154 results about "RNase H" patented technology

Oligonucleotides and other macromolecules are provided which have increased nuclease resistance, substituent groups for increasing binding affinity to complementary strand, and subsequences of 2′-deoxy-erythro-pentofuranosyl nucleotides that activate RNase H. Such oligonucleotides and macromolecules are useful for diagnostics and other research purposes, for modulating the expression of a protein in organisms, and for the diagnosis, detection and treatment of other conditions susceptible to oligonucleotide therapeutics.

The present invention pertains to novel oligonucleotide compounds for use in various biological assays, such as nucleic acid amplification, ligation and sequencing reactions. The novel oligonucleotides comprise a ribonucleic acid domain and a blocking group at or near the 3′ end of the oligonucleotide. These compounds offer an added level of specificity previously unseen. Methods for performing nucleic acid amplification, ligation and sequencing are also provided. Additionally, kits containing the oligonucleotides are also disclosed herein.

Methods and compositions are disclosed for controlling expression of TNF receptors (TNFR1 and TNFR2) and of other receptors in the TNFR superfamily using compounds that modulate splicing of pre-mRNA encoding these receptors. More specifically these compounds cause the removal of the transmembrane domains of these receptors and produce soluble forms of the receptor which act as an antagonist to reduce TNF-α activity or activity of the relevant ligand. Reducing TNF-α activity provides a method of treating or ameliorating inflammatory diseases or conditions associated with TNF-α activity. Similarly, diseases associated with other ligands can be treated in like manner. In particular, the compounds of the invention are splice-splice switching oligomers (SSOs) which are small molecules that are stable in vivo, hybridize to the RNA in a sequence specific manner and, in conjunction with their target, are not degraded by RNAse H.

The present invention provides a new method for producing amplified RNA from a selected set of cells. This method combines and utilizes known methods in a novel way to produce the gene expression profiles. The methods of the present invention utilize thermostable DNA polymerases and RNase H to produce high fidelity second strand synthesis of nucleic acids from selected cells in a highly efficient mariner and in substantially reduced time.

The present invention pertains to a method to isolate, separate, enrich or amplify a targeted nucleotide polymer such as mRNA through selective reverse transcription of the targeted polymer into cDNA from a sample comprising of chemically identical or similar polynucleotide polymers such as rRNA. The enrichment of the targeted nucleic acid such as mRNA is accomplished by blocking the reverse transcription of undesired rRNA while allowing unrestricted reverse transcription of the targeted polymer. The invention also embodies that the cleavage of the non-targeted nucleic acid such as rRNA bound to an oligonucleotide through enzymatic activity (RNase H). The invention further embodies methods and kits to accomplish the utility of the invention through the following steps 1) 3′ tailing of chemically identical or similar nucleotide polymers in a sample that includes bacterial mRNA 2) a 3′ tail capable of binding to a oligo-dN primer 3) at least one oligonucleotide capable of preventing the extension of oligo-dN bound to at least one non-targeted nucleotide polymers by a DNA polymerase such as a reverse transcriptase without restricting conversion of bacterial mRNA into cDNA 4) where the non-targeted molecule is prevented as a template for cDNA synthesis by enzymatic cleavage (RNase H) of template (rRNA)-oligonucleotide hybrid 5) where the reverse transcriptase is physically blocked by the oligonucleotide bound to the non-targeted nucleic acids such as rRNA 5) purification of the selectively transcribed cDNA. In further embodiments of the present invention, methods and composition to enable the study of bacterial transcriptomics-an analysis of genes expressed by a bacterial infection of a host, an isolated bacterial culture or a bacterial community, such as recovered from soil, intestine, mouth, biofilm, water etc are also included for use in DNA-chip or sequencing analyses.

Modified oligonucleotides containing both A-form conformation geometry and B-from conformation geometry nucleotides are disclosed. The B-form geometry allows the oligonucleotide to serve as substrates for RNase H when bound to a target nucleic acid strand. The A-form geometry imparts properties to the oligonucleotide that modulate binding affinity and nuclease resistance. By utilizing C2' endo sugars or O4' endo sugars, the B-form characteristics are imparted to a portion of the oligonucleotide. The A-form characteristics are imparted via use of either 2'-O-modified nucleotides that have 3' endo geometries or use of end caps having particular nuclease stability or by use of both of these in conjunction with each other.

Modified oligonucleotides containing both A-form conformation geometry and B-from conformation geometry nucleotides are disclosed. The B-form geometry allows the oligonucleotide to serve as substrates for RNase H when bound to a target nucleic acid strand. The A-form geometry imparts properties to the oligonucleotide that modulate binding affinity and nuclease resistance. By utilizing C2′ endo sugars or O4′ endo sugars, the B-form characteristics are imparted to a portion of the oligonucleotide. The A-form characteristics are imparted via use of either 2′-O-modified nucleotides that have 3′ endo geometries or use of end caps having particular nuclease stability or by use of both of these in conjunction with each other.

The invention discloses a CRISPR-Cas based technology for normal-temperature/isothermal rapid detection of ribonucleic acid and a detection method. The invention aims to perform in-vitro ribonucleic acid amplification on multiple disclosed gentically engineered enzymes and chemical components and to realize amplification and detection of specific ribonucleic acid (RNA) or desoxyribonucleic acid (DNA) quickly in one step or two steps in normal-temperature/isothermal condition so that the detection of each nucleic acid is faster and more convenient. The method comprises the following steps: (1)performing nucleic acid extraction to obtain the RNA, single-stranded DNA or double-stranded DNA of a to-be-detected sample; (2) conducting a reaction with to-be-detected nucleic acid by using the combined enzyme of reverse transcriptase, transcriptase, ribonuclease H and CRISPR-associated protein 13 as well as a nucleic acid fluorescent probe in an isothermal condition, wherein if the to-be-detected nucleic acid is DNA, a pre-denaturation step is added before the reaction; (3) detecting the fluorescence signal to judge whether target nucleic acid exists in the to-be-detected sample.

The present invention relates to oligonucleotides for modulation of target RNA activity. Thus, the invention provides oligonucleotides that bind to microRNA binding sites of target RNA. The oligonucleotides may activate RNase H or RNAi. In a preferred embodiment, the oligonucleotides prevents a microRNA from binding to its binding site of the target RNA and thereby prevent the microRNA from regulating the target RNA. Such oligonucleotides have uses in research and development of new therapeutics.

The present invention provides oligomeric compounds and uses thereof. In certain embodiments, such oligomeric compounds are useful as antisense compounds. Certain such antisense compounds are useful as RNase H antisense compounds or as RNAi compounds.

The invention provides a class of oligonucleotide that is optimized to target a specific RNA for RNAse H degradation and to be itself resistant to degradation within in plasma and within eukaryotic, especially mammalian cells. The oligonucleotides of the invention contain no naturally occurring 5'->3'-linked nucleotides. Rather, the invention provides oligonucleotides having two types of nucleotides: 2'-deoxyphosphorothioate, which activate RNase H, and 2'-modified nucleotides, which do not. The linkages between the 2'-modified nucleotides can be phosphodiesters, phosphorothioate or P-ethoxyphosphodiester. Activation of RNAse H is accomplished by a contiguous, RNAse H-activating region, which contains between three and five 2'-deoxyphosphorothioate nucleotides to activate bacterial RNAse H and between five and ten 2'-deoxyphosphorothioate nucleotides to activate eukaryotic and, particularly, mammalian RNAse H. Protection from degradation is accomplished by making the 5' and 3' terminal bases highly nuclease resistant and, optionally, by placing a 3' terminal blocking group.

The present invention pertains to novel oligonucleotide compounds for use in various biological assays, such as nucleic acid amplification, ligation and sequencing reactions. The novel oligonucleotides comprise a ribonucleic acid domain and a blocking group at or near the 3′ end of the oligonucleotide. These compounds offer an added level of specificity previously unseen. Methods for performing nucleic acid amplification, ligation and sequencing are also provided. Additionally, kits containing the oligonucleotides are also disclosed herein.

The present invention provides methods of cleaving a nucleic acid strand to initiate, assist, monitor or perform biological assays.

Antisense polynucleotides and their use in pharmaceutical compositions to induce exon skipping in targeted exons of the gamma sarcoglycan gene are provided, along with methods of preventing or treating dystrophic diseases such as Limb-Girdle Muscular Dystrophy. One aspect the disclosure provides an isolated antisense polynucleotide wherein the polynucleotide specifically hybridizes to an exon target region of a gamma sarcoglycan RNA, wherein the exon is selected from the group consisting of exon 4 (SEQ ID NO:1), exon 5 (SEQ ID NO: 2), exon 6 (SEQ ID NO: 3), exon 7 (SEQ ID NO: 4) and a combination thereof. In some embodiments, the antisense polynucleotide cannot form an RNase H substrate, and in further embodiments the antisense polynucleotide comprises a modified polynucleotide backbone.

The present disclosure encompasses systems, and their methods of use, for detecting a target analyte, the systems comprising: (a) a first oligonucleotide probe comprising a reporter oligonucleotide-binding arm complementary to the nucleotide sequence of a first region of a reporter oligonucleotide and an analyte-binding arm selectively binding to a first region of a target analyte, a second oligonucleotide probe comprising a reporter oligonucleotide-binding arm having a nucleotide sequence complementary to the nucleotide sequence of a second region of a reporter oligonucleotide, and an analyte-binding arm having a nucleotide sequence characterized as selectively binding to a second region of a target analyte; and a reporter oligonucleotide comprising a region complementary to the reporter oligonucleotide-binding arm of the first oligonucleotide probe, a second region complementary to the reporter oligonucleotide-binding arm of the second oligonucleotide probe, a fluorophore and a quencher disposed on the reporter oligonucleotide and a cleavable site disposed between the fluorescent label and the quencher. The cleavable site of the reporter oligonucleotide when in the presence of a target analyte can be cleaved by an enzyme such as a restriction endonuclease, an RNase H, a Flap-endonuclease-1 (FEN-1), and a DNA glycosylase.

The invention discloses a method of detecting the UDG activity by enzyme-mediated two-step serial signal amplification based on excision repair. The method comprises the following steps: (1) adding a UDG active substrate in an excision reaction buffer solution to carry out excision repair reaction, excising a uracil base of the UDG active substrate, and leaving an abasic site; and (2) adding an excision repair reaction product in an amplification reaction buffer solution to carry out enzyme-assisted two-step serial signal amplification reaction, namely inducing strand displacement reaction and index amplification reaction, generating strengthened fluorescence signals in a circulation manner, and determining the UDG activity through weakness of the fluorescence signals. According to the method provided by the invention, ultrahigh sensitive detection to the activity of uracil DNA glycosylase (UDG) is realized by utilizing high amplification efficiency of constant-temperature index amplification reaction and specific circulation digestion of ribonuclease H.

The current invention provides for methods and medicaments that apply an oligonucleotide comprising aninosine and/or an uracile and/or a nucleotide containing a base able to form a wobble base pair, said oligonucleotide being preferably RNAse H substantially independent and being complementary only to a repetitive sequence in a human gene transcript, for the manufacture of a medicament for the diagnosis, treatment or prevention of a cis-element repeat instability associated genetic disorders in humans. The invention hence provides a method of treatment for cis-element repeat instability associated genetic disorders. The invention also pertains to a modified oligonucleotide which can be applied in a method of the invention to prevent the accumulation and/or translation of repeat expanded transcripts in cells.

The present invention describes oligonucleotides that bind to microRNA target sites in target RNAs, such as mRNAs. The oligonucleotides of the invention may mediate RNase H degradation of the target RNA, mediate RNAi of the target RNA or prevent microRNA regulation of the target RNA. The oligonucleotides of the invention are useful e.g. as research tools for studying microRNA:mRNA interactions andfor therapeutic development. The present invention also describes methods of identifying microRNA target sites, methods of validating microRNA target sites, methods of identifying oligonucleotides ofthe invention and methods of modulating the activity of a target RNA using the oligonucleotides of the invention.