determining region (CDR) such as a CDR3 peptide), or a constrained FR3-CDR3-FR4 peptide. Other engineered molecules, such as domain-specific antibodies, single domain antibodies, domain-deleted antibodies, chimeric antibodies, CDR-grafted antibodies, diabodies, triabodies, tetrabodies, minibodies, nanobodies (e.g., monovalent nanobodies, bivalent nanobodies, etc.), small modular immunopharmaceuticals (SMIPs), and shark variable IgNAR domains, are also encompassed within the expression “antigen-binding fragment,” as used herein.

[0023] An antigen-binding fragment of an antibody will typically comprise at least one variable domain. The variable domain may be of any size or amino acid composition and will generally comprise at least one CDR which is adjacent to or in frame with one or more framework sequences. In antigen-binding fragments having a VH domain associated with a VL domain, the VH and VL domains may be situated relative to one another in any suitable arrangement. For example, the variable region may be dimeric and contain VH-VH, VH-Vror VL-VL dimers. Alternatively, the antigen-binding fragment of an antibody may contain a monomeric VH or VL domain. In certain embodiments, an Ab or Ag-binding fragment of the present disclosure specifically binds to a double-stranded deoxyribonucleic acid (DNA) strand.

[0024] As used herein, the term “antigen” or “Ag”, as used herein, refers to an immunogenic molecule that provokes an immune response. This immune response may involve Ab production, activation of specific immunologically-competent cells, activation of complement, Ab-dependent cytotoxicicity, or any combination thereof. An antigen (Ag-immunogenic molecule) is a double-stranded deoxyribonucleic acid (DNA) strand. It is readily apparent that an Ag can be synthesized, produced recombinantly, or derived from a biological sample. Exemplary biological samples that can containone or more Ags include tissue samples, stool samples, cells, biological fluids, or combinations thereof. Ags can be produced by cells that have been modified or genetically engineered to express an Ag. Ags can also be present in a virion, or expressed or presented on the surface of a cell infected by a DNA virus.

[0025] As used herein, the phrase “bispecific antibody”, “bivalent antibody” includes an antibody (Ab) capable of selectively binding two epitopes, and “multivalent” to two or more epitopes. Bispecific Abs include fragments of two different monoclonal Abs and generally comprise two nonidentical heavy chains derived from the two different monoclonal Abs, with each heavy chain specifically binding a different epitope - either on two different molecules (e.g., different epitopes on two different immunogens) or on the same molecule. Bispecific Abs can be made, for example, by combining heavy chains that recognize different epitopes of the same or different immunogen. For example, nucleic acid sequences encoding heavy chain variable sequences that recognize different epitopes of the same or different immunogen can be fused to nucleic acid sequences encoding the same or different heavy chain constant regions, and such sequences can be expressed in a cell that expresses an immunoglobulin light chain. A typical bispecific Ab has two heavy chains each having three heavy chain CDRs, followed by (N-terminal to C-terminal) a CHI domain, a hinge, a CH2 domain, and a CH3 domain, and an immunoglobulin light chain that either does not confer epitopebinding specificity but that can associate with each heavy chain, or that can associate with each heavy chain and that can bind one or more of the epitopes bound by the heavy chain epitope-binding regions, or that can associate with each heavy chain and enable binding or one or both of the heavy chains to one or both epitopes.

[0026] As used herein, the term “epitope” or “antigenic epitope” includes any molecule, structure, amino acid sequence, or protein determinant that is recognized and specifically bound by a cognate binding molecule, such as an immunoglobulin, or other binding molecule, domain, or protein. Epitopic determinants generally contain chemically active surface groupings of molecules, such as amino acids or sugar side chains, and can have specific three-dimensional structural characteristics, as well as specific charge characteristics. Where an Ag comprises a peptide or protein, the epitope can be comprised of consecutive amino acids (e.g., a linear epitope), or can be comprised of amino acids from different parts or regions of the protein that are brought into proximity by protein folding (e.g., a discontinuous or conformational epitope), or non-contiguous amino acids that are in close proximity irrespective of protein folding.

[0027] As used herein, the term “host” refers to a cell or microorganism targeted for genetic modification with a heterologous nucleic acid molecule to produce a polypeptide of interest (e.g., an antibody of the present disclosure). A host cell may include any individual cell or cell culture which may receive a vector or the incorporation of nucleic acids or express proteins. The term also encompasses progeny of the host cell, whether genetically or phenotypically the same or different. Suitable host cells may depend on the vector and may include mammalian cells, animal cells, human cells, simian cells, insect cells, yeast cells, and bacterial cells. These cells may be induced to incorporate the vector or other material by use of a viral vector, transformation via calcium phosphate precipitation, DEAE-dextran, electroporation, microinjection, or other methods. See, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual 2d ed. (Cold Spring Harbor Laboratory, 1989).

[0028] As used herein, the term “Fab” (fragment antigen binding) refers to the part of an Ab that binds to Ag and includes the variable region and CHI of the heavy chain linked to the light chain via an inter-chain disulfide bond. Each Fab fragment is monovalent with respect to Ag binding, i.e., it has a single Ag-binding site. Pepsin treatment of an Ab yields a single large F(ab')2 fragment that roughly corresponds to two disulfide linked Fab fragments having divalent Ag-binding activity and is still capable of cross-linking Ag. Both the Fab and F(ab')2 are examples of “Ag-binding fragments.” Fab' fragments differ from Fab fragments by having additional few residues at the carboxy terminus of the CHI domain including one or more cysteines from the Ab hinge region. Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab')2 Ab fragments originally were produced as pairs of Fab' fragments that have hinge cysteines between them. Other chemical couplings of Ab fragments are also known. Fab fragments may be joined, e.g., by a peptide linker, to form a single chain Fab, also referred to herein as “scFab.” In these embodiments, an inter-chain disulfide bond that is present in a native Fab may not be present, and the linker serves in full or in part to link or connect the Fab fragments in a single polypeptide chain.

[0029] As used herein, the term “Fv” is a small Ab fragment that contains a complete Ag-recognition and Ag-binding site. This fragment generally consists of a dimer of one heavy- and one light-chain variable region domain in tight, non-covalent association. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an Ag) has the ability to recognize and bind Ag, although typically at a lower affinity than the entire binding site.

[0030] As used herein, the term “single-chain Fv” also abbreviated as “sFv” or “scFv”, are Ab fragments that comprise the VH and VL antibody domains connected into a single polypeptide chain. In some embodiments, the scFv polypeptide comprises a polypeptide linker disposed between and linking the VH and VL domains that enables the scFv to retain or form the desired structure for Ag binding. Such a peptide linker can be incorporated into a fusion polypeptide using standard techniques well known in the art. Additionally or alternatively, Fv can have a disulfide bond formed between and stabilizing the VH and the VL. For a review of scFv, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer- Verlag, New York, pp. 269- 315 (1994); Borrebaeck 1995, infra. In certain embodiments, the Ab or Ag-binding fragment comprises a scFv comprising a VH domain, a VL domain, and a peptide linker linking the VH domain to the VL domain. In particular embodiments, a scFv comprises a VH domain linked to a VL domain by a peptide linker, which can be in a VH-linker-VL orientation or in a VL-linker-VH orientation. Any scFv of the present disclosure may be engineered so that the C-terminal end of the VL domain is linked by a short peptide sequence to the N-terminal end of the VH domain, or vice versa (i.e., (N)VL(C)-linker-(N)VH(C) or (N)VH(C)-linker-(N)VL(C). Alternatively, in some embodiments, a linker may be linked to an N-terminal portion or end of the VH domain, the VL domain, or both. scFv can be constructed using any combination of the VH and VL sequences or any combination of the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences disclosed herein.

[0031] As used herein, a “monoclonal antibody” refers to an Ab obtained from a population of substantially homogeneous Abs, e.g., the individual Abs comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts. In contrast to polyclonal Ab preparations, which typically include different Abs directed against different determinants (epitopes), each monoclonal Ab is directed against a single determinant on the Ag (epitope). The modifier “monoclonal” indicates the character of the Ab as being obtained from a substantially homogeneous population of Abs, and is not to be construed as requiring production of the Ab by any particular method. For example, the monoclonal Abs to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler and Milstein, 1975, Nature, 256:495, or may be made by recombinant DNA methods such as described in U.S. Pat. No. 4,816,567. The monoclonal Abs may also be isolated from phage libraries generated using the techniques described in McCafferty et al., 1990, Nature, 348:552-554, for example. Other methods are known in the art and are contemplated for use herein.

[0032] As used herein, the term “neutralizing antibody” is an Ab that can neutralize, i.e., prevent, inhibit, reduce, impede, or interfere with, the ability of a pathogen to initiate and / or perpetuate an infection in a host. The terms “neutralizing Ab” and “an Ab that neutralizes” or “Abs that neutralize” are used interchangeably herein. In any of the presently disclosed embodiments, the Ab or Ag-binding fragment is capable of preventing and / or neutralizing a DNA virus infection in an in vitro model of infection and / or in an in vivo animal model of infection and / or in a human.

[0033] As used herein, the terms “nucleic acid molecule” or “polynucleotide” or “polynucleic acid” refers to a polymeric compound including covalently linked nucleotides, which can be made up of natural subunits (e.g., purine or pyrimidine bases) or non-natural subunits (e.g., morpholine ring). Purine bases include adenine, guanine, hypoxanthine, and xanthine, and pyrimidine bases include uracil, thymine, and cytosine. Nucleic acid molecules include polyribonucleic acid (RNA), which includes mRNA, microRNA, siRNA, viral genomic RNA, and synthetic RNA, and polydeoxyribonucleic acid (DNA), which includes cDNA, genomic DNA, and synthetic DNA, either of which may be single or double-stranded. If single-stranded, the nucleic acid molecule may be the coding strand or non-coding (anti-sense) strand. A nucleic acid molecule encoding an amino acid sequence includes all nucleotide sequences that encode the same amino acid sequence. Some versions of the nucleotide sequences may also include intron(s) to the extent that the intron(s) would be removed through co- or post-transcriptional mechanisms. In other words, different nucleotide sequences may encode the same amino acid sequence as the result of the redundancy or degeneracy of the genetic code, or by splicing.

[0034] Variants of nucleic acid molecules of this disclosure are also contemplated. Variant nucleic acid molecules are at least 70%, 75%, 80%, 85%, 90%, and are preferably 95%, 96%, 97%, 98%, 99%, or 99.9% identical a nucleic acid molecule of a defined or reference polynucleotide as described herein, or that hybridize to a polynucleotide under stringent hybridization conditions of 0.015M sodium chloride, 0.0015M sodium citrate at about 65-68° C. or 0.015M sodium chloride, 0.0015M sodium citrate, and 50% formamide at about 42° C. Nucleic acid molecule variants retain the capacity to encode a binding domain thereof having a functionality described herein, such as binding a target molecule.

[0035] As used herein, the term “percent sequence identity” refers to a relationship between two or more sequences, as determined by comparing the sequences. Preferred methods to determine sequence identity are designed to give the best match between the sequences being compared. Forexample, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment). Further, non-homologous sequences may be disregarded for comparison purposes. The percent sequence identity referenced herein is calculated over the length of the reference sequence, unless indicated otherwise. Methods to determine sequence identity and similarity can be found in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using a BLAST program (e.g., BLAST 2.0, BLASTP, BLASTN, orBLASTX). The mathematical algorithm used in the BLAST programs can be found in Altschul et al., Nucleic Acids Res. 25:3389-3402, 1997. Within the context of this disclosure, it will be understood that where sequence analysis software is used for analysis, the results of the analysis are based on the “default values” of the program referenced. “Default values” mean any set of values or parameters which originally load with the software when first initialized.

[0036] As used herein, the term “pharmaceutical composition” comprises the combination of an active agent, such as any one or more of the presently disclosed Abs, Ag-binding fragments, polynucleotides, peptides, vectors, or host cells, singly or in any combination, and can further comprise a pharmaceutically acceptable carrier, excipient, or diluent, inert or active, in a sterile composition suitable for diagnostic or therapeutic use in vitro, in vivo or ex vivo. Carriers, excipients, and diluents are discussed in further detail herein. Such compositions comprising the disclosed Ab, Ag-binding fragment, polynucleotide, vector, host cell, peptides, or composition of the present disclosure may also be administered simultaneously with, prior to, or after administration of one or more other therapeutic agents such as anti-viral or anti-inflammatory agents.

[0037] As used herein, the terms “pharmaceutically acceptable carrier” or “pharmaceutical acceptable excipient” includes any material which, when combined with an active ingredient, allows the ingredient to retain biological activity and is non-reactive with the subject's immune system. This further includes materials from such compounds that are appropriate for use in pharmaceutical contexts, i.e., materials which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit / risk ratio. Examples include, but are not limited to, any of the standard pharmaceutical carriers such as a phosphate buffered saline solution, water, emulsions such as oil / water emulsion, and various types of wetting agents. Preferred diluents for aerosol or parenteral administration are phosphate buffered saline or normal (0.9%) saline.Compositions comprising such carriers are formulated by well-known conventional methods (see, for example, Remington's Pharmaceutical Sciences, 18th edition, A. Gennaro, Ed., Mack Publishing Co., Easton, Pa., 1990; and Remington, The Science and Practice of Pharmacy 20th Ed. Mack Publishing, 2000).

[0038] As used herein, the terms “protein” or “polypeptide” refers to a polymer of amino acid residues. Proteins apply to naturally occurring amino acid polymers, as well as to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, and non-naturally occurring amino acid polymers. Variants of proteins, peptides, and polypeptides of this disclosure are also contemplated. In certain embodiments, variant proteins, peptides, and polypeptides comprise or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.9% identical to an amino acid sequence of a defined or reference amino acid sequence as described herein.

[0039] As used herein, the term “specifically binds” refers to an association or union of an antibody or antigen-binding fragment to an antigen with an affinity or Ka(i.e., an equilibrium association constant of a particular binding interaction with units of 1 / M) equal to or greater than 105M1(which equals the ratio of the on-rate [Kon] to the off rate [Koir] for this association reaction), while not significantly associating or uniting with any other molecules or components in a sample. Alternatively, affinity may be defined as an equilibrium dissociation constant (Kd) of a particular binding interaction with units of M (e.g., 105M to 1013M). Antibodies may be classified as “high- affinity” antibodies or as “low-affinity” antibodies. “High-affinity” antibodies refer to those antibodies having a Kaof at least 107M at least I OXM at least IO9M at least 10'° M at least 1011M ', at least 10l 2M ’, or at least 1013M “Low-affinity” antibodies refer to those antibodies having a Kaof up to 107M ', up to I O6M ', up to IO7M Alternatively, affinity may be defined as an equilibrium dissociation constant (Ka) of a particular binding interaction with units of M (e.g., 107M to 10l 3M).

[0040] In some contexts, Ab and Ag-binding fragments may be described with reference to affinity and / or to avidity for antigen. Unless otherwise indicated, avidity refers to the total binding strength of an Ab or Ag-binding fragment thereof to Ag, and reflects binding affinity, valency of the Ab or antigen-binding fragment (e.g., whether the antibody or antigen-binding fragment comprises one, two, three, four, five, six, seven, eight, nine, ten, or more binding sites), and, for example, whether anotheragent is present that can affect the binding (e.g., a non-competitive inhibitor of the antibody or antigen-binding fragment).

[0041] As used herein, the phrases “therapeutically effective amount” and “therapeutic level” mean that drug dosage or plasma concentration in a subject, respectively, that provides the specific pharmacological effect for which the drug is administered in a subject in need of such treatment, i.e., to reduce, ameliorate, or eliminate the symptoms or effects of infection with a DNA virus. It is emphasized that a therapeutically effective amount or therapeutic amount of an antibody will not always be effective in treating the conditions / diseases described herein, even though such dosage is deemed to be a therapeutically effective amount by those of skill in the art. The therapeutically effective amount may vary based on the route of administration and dosage form, the age and weight of the subject, and / or the subject’s condition, including DNA virus variants and severity of the infection, among other factors. The human subject treated according to the present disclosure include an infant, a child, a young adult, an adult of middle age, or an elderly person. The human subject treated according to the present disclosure include those less than 1 year old, or those 1 to 5 years old, or those between 5 and 125 years old (e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, or 125 years old, including any and all ages therein or there between). The human subject treated includes male and female.

[0042] As used herein, the terms “treat”, “treating”, and “treatment” refer to therapeutic or preventative measures described herein. The methods of “treatment” employ the administration of an Ab to a subject having a disease or disorder, or predisposed to having such a disease or disorder, in order to prevent, cure, delay, reduce the severity of, or ameliorate, partially or completely alleviate one or more symptoms of the disease or disorder or recurring disease or disorder, or in order to prolong the survival of a subject beyond that expected in the absence of such treatment. Treatment may be administered to a subject who does not exhibit signs of a disease, disorder, and / or condition or to a subject who exhibits only early signs of the disease, disorder, and / or condition, for example, for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, and / or condition.

[0043] As used herein, the terms “vector” or “expression vector” refers to a DNA construct containing a nucleic acid molecule that is operably linked to a suitable control sequence capable of effecting the expression of the nucleic acid molecule in a suitable host. Such control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequenceencoding suitable mRNA ribosome binding sites, and sequences that control termination of transcription and translation. The vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert. Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself or deliver the polynucleotide contained in the vector into the genome without the vector sequence. In the present specification, “plasmid,” “expression plasmid,” “virus,” and “vector” are often used interchangeably.

[0044] General Methods for monoclonal antibody production: It will be understood that monoclonal Abs binding to double-stranded deoxyribonucleic acid (DNA) strands will have utility in several applications. These include the production of diagnostic kits for use in detecting and diagnosing disease. In these contexts, one may link such Abs to diagnostic or therapeutic agents, or use them as capture agents or competitors in competitive assays. Means for preparing and characterizing Abs are well known in the art (see, e.g., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; U.S. Patent 4,196,265).

[0045] The methods for generating monoclonal antibodies (Mabs) generally begin along the same lines as those for preparing polyclonal Abs. The first step for both these methods is immunization of an appropriate host or identification of subjects who are immune due to prior natural infection. In the case of human monoclonal Abs, one may instead simply look for an individual already known to have generated an immune response, in this case, to have been exposed to a DNA virus, or others.

[0046] Monoclonal Abs useful in the present invention may be prepared by the hybridoma methodology first described by Kohler et al., Nature 256:495 (1975), or may be made using recombinant DNA methods in bacterial, eukaryotic animal, or plant cells (see, e g., U.S. Pat. No. 4,816,567). Monoclonal Abs may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991), for example. Monoclonal Abs may also be obtained using methods disclosed in PCT Publication No. WO 2004 / 076677A2, relevant portions incorporated herein by reference.

[0047] It also is contemplated that a molecular cloning approach may be used to generate monoclonal Abs. For this, RNA can be isolated from the hybridoma line and the antibody genes obtained by RT- PCR and cloned into an immunoglobulin expression vector. Alternatively, combinatorial immunoglobulin phagemid libraries are prepared from RNA isolated from the cell lines and phagemids expressing appropriate antibodies are selected by panning using viral antigens. Theadvantages of this approach over conventional hybridoma techniques are that approximately 104times as many antibodies can be produced and screened in a single round, and that new specificities are generated by H and L chain combination which further increases the chance of finding appropriate antibodies.

[0048] Other U.S. patents, each incorporated herein by reference, that teach the production of antibodies useful in the present invention include: U.S. Patent 5,565,332, which describes the production of chimeric antibodies using a combinatorial approach; U.S. Patent 4,816,567 which describes recombinant immunoglobulin preparations; U.S. Patent 4,867,973 which describes antibody -therapeutic agent conjugates; and U.S. Patent 8,563,305 which describes methods for rapidly producing monoclonal antibodies.

[0049] Lymphoprep and B-Cell Enrichment1. Collect blood 7 days post-vaccination into acid citric dextrose blood collection tubes (typically one for ELISpot, four for sort, 40-50 ml of blood total).2. Add RosetteSep at 2.5 pl / mL to whole blood. Mix well. Best results occur if the lymphoprep is begun immediately after collection of the blood but may be done within 18 h of collection. If necessary store blood overnight, store as whole blood at 4° C. and perform lymphoprep immediately prior to staining and cell sorting. The antibody-secreting cells (ASCs) can become unstable and die when removed from whole blood and stored overnight or when frozen.3. Incubate at room temperature (20-25° C.) for 20 min.4. Dilute the blood with an equal volume of PBS.5. Add 15 ml of LSM to a separate 50-ml conical tube. Carefully layer diluted blood over the LSM. Layer no more than 30 ml of diluted blood over 15 ml of LSM. Use multiple tubes if necessary.6. Centrifuge for 30 min at 800 g at room temperature with no brake.7. After centrifugation, the enriched PBMCs will form a band at the interface between the serum and the LSM. Remove this band with a Pasteur pipette and transfer to a new 50-ml centrifuge tube.8. Rinse the enriched PBMCs by diluting to 50 ml with PBS, centrifuge for 5-10 min at 800 g at room temperature with no brake, then remove the supernatant.9. If using more than one tube, combine the cells. Repeat Step 8, decreasing the centrifugation speed to 360 g. Brake may be used.

[0050] Staining and Flow Cytometry10. To ensure that enough ASCs are obtained from the sorting process, begin with 4-8 million of enriched PBMCs prepared in Steps 1-9.11. If the cells appear bloody (i.e., contain significant amounts of red blood cells), clear with ACK buffer (add 1 ml of ACK for 1-2 min). Wash the cells twice with PBS. Filter the cells through a 40-mm cell strainer to remove clumps.12. Resuspend approximately 3 million cells in 100 pl of staining buffer; these are the cells that will be used for sorting. In addition, prepare one aliquot of cells (about 0.5 x 106cells in 100 pl of staining buffer) for each fluorophore to be tested in Step 13 and one aliquot of cells that will remain unstained. These compensation controls will be used to adjust the sensitivity of the flow cytometer detectors to avoid overlap of the emission spectra when the various fluorophores are combined. All buffers for staining should contain 2% FCS (vol / vol) in PBS to block nonspecific staining.13. Add the following antibodies to the aliquot of cells for sorting: CD3 FITC; anti-CD27 PE; anti-CD38 APC-Cy5.5; anti-CD20 FITC; anti-CD19 PE-Alexa Fluor 610; mouse anti-human IgM-biotin and anti-IgG-Alexa 647. In addition, add one of the fluor ophore-conjugated antibodies to each of the compensation control aliquots of cells prepared in Step 12. The specific amounts of each antibody used should be titrated to give distinct single color populations before setting up a new experiment. Appropriate species-specific isotype control antibodies should be used to distinguish specifically stained populations from any background staining that might occur.14. Incubate the cells for 30 min at 4° C.15. Wash twice with 200 pl of 2% FCS in PBS.16. Add 1 :500 Streptavidin PE-Cy7 and incubate for 20 min at 4° C.17. Wash twice again; pass the cells through another cell strainer to avoid clogs in the cytometer.18. ASCs were gated as IgG+ / CD19+ / C D3- / CD20 low / CD27high / CD38high.19. Bulk sort the cells into tubes containing 2% FCS in PBS buffer collecting the cells gated as above.20. Re-sort the cells on forward versus side scatter (live cell gate with doublet discrimination) into single cell PCR plates containing 10 pl of RNase-inhibiting RT-PCR catch buffer. To facilitate the RT-PCR step, sort only into half of the plate and do not put cells in Row H (catch buffer should be added to this row to allow for PCR negative controls). Immediately seal each plate with a microseal foil label and place on dry ice until the cell sorting is finished when plates can be placed in a -80° C. freezer. Use RNase-free precautions for Step 20. As the catch buffer is hypotonic, the cells are lysed, and with immediate freezing, their RNA is protected by the included RNase inhibitor. It is necessary to use multiple buffer controls (row H) because the likelihood of PCR contamination increases substantially with the many cycles of PCR required to amplify the variable genes from single B cells. At this point, the plates may be stored for months to several years if they are immediately flash frozen on dry ice after the collection and kept at -80° C.

[0051] Reverse Transcription, Nested and Cloning PCRs21. Thaw a half-plate of single cells on ice and prepare the RT-PCR master mix following the Bio-Rad iScript cDNA synthesis kit protocol. The program for the PCR machine is also as per the iScript protocol (also see Table 1). Each kit provides enough to process two halfplates. Add 10 pl of master mix to each well (now containing 20 pl of product). RNase-free precautions should be used for this step. When the program is complete, it is best to proceed with the next step (1st PCR, step 22), or immediately store the plate at -20°C until ready to proceed. The protocol here only details the PCRs for IgG heavy chain and Kappa and Lambda light chain, as that is sufficient to amplify most antibodies of interest. However, there is enough master mix to do 5-6 subsequent reactions. These could include IgA and IgM heavy chains if not these are not well discriminated during the FACS sort and / or any other gene of interest (i.e., cytokines).22. For the next PCR step (termed 1st PCR), prepare IgG heavy chain, kappa light chain, and lambda light chain master mixes (see Table 2 for master mixes and Table 3 for primer sequences for steps 22 and 23). Note that doing these simultaneously will require at least 2 PCR machines (the heavy chain program and light chain program are different, however the kappa and lambda mixes from each half plate can be combined onto a full plate and run simultaneously). Add 37 pl of IgG heavy master mix into 48 wells of a fresh 96 well plate. Add 3 pl of cDNA (per well) from step 21 to each well. Similarly add 37 pl of kappa light chain master mix and 3 pl of cDNA (per well) from step 21 and add 37 pl of lambda light chain master mix and 3 pl of cDNA (per well) from step 21. Remember that the 48 kappa and 48 lambda wells can be added to the same 96 well plate. Affix dome cap strip lids to the plate and place in the PCR machines. The PCR machine programs are listed in Table 1. After the program is complete, it is best to immediately run the 2nd PCR, if this is not possible, the plate can be stored at -20°C until ready to proceed.

[0052] Table 1. cDNA Synthesis Program23. For the second PCR step with degenerate V-gene primers (termed 2nd PCR), again prepare IgG heavy chain, kappa light chain, and lambda light chain master mixes (see Table 2 for master mixes and Table 3 for primer sequences for steps 22 and 23). The 2nd PCR program is the same for all three combinations and thus if desired 48 heavy chain and 48 light chain wells can be combined onto the same plate and run in the same PCR machine. For all mixes, add 36 pl of master mix to each well. Then add 4 pl of template from the 1st PCR plate being careful to keep the 48 heavy chain wells and 48 light chain wells distinct. Affix dome cap strip lids to the plate and place in the PCR machines. The PCR machine programs are listed in Table 1.24. When the 2nd PCR program is complete, make a 1% Agarose gel in TAE buffer (large enough for 96 wells). Run 1 pl from each well with the proper loading dye and marker. Positive wells have a band around 400 bp indicating successful amplification of an antibody gene. Wells positive for both a heavy and a light chain are noted for the following steps. We suggest proceeding with the PCR cleanup, but the plate can be frozen at -20°C until ready to proceed if necessary.25. Based on the number of positive wells, one of two methods can be used for the cleanup to prepare for sequencing. Although for a typical experiment, a large number (>70% of total single cells) are positive, occasionally with certain vaccines and certain vaccinees there may only be a few positive cells. If there are only a handful of positive wells, we suggest using a QIAquick PCR purification kit. If there are a large number of positives or you are processing a large number of plates simultaneously, we suggest an ‘entire plate’ ethanol precipitation as described here. Spin the second PCR plate on a swinging plate base at 800 rpm for 30 seconds. Add 75 pl of freshly made ethanol / 0. 12M sodium acetate to each well. This solution is made with a stock solution of 3M sodium acetate at pH 4.5 (dissolve 408.24g of sodium acetate trihydrate in about 600 ml of purified water, adjust the pH to 4.5 with glacial acetic acid and bring to a final volume of IL with purified water). Combine 15.7 ml of 100% ethanol, 660 pl of 3M sodium acetate and 175 pl of purified water; this makes 16.5 ml, enough for two 96- well plates. Leaving the plate uncovered, spin immediately at 3200 rpm in a centrifuge precooled to 4 °C for 35 minutes. Decant the ethanol / sodium acetate solution by placing the plate upside down on a paper towel in the swinging plate base, still cooled to 4 °C, then allow thecentrifuge to spin up to 900rpm (about 5 seconds) and immediately stop the centrifuge. Flip the plate back over onto the benchtop. Rinse the plate by adding 70 pl of freshly prepared 70% ethanol, again centrifuging at 3200 rpm at 4 °C for 15 minutes, then flipping the plate onto a paper towel and spinning up to 900 rpm and stopping as above. Flip the plates over again, protect from dust with a paper towel and allow to air dry on the benchtop for an hour. Finally, resuspend the dried DNA is in 35 pl of sterile water per well. Wells corresponding to positive cells are transferred to 1.5ml labeled Eppendorf tubes.26. Sequence each purified well with conventional ABI / Sanger sequencing. The ‘reverse’ primer for the 2nd PCR is also used to sequence (nested rev, 3’CK494-516, and CL int rev for heavy, kappa, and lambda respectively). After sequencing, the raw sequences are submitted to IMGT / Vquest with the output formatted for analysis and cataloging.27. Prepare the cloning PCR master mixes as detailed in the Table 3. To ensure that the master mix is not contaminated, prepare each master mix with enough volume to have one buffer control. Many of the primers for the cloning PCR are used for several gene families as they prime conserved sequences. The targeted gene segments are all indicated in the name of the primer in Table 1. For example, the 5' Agel VH1 / 5 / 7 primer is used for any gene from the VH1, VHS or VH7 families; the 5' Agel VH3-9 / 30 / 33 primer is used for either VH3-9, VH3- 30 65 or VH3-33 genes; the 3' RSRII Jk 1 / 2 / 4 primer is used for either Jk 1, Jk 2 or Jk 4.28. Add 1 pl of the RT product to each 24 pl of cloning PCR mix and apply dome caps as in Step 22. Products should be checked on a gel to ensure that a band is present and that the controls are not contaminated as described in Step 25. Run the PCR using the following conditions: 95° C for 4 min, 35 cycles of 95°C for 1 min, 57°C for 1 min and 72°C for 1.5 min.

[0053] Table 2.

[0054] PCR Purification29. Follow the protocol outlined in the QIAquick PCR Microcentrifuge Protocol with one exception: to elute the DNA, apply 31 pl of PCR water to the column, let the column sit for 1 min and then centrifuge. For all centrifuging steps, centrifuge for 60 s at 17,900 g (13,000rpm) at room temperature as per Qiagen protocol. PCR products may be stored for up to 1 month at 20°C. First digestion of gamma, kappa or lambda chain variable gene inserts.30. For all inserts: add 3.5 pl of NEB buffer 1 and 1 pl of Agel to purified PCR products (use manufacturer recommended appropriate buffers for the restriction system utilized).31 . Mix the sample by pipetting up and down.32. Overlay the sample with 40 pl of sterile mineral oil.33. Incubate the samples for 4 h or overnight in a 37°C water bath or heat block.

[0055] Digestion Purification34. Purify using the same protocol as the 'PCR purification' in Step 29.

[0056] Second Digestion35. For a gamma chain insert, add 3.5 pl NEB buffer3, 0.35 pl BSA and 1 pl Sall to the purification product. For a kappa chain insert, add 3.5 pl NEB buffer 3 and 1 pl RSRII to the purification product. For a lambda chain insert, add 3.5 pl NEB buffer 2, 0.35 pl BSA and 1 pl Xhol to the purification product.36. Overlay the sample with 40 pl of sterile mineral oil.37. Incubate the sample for 4 h or overnight in a water bath. For kappa inserts, incubate at 55°C. For gamma and lambda inserts, incubate at 37°C.

[0057] Gel Purification38. Run all samples on a 1% agarose gel (wt / vol). The insert band will be approximately 400 bp in length.39. Follow the protocol outlined in the QIAquick Gel Extraction Kit (using a microcentrifuge) with one exception: to elute the DNA, apply 34 pl of EB buffer to the column, let the column sit for 1 min and centrifuge. Note: all centrifuge steps are carried out for 60 s. After excising the insert band from the gel, you may store it at 4°C overnight before proceeding with the remaining gel purification protocol. The final product may be stored for up to 1 year at -20°C.

[0058] Ligation40. Vector and insert DNA concentrations should be calculated from the A260 reading of a spectrophotometer (an A260 of 1.0 is 50 mg / ml of pure double stranded 20 DNA). A five-foldmolar excess of insert to vector should be used. As the vector is approximately 5,700 bp and the insert is typically 350-400 by (variance is due to the CDR3 junction), a 3 : 1 ratio of vector to insert can be used.41. Add 1 pl of vector (from a 1 pg / ml stock), 1 pl of T4 DNA ligase buffer, 1 pl of T4 ligase and an appropriate volume of the insert purification product to equal 0.3 mg into a clean 0.5 microcentrifuge tube.42. Add PCR water to a final volume of 10 mL. Incubate the sample overnight in a bench-top temperature controlled mini-fridge or for 2 h at room temperature.

[0059] Transformation of DH5a Cells43. Follow the protocol included with the DH5a cells with the following exceptions: use 25 pl of DH5a cells and 3 pl of DNA, and plate the cells on an LB plate containing 50 pg / ml of ampicillin. Incubate the cultures for 2-3 h in SOC media at 37° C, and plate 100 pl of the transformation culture. Incubate the plates overnight at 37° C.44. Choose four colonies from the plate to ensure a consensus variable gene sequence is identified. For each colony, inoculate one 14-ml round-bottom tube containing 5 ml of LB broth and ampicillin (50 pg / ml).45. Incubate the tubes overnight, shaking at 225 r.p.m. on an orbital shaker, at 37° C.46. Make glycerol stocks of each culture by transferring 300 ml of 1 : 1 sterile LB / glycerol and 700 ml of the confluent culture to a 2-ml tube, mix well and freeze at -80°C. These glycerol stocks are still viable after several years at -80°C.

[0060] Miniprep47. Pellet bacteria by centrifuging the culture tubes (prepared in Steps 44 and 45) for 10 min at 800 g. Discard the supernatant.48. Follow the protocol outlined in the QIAprep Spin Mini- 55 prep Kit Handbook (using a microcentrifuge) with one exception: elute the DNA with 40 pl of EB buffer. Note: all centrifuge steps are carried out for 60 s.49. Sequence the eluted DNA with the AbVec primer.

[0061] Maxiprep50. Compare the four mini-prep sequences using DNA sequence alignment software (Such as ClustalW: www.ebi.ac.uk / Tools / clustalw2 / index.html). It is expected that some sequences will have accumulated base exchanges due to PCR errors but one of the four samples typically represents the consensus.51. With a scraping from the glycerol stock of the colony of choice, inoculate one 14-ml round-bottom tube containing 5 ml of LB broth with ampicillin (50 pg / ml).52. Incubate the tubes for 4-5 h, shaking at 225 rpm on an orbital shaker, at 37°C.53. Transfer the cultures to 500-ml flasks containing 250 ml of LB broth and ampicillin (50 pg / ml). Incubate the flasks overnight, shaking at 225 rpm on an orbital shaker, at 37°C.54. Follow the protocol outlined in the Genopure Plasmid Maxi Kit with the following exception: re-dissolve the plasmid DNA pellet in 400 pl of pre-warmed (50°C) elution buffer.

[0062] Transfection of 293 A Cells55. 293A cells should be grown and passaged as per the product sheet from Invitrogen. Ensure that 293 A cells are 80-90% confluent and evenly spread out across the 150 mm x 25 mm tissue culture plate. It is important that the passage number for the 293A cells be kept below 30 passages; otherwise, the cells may not efficiently produce the antibody.56. Warm DMEM media to room temperature; thaw PEI solution, heavy chain and light chain DNA.57. For each plate to be transfected, aliquot 2.4 ml of DMEM into a conical vial. Add 9 pg of heavy chain DNA and 9 pg of light chain DNA per plate to the DMEM.58. Add 100 ml of PEI solution per plate to the prepared DMEM and DNA mixture. Immediately vortex. Incubate at room temperature for 15 min.59. Remove all but 18 ml of the culture media from each plate to be transfected.60. Gently add 2.5 ml of PEI mixture to each plate, rocking the plate to ensure even distribution.61. Incubate the cells with the PEI mixture in an incubator at 37° C with 5% CO2 for 24 h.62. Change the culture media to basal media (20-25 ml per plate).63. Collect the media from the plates 4 d later. The supernatant may be stored at 4° C for several months if NaN.i is added at a concentration of 0.05% (wt / vol). For some applications (i.e., ELISA), the antibody-containing supernatant is sufficient for testing the Mabs and the protein purification steps (Steps 64-77) can be optional. However, for long-term storage and more flexibility the antibodies are preferably purified.

[0063] Protein Purification64. Prepare protein A agarose beads by adding approximately 1.5 ml of suspended beads to 50 ml of PBS in a 50-ml conical tube.65. Centrifuge the tubes of beads for 10 min at 2,100 g at room temperature with no brake. Remove the PBS with an aspirator. Do not use brake on any of the centrifugations involving the agarose beads, as braking can damage the beads. Even slight breaking at the end of the spin can cause the beads to fluff, making it difficult to cleanly remove the supernatant.66. Rinse each tube of beads with PBS (fill each tube with 50 ml of PBS and repeat Step 65).67. Centrifuge the media collected from the transfection for 10 min at 900 g at room temperature, and then transfer the media from two plates (25 ml from each plate) to each tube of beads.68. Incubate the media with the beads for 1-2 h at room temperature or overnight at 4°C with slow agitation using a variable speed angle rocker. It works well to stabilize the tubes in a horizontal position.69. Centrifuge the tubes of beads for 10 min at 2,100 g at room temperature with no brake. Remove the media with an aspirator.70. Add 35 ml of 1 M NaCl to each tube. Centrifuge the tubes of beads for 10 min at 2,100 g at room temperature with no brake. Remove the 1 M NaCl with an aspirator.71. Rinse each tube of beads with PBS (fill each tube with 35 ml of PBS and repeat Step 65).72. Repeat Step 65.73. Add 3-5 ml of 0.1 M glycine-HCl to each tube. Incubate on a tabletop shaker for 15 min.74. Centrifuge the tubes of beads for 10 min at 2,100 g at room temperature with no brake. Transfer the glycine-HCl to a new vial. The time the antibodies are at low pH should be minimized as much as possible.75. Adjust the pH to 7-7.4 with 1 M Tris-HCI. If there are beads in the vial, centrifuge the tubes for 10 min at 2, 100 g at room temperature with no brake.76. Transfer the neutralized sample to the top of an Amicon protein concentrator; add PBS to a final volume of 15 ml. Centrifuge the concentrator for 8-12 min at 2,100 g at room temperature with brake on, until a volume of 0.5-1.0 ml is reached.77. Transfer the concentrated antibody sample from the concentrator into a clean 1.5-ml tube. If desired, preserve the antibody by adding NaN? to 0.05% (wt / vol). Note that biological assays using live cells (i.e., viral infection neutralization assays) are sensitive to NaNs.78. To reuse the beads (up to 10 times as suggested by the manufacturer), add 15 ml of 0.1 M glycine-HCl to each 30 tube of beads after 3-5 ml containing the antibody fraction is removed. Incubate on a tabletop shaker for 30 min, centrifuge for 10 min at 2, 100 g at room temperature with no brake, remove the glycine-HCI with an aspirator, and then rinse twice with PBS (according to Step 89). Store in conical vials with 50 ml of PBS containing 0.05% NaNs at 4°C for up to 6 months.

[0064] Protein Quantification79. Follow the protocol included with the EZQ Protein Quantification Kit with the following exception: stain the paper for 60 min. Protein concentrations can be checked using an alternative quantification method, such as anti-IgG ELISA assays relative to a good IgG standard, the Qubit Protein Quantification Kit or a spectrophotometer. For critical applications, verify the concentrations by more than one method.

[0065] Gel Confirmation of Protein Quality80. Run the resulting purified antibodies on an SDS-PAGE gel (12% gel (vol / vol), 4% stacking (vol / vol), reducing conditions). The resulting bands for heavy chain will be between 50 and 60 kDa and the light chain will be between 20 and 25 kDa.

[0066] Reagents for Steps 1-80.

[0067] Ig gamma, Ig kappa and Ig lambda expression vectors: The expression vectors contain a murine immunoglobulin signal peptide sequence and variable-gene cloning sites upstream of the appropriate human immunoglobulin constant regions followed by an SV40 polyadenylation sequence. Transcription is under the HCMV (human cytomegalovirus immediate- early) promoter and clonesare selected based on ampicillin resistance. The antibody variable-heavy and variable-light rearranged genes from each single cell are cloned into the respective vectors in frame with the signal peptide and constant region genes. These vectors are then co-transfected into the 293A cell line for expression. The resultant antibodies are properly trafficked and secreted after cleavage of the signal peptide, resulting in fully human IgG / kappa or IgG / lambda amino acid sequences. The vector sequences are available through the NCBI GenBank (accession numbers: FJ475055, FJ475056 and FJ517647).

[0068] Basal media: An aliquot of 250 ml each of sterile RPMI and DMEM; 3.75 ml of antibiotic / antimycotic and 5 ml each of L-glutamine (200 mM), lOOx Nutridoma and sodium pyruvate (100 mM) was used. Basal media must be made fresh every 7 d. L-Glutamine can be stored at -20° C for up to 1 year, Nutridoma can be stored at room temperature (20-25° C) for up to 1 year and sodium pyruvate can be stored for up to 6 months at 4° C.

[0069] 0.1 M glycine-HCI: 0.1 M glycine solution is equilibrated to pH 2.7 with 12 M HC1 and filter sterilized. Solution can be stored up to 60 d at room temperature.

[0070] IM Tris-HCl: IM Tris solution is equilibrated to pH 9.0 with HC1 and filter sterilized. Solution can be stored up to 60 d at 4° C.

[0071] ACK lysing buffer: 0.15 M NH4C1, 10 mM KHCO3 and 0.1 mM Na2EDTA. Adjust pH to 7.2-7.4 with IM HC1 and filter sterilized. Solution can be stored up to 1 year at room temperature (20- 25° C).

[0072] LB agar plates: LB agar dissolved in dH2O according to package directions and autoclaved. When cooled to 45° C, 50 pg / ml ampicillin is added. Dispense 20-25 ml agar solution into 100 mm x 15 mm petri dishes. Cool and store at 4° C for up to 6 months.

[0073] AEC substrate: Prepare AEC stock (20 mg / ml AEC in dimethylformamide). Dilute AEC from stock to 0.3 mg / ml in 0.1 M sodium acetate buffer (pH 5.0) just prior to use. Filter sterilized with a 0.45-mm syringe filter. The stock solution may be made and stored for up to 2 months. The diluted solution must be made fresh each time used.

[0074] RNAse-inhibiting RT-PCR catch buffer: To 5 ml of RNAse-free water, add 50 pl of IM Tris pH 8.0 and 125 pl of Rnasin. Keep on ice. This makes enough for 10 half plates. Catch buffer must be made fresh each time used.

[0075] PEI solution: prepare a 1 mg / ml PEI solution in lOOmL dPEO. Heat to 80° C (do not boil) to allow all of the PEI to dissolve, then allow to cool. Adjust pH to 7.2 with HC1. Filter sterilize with a 0.45-mm syringe filter. Store aliquots at -20° C. for up to 1 year.

[0076] Table 3. PCR oligonucleotides sequences, SEQ ID NOS: 41-87 (left column, right column, and the three (3) bottom primers, respectively).

[0077] Exemplary Anti-DNA Antibodies - CDR Sequences

[0078] DNA binding human antibodies were screened using an OriGene Technologies Double- Stranded DNA ELISA KIT, Cat# EA100918 (OriGene Technologies, USA). The manufacturer’s instructions were followed with the exception that in the Assay Procedure the following steps weremodified as follows: (1) Step 2, the instructions are to dilute sample 1 :21, but rather, the antibodies were diluted to 10 ug / ml. (2) In step 9, the suggested range for dual -wavelength with a reference filter at 600 / 650 nm; the present inventors used dual-wavelength with a reference filter at 450 / 650 nm (within the suggested range).

[0079] Provided herein are sequences for exemplary human anti-DNA antibodies of the disclosure.Included are complementarity determining region (CDR) sequences and the variable heavy and light domain sequences (VH, VL) that constitute the DNA antigen binding domains of the disclosure. The discovery of these antibodies is detailed in the Examples section.

[0080] As referred below, a light chain variable (VL) domain CDR1 region is referred to as CDR-L1; a VL CDR2 region is referred to as CDR-L2; a VL CDR3 region is referred to as CDR-L3; a heavy chain variable (VH) domain CDR1 region is referred to as CDR-H1; a VH CDR2 region is referred to as CDR-H2; and a VH CDR3 region is referred to as CDR-H3. Table 1 provides exemplary CDR combinations of antibodies of the disclosure.

[0081] Table 4. Antibody heavy and light chain complementarity determining regions (CDR).

[0082] In some embodiments, provided herein is an anti-DNA antibody, wherein the antibody comprises the amino acid sequences of the following three VH CDRs: SEQ ID NO: 1, 2, 3; 11, 12,13; 21, 22, 23; or 31, 32, 33; and comprises the amino acid sequences of the following three VL CDRs SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38.

[0083] Exemplary Anti-DNA Antibodies - Variable Region Sequences

[0084] The term variable domain and variable region are used interchangeably and refer to the portions of the light and heavy chains of an antibody that include the complementarity determining regions and framework regions (FRs).

[0085] In some embodiments, an anti-DNA antibody of the disclosure comprises the combination of VH / VL variable chain sequences of any one of the combinations listed in Table 5.

[0086] Table. 5. Antibody amino acid and nucleic acid sequences.

[0087] In some embodiments, provided herein is an anti-DNA antibody, wherein the heavy chain variable domain (VH) of the antibody comprises the amino acid sequence of SEQ ID NO: 4, 14, 24, or 34; and / or wherein the light chain variable domain (VL) of the antibody comprises the amino acid sequence of SEQ ID NO: 9, 19, 29, or 39.

[0088] Exemplary Tandem scFvc anti-DNA Antibodies

[0089] In some embodiments, the disclosure provides for scFv antibodies. In some embodiments, the disclosure provides for tandem scFv-Fc antibodies that are composed two or more scFv binding sites in tandem on each antibody arm, optionally linked by a linker, optionally a flexible linker. In someembodiments, a tandem scFV antibody has a total of four or more scFv binding sites in a single scFv- Fc formatted antibody.

[0090] The VH1 and the VL1 of each scFvl may be connected by a linker, e.g., a flexible linker.

[0091] The scFvs on each antibody arm may be connected by a linker, e.g., a flexible linker. An exemplary linker comprises the following amino acid sequence: GGGGSGGGGSGGGGS; SEQ IDNO:116.

[0092] In exemplary embodiments, provided herein is a single-chain Fv (scFv) anti-DNA antibody, wherein the heavy chain variable domain (VH) of the antibody comprises the amino acid sequence of SEQ ID NO: 4, 14, 24, 34; wherein the light chain variable domain (VL) of the antibody comprises the amino acid sequence of SEQ ID NO: 9, 19, 29, 39; wherein the scFv are linked with a linker comprising the following amino acid sequence: GGGGSGGGGSGGGGS; SEQ ID NO: 116.

[0093] Additional oligonucleotides for use with the invention are listed as SEQ ID NOS: 73-100, which include the restriction enzyme cleavage site and the location on the antibody, as follows in Table 6.

[0094] Table 6. Additional oligonucleotides, SEQ ID NOS: 88-115.

[0095] As embodied and broadly described herein, an aspect (or object) of the present disclosure can be used individually, or in combination, as follows. The present disclosure relates to an antibody (Ab), an antigen (Ag)-binding fragment, a single chain, a bivalent, or a multivalent antibody capable of binding to a double-stranded deoxyribonucleic acid (DNA) strand comprising, consisting essentially of, or consisting of: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively. In one aspect, the Ab or fragment thereof is a human Ab or a human Ag-binding fragment. In another aspect, the Ab or fragment thereof comprises: a VHsequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39. In another aspect, at least one of: the Ab, Ab fragment, single chain, bivalent, or multivalent antibody neutralizes a DNA virus infection: (i) in an in vitro model of infection; (ii) in an in vivo animal model of infection; (iii) in a human; or (iv) any combination of (i)-(iii); or further comprising a second agent as a fusion protein, or conjugated to the Ab, Ab fragment, single chain, bivalent, or multivalent antibody. In another aspect, the Ab or fragment thereof comprises a monoclonal Ab, a single chain Ab, a Fab, a Fab’, an F(ab’)2, an Fv, an scFv, or a scFab. In another aspect, the Ab, single chain, bivalent, or multivalent antibody is an IgGl, IgG2, IgG3, IgG4, IgAl, IgA2, IgM, IgE, or IgD isotype. In another aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a hybridoma or engineered cell comprising a polynucleotide encoding the Ab, binding fragment, single chain, bivalent, or multivalent antibody described hereinabove. In another aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a nucleic acid molecule encoding the Ab or fragment. In another aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a vector comprising the nucleic acid molecule. In another aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a host cell comprising the vector. In another aspect, the antibody is prepared by a method comprising: obtaining the host cell; culturing the host cell in a medium under conditions permitting expression of the Ab, binding fragment, single chain, bivalent, or multivalent antibody encoded by the vector; and purifying the Ab, binding fragment, single chain, bivalent, or multivalent antibody thereof from the cultured cell or a medium thereof. In another aspect, the antibody further comprises a pharmaceutically acceptable carrier or excipient. In another aspect, the antibody further comprises a second therapeutic agent, wherein the second therapeutic agent is selected from the group consisting of: an anti-inflammatory agent, or an anti-viral agent.

[0096] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of treating a mammalian or human subject infected with a DNA virus or preventing infection of the DNA virus in a subject at risk of infection with the DNA virus comprising, consisting essentially of, or consisting of: administering to a subject in need thereof a therapeutically effectiveamount of a Ab, binding fragment, single chain, bivalent, or multivalent antibody specific to DNA and having antibody comprises the amino acid sequences of the following three VH CDRs: SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33; and comprises the amino acid sequences of the following three VL CDRs SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38. In one aspect, the Ab, binding fragment, single chain, bivalent, or multivalent antibody capable of binding to DNA comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively. In another aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39.

[0097] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of detecting DNA in a mammalian or human subject comprising, consisting essentially of, or consisting of, the steps of: (a) contacting a sample from the subject suspected of having DNA; and (b) detecting binding of a Ab, binding fragment, single chain, bivalent, or multivalent antibody to DNA in the sample, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody is capable of binding to DNA comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)H1, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively. In another aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acidsequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39. sample is selected from a nasopharyngeal swab, a nares swab, saliva, urine, tears, cerebrospinal fluid, amniotic fluid, serum, plasma, whole blood, bronchopulmonary lavage, vaginal sampling and a rectal / stool sampling obtained from the subject. In another aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39. Ab, binding fragment, single chain, bivalent, or multivalent antibody is conjugated to at least one of: a nanoparticle, a liposome, or a detectable label, and wherein the detectable label comprises a radioactive tag, a fluorescent tag, a biological, or an enzymatic tag.

[0098] As embodied and broadly described herein, an aspect of the present disclosure relates to a kit for the detection of DNA in a subject comprising, consisting essentially of, or consisting of: (a) an Ab, binding fragment, single chain, bivalent, or multivalent antibody capable of binding to the DNA, (b) a suitable container, and (c) an immunodetection reagent, wherein the Ab or Ag-binding fragment capable of binding to the DNA comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)H1, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively. In one aspect, the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39. at least one of: the Ab, binding fragment, single chain, bivalent, or multivalent antibody are affixed to a support selected from one or more beads, a dipstick, a filter, a membrane, a plate, a chip, or a column matrix; the immunodetection reagent comprises atleast a second Ab that binds an immunocomplex formed when the Ab, binding fragment, single chain, bivalent, or multivalent antibody binds DNA; the kit further comprises, consists essentially of, or consists of DNA for use as a standard; or wherein at least one of the Ab, binding fragment, single chain, bivalent, or multivalent antibody, or the immunodetection reagent are linked to a detectable label, and the detectable label comprises a radioactive tag, a fluorescent tag, a biological, or an enzymatic tag.

[0099] As embodied and broadly described herein, an aspect of the present disclosure relates to an isolated nucleic acid molecule, a group of isolated nucleic acid molecules, or a vector encoding an antibody, binding fragment, single-chain, bivalent, or multivalent antibody comprising, consisting essentially of, or consisting of: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)H1, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively; a VH sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO.: 5, 15, 25, or 35; and a VL sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO.: 10, 20, 30, or 40; or the single-chain, bivalent, or multivalent antibody encoding nucleic acid sequence that comprises: a VH sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 99%, or 100% identity to SEQ ID NO.: 5, 15, 25, or 35; and a VL sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 99%, or 100% identity to SEQ ID NO.: 10, 20, 30, or 40.

[0100] As embodied and broadly described herein, an aspect of the present disclosure relates to an isolated host cell comprising the nucleic acid molecule, the group of isolated nucleic acid molecules, or the vector disclosed herein.

[0101] It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method, kit, reagent, or composition of the invention, and vice versa. Furthermore, compositions of the invention can be used to achieve methods of the invention.

[0102] It will be understood that particular embodiments described herein are shown by way of illustration and not as limitations of the invention. The principal features of this invention can be employed in various embodiments without departing from the scope of the invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerousequivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the claims.

[0103] All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

[0104] The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and / or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” The use of the term “or” in the claims is used to mean “and / or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and / or.” Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.

[0105] As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. In embodiments of any of the compositions and methods provided herein, “comprising” may be replaced with “consisting essentially of’ or “consisting of’. As used herein, the phrase “consisting essentially of’ requires the specified integer(s) or steps as well as those that do not materially affect the character or function of the claimed invention. As used herein, the term “consisting” is used to indicate the presence of the recited integer (e.g., a feature, an element, a characteristic, a property, a method / process step or a limitation) or group of integers (e.g., feature(s), element(s), characteristic(s), property(ies), method / process steps or limitation(s)) only.

[0106] The term “or combinations thereof’ as used herein refers to all permutations and combinations of the listed items preceding the term. For example, “A, B, C, or combinations thereof’ is intended to include at least one of A, B, C, AB, AC, BC, or ABC, and if order is important in a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing with this example, expressly included are combinations that contain repeats of one or more item or term, such as BB, AAA, AB, BBC,AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan will understand that typically there is no limit on the number of items or terms in any combination, unless otherwise apparent from the context.

[0107] As used herein, words of approximation such as, without limitation, “about”, "substantial" or "substantially" refers to a condition that when so modified is understood to not necessarily be absolute or perfect but would be considered close enough to those of ordinary skill in the art to warrant designating the condition as being present. The extent to which the description may vary will depend on how great a change can be instituted and still have one of ordinary skilled in the art recognize the modified feature as still having the required characteristics and capabilities of the unmodified feature. In general, but subject to the preceding discussion, a numerical value herein that is modified by a word of approximation such as “about” may vary from the stated value by at least ±1, 2, 3, 4, 5, 6, 7, 10, 12 or 15%.

[0108] Additionally, the section headings herein are provided for consistency with the suggestions under 37 CFR 1.77 or otherwise to provide organizational cues. These headings shall not limit or characterize the invention(s) set out in any claims that may issue from this disclosure. Specifically and by way of example, although the headings refer to a “Field of Invention,” such claims should not be limited by the language under this heading to describe the so-called technical field. Further, a description of technology in the “Background of the Invention” section is not to be construed as an admission that technology is prior art to any invention(s) in this disclosure. Neither is the “Summary” to be considered a characterization of the invention(s) set forth in issued claims. Furthermore, any reference in this disclosure to “invention” in the singular should not be used to argue that there is only a single point of novelty in this disclosure. Multiple inventions may be set forth according to the limitations of the multiple claims issuing from this disclosure, and such claims accordingly define the invention(s), and their equivalents, that are protected thereby. In all instances, the scope of such claims shall be considered on their own merits in light of this disclosure, but should not be constrained by the headings set forth herein.

[0109] All of the compositions and / or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and / or methods and in the steps or in the sequence of steps of the method described herein without departing from theconcept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

[0110] To aid the Patent Office, and any readers of any patent issued on this application in interpreting the claims appended hereto, applicants wish to note that they do not intend any of the appended claims to invoke paragraph 6 of 35 U.S.C. § 112, U.S.C. § 112 paragraph (f), or equivalent, as it exists on the date of filing hereof unless the words “means for” or “step for” are explicitly used in the particular claim.

[0111] For each of the claims, each dependent claim can depend both from the independent claim and from each of the prior dependent claims for each and every claim so long as the prior claim provides a proper antecedent basis for a claim term or element.

Claims

What is claimed is:

1. An antibody (Ab), an antigen (Ag)-binding fragment, a single chain, a bivalent, or a multivalent antibody capable of binding to a double-stranded deoxyribonucleic acid (DNA) strand comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)H1, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively.

2. The antibody of claim 1, wherein the Ab or fragment thereof is a human Ab or a human Ag- binding fragment.

3. The antibody of claim 1, wherein the Ab or fragment thereof comprises: a VH sequence comprising the amino acid sequence of SEQ ID NO.: 4, 14, 24, or 34, and a VL sequence comprising the amino acid sequence of SEQ ID NO.: 9, 19, 29, or 39; or wherein the Ab or fragment thereof in which (i) the VH comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 4, 14, 24, or 34; and / or (ii) the VL comprises or consists of an amino acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence set forth in SEQ ID NO: 9, 19, 29, or 39.

4. The antibody of claim 1, wherein at least one of: the Ab, Ab fragment, single chain, bivalent, or multivalent antibody neutralizes a DNA virus infection: (i) in an in vitro model of infection; (ii) in an in vivo animal model of infection; (iii) in a human; or (iv) any combination of (i)-(iii); or further comprising a second agent as a fusion protein, or conjugated to the Ab, Ab fragment, single chain, bivalent, or multivalent antibody.

5. The antibody of claim 1, wherein the Ab or fragment thereof comprises a monoclonal Ab, a single chain Ab, a Fab, a Fab’, an F(ab’)2, an Fv, an scFv, or a scFab.

6. The antibody of claim 1, wherein the Ab, single chain, bivalent, or multivalent antibody is an IgGl, IgG2, IgG3, IgG4, IgAl, IgA2, IgM, IgE, or IgD isotype.

7. The antibody of claim 1, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a hybridoma or engineered cell comprising a polynucleotide encoding the Ab, binding fragment, single chain, bivalent, or multivalent antibody thereof.

8. The antibody of claim 7, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a nucleic acid molecule encoding the Ab or fragment.

9. The antibody of claim 8, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a vector comprising the nucleic acid molecule.

10. The antibody of claim 9, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody is expressed by a host cell comprising the vector.

11. The antibody of claim 10, prepared by a method comprising: obtaining the host cell; culturing the host cell in a medium under conditions permitting expression of the Ab, binding fragment, single chain, bivalent, or multivalent antibody encoded by the vector; and purifying the Ab, binding fragment, single chain, bivalent, or multivalent antibody thereof from the cultured cell or a medium thereof.

12. The antibody of claim 1, further comprising a pharmaceutically acceptable carrier or excipient.

13. The antibody of claim 12, further comprising a second therapeutic agent, wherein the second therapeutic agent is selected from the group consisting of: an anti-inflammatory agent, or an antiviral agent.

14. A method of treating a mammalian or human subject infected with a DNA virus or preventing infection of the DNA virus in a subject at risk of infection with the DNA virus comprising administering to a subject in need thereof a therapeutically effective amount of a Ab, binding fragment, single chain, bivalent, or multivalent antibody specific to DNA and having antibody comprises the amino acid sequences of the following three VH CDRs: SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33; and comprises the amino acid sequences of the following three VL CDRs SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38.

15. The method of claim 14, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody capable of binding to DNA comprising:a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively.

16. A method of detecting DNA in a mammalian or human subject comprising the steps of:(a) contacting a sample from the subject suspected of having DNA; and(b) detecting binding of a Ab, binding fragment, single chain, bivalent, or multivalent antibody to DNA in the sample, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody is capable of binding to DNA comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31 , 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively.

17. The method of claim 16, wherein the sample is selected from a nasopharyngeal swab, a nares swab, saliva, urine, tears, cerebrospinal fluid, amniotic fluid, serum, plasma, whole blood, bronchopulmonary lavage, vaginal sampling and a rectal / stool sampling obtained from the subject.

18. The method of claim 16, wherein the Ab, binding fragment, single chain, bivalent, or multivalent antibody is conjugated to at least one of: a nanoparticle, a liposome, or a detectable label, and wherein the detectable label comprises a radioactive tag, a fluorescent tag, a biological, or an enzymatic tag.

19. A kit for the detection of DNA in a subject comprising: (a) an Ab, binding fragment, single chain, bivalent, or multivalent antibody capable of binding to the DNA, (b) a suitable container, and(c) an immunodetection reagent, wherein the Ab or Ag-binding fragment capable of binding to the DNA comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)Hl, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, anda light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively.

20. The kit of claim 19, wherein at least one of: the Ab, binding fragment, single chain, bivalent, or multivalent antibody are affixed to a support selected from one or more beads, a dipstick, a filter, a membrane, a plate, a chip, or a column matrix; the immunodetection reagent comprises at least a second Ab that binds an immunocomplex formed when the Ab, binding fragment, single chain, bivalent, or multivalent antibody binds DNA; the kit further comprises DNA for use as a standard; or wherein at least one of the Ab, binding fragment, single chain, bivalent, or multivalent antibody, or the immunodetection reagent are linked to a detectable label, and the detectable label comprises a radioactive tag, a fluorescent tag, a biological, or an enzymatic tag.

21. An isolated nucleic acid molecule, a group of isolated nucleic acid molecules, or a vector encoding an antibody, binding fragment, single-chain, bivalent, or multivalent antibody comprising: a heavy chain variable domain (VH) that comprises complementarity determining region (CDR)H1, CDRH2, and CDRH3 amino acid sequences set forth in SEQ ID NO: 1, 2, 3; 11, 12, 13; 21, 22, 23; or 31, 32, 33, respectively, and a light chain variable domain (VL) that comprises CDRL1, CDRL2, and CDRL3 amino acid sequences set forth in SEQ ID NO: 6, 7, 8, 16, 17, 18, 26, 27, 28; or 36, 37, 38, respectively; a VH sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO.: 5, 15, 25, or 35; and a VL sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO.: 10, 20, 30, or 40; or the single-chain, bivalent, or multivalent antibody encoding nucleic acid sequence that comprises: a VH sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 99%, or 100% identity to SEQ ID NO.: 5, 15, 25, or 35; and a VL sequence comprising the nucleic acid sequence having at least 85%, 90%, 95%, 99%, or 100% identity to SEQ ID NO.: 10, 20, 30, or 40.

22. An isolated host cell comprising the nucleic acid molecule, the group of isolated nucleic acid molecules, or the vector of claim 21.

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