12 results about "Single strand dna" patented technology

Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and / or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.

Engineered filamentous bacteriophage particle are provided, and DNA extracted from such phage particles, including: (a) a filamentous bacteriophage capsid comprising a peptide antigen displayed on a surface of the capsid; and (b) a single stranded DNA molecule (ssDNA) encapsulated within the capsid, wherein the single stranded DNA molecule; wherein (i) the ssDNA comprises at least 12% unmethylated CG dinucleotides; (ii) the ssDNA comprises sequences encoding bacteriophage (A) fl-ori, (B) fl-term, and (C) packaging signal; and (iii) the ssDNA comprises less than 50% bacteriophage ssDNA.

Current minicircle production methods are slow, expensive, and difficult to perform under GMP conditions because, in most cases, the product is derived from bacteria. In contrast, HTLA-and CHTLA-based synthetic circular supercoiled DNA production can be done completely in a test tube, using chemically or enzymatically synthesized oligonucleotides, long single stranded DNA, and / or double stranded DNA.

Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and / or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.

Described herein are various methods of removing uracils due to the deamination of unmethylated cytosines in an assay using engineered cytosine deaminases to deaminate methylated cytosines. The Chemoenzymatic Uracil Replacement of Nucleobases (ChURN) method includes providing a sample comprising single stranded DNA library fragments in which a cytosine deaminase has deaminated methylated cytosines; contacting the sample with an uracil DNA glycosylase (UDG) to deglycosylate uracil residues to form abasic sites having a hemiacetal formation within the single stranded DNA library fragments; contacting the sample with a reactive cytosine nucleobase analog to install a cytosine at abasic sites thru a noncanonical linkage; and subjecting the sample to polymerase chain reaction (PCR) amplification resulting in double stranded DNA corrected library fragments. The Uracil Enzymatic Removal and Substitution at Errors (U-ERASE) method includes providing a sample comprising single stranded DNA library fragments in which a cytosine deaminase has deaminated methylated cytosines, synthesizing double stranded DNA library fragments in which the second strand is tagged to facilitate its downstream degradation, treating the double stranded DNA library fragments with an uracil DNA glycosylase and an endonuclease resulting in the removal of uracil bases and single nucleotide gaps at those sites, and repairing the single nucleotide gaps through treatment with a polymerase, dCTP, and a ligase, resulting in replacement of false positive uracil bases with a mismatched base, such as cytosine. Subsequently, the second strand is selectively degraded, allowing for selective amplification of the original DNA strand via PCR.

The present invention provides a novel in vitro method of selecting DNAzymes with self-cleaving activity, novel DNAzymes and their use for the production of single stranded DNA.

The present invention relates to a method for generating a single stranded DNA (ssDNA) molecule from a cyclic double stranded DNA (dsDNA) molecule.

The present invention is directed to methods for generating one or more genetically modified cells by using a circular single stranded DNA (CiSSD) as a donor template and targeting genome modification. These methods include transferring one or more DNA polynucleotides into the cell for site-specific nuclease-mediated DNA repair and selecting one or more cells having the transferred DNA incorporated into the cell's genome.

A composition comprising a complex containing a polynucleotide of interest and a carrier is provided. The surface of the complex is coated covalently or non-covalently with a CD22 receptor ligand and can target CD22 on cells. The carrier may contain a polymer, a lipid, or a protein. The polynucleotide of interest may contain, for example, plasmid DNA (pDNA), linear double stranded DNA (dsDNA), linear single stranded DNA (ssDNA), messenger RNA (mRNA), small hairpin RNA (shRNA), or small interfering RNA (siRNA) that alters level or activity of a target molecule in B cells. Methods of delivering a polynucleotide of interest to a CD22 expressing cell, and methods of treating a B cell-associated disease (such as acute lymphoblastic leukemia) in a subject using the composition are also provided.

Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and / or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.

Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and / or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incoporated into the target DNA molecule.

The present disclosure describes a system and methods for the generation of DNA strands and querying a DNA database rapidly and accurately. The method disclosed includes the generating at least one database single stranded DNA (ssDNA) strand, includes a plurality of functional oligonucleotides separated by introns. On one end of each intron there is a donor fluorophore and on the other end is an acceptor fluorophore. A query ssDNA strand is also generated that includes a series of complimentary oligonucleotides, which can hybridize with the functional oligonucleotides of the database ssDNA strand. Hybridization causes the intron regions of the database ssDNA strand to fold resulting in the donor fluorophore and acceptor fluorophore being placed in close proximity to one another. The close proximity enables Förster Resonance Energy Transfer (FRET) phenomena to occur, which is detected using a photodetector.