Abstract: Modified nucleotides, and methods to modify nucleotides with a moiety or label, such as biotin, that permits their detection and results in a modified nucleotide, and methods of use of the modified nucleotide in quantitative and qualitative assays.

Abstract: The invention provides a novel truncated mutated T4 RNA ligase 2. In addition, methods are provided for ligating pre-adenlylated donor molecules to the 3? hydroxyl group of RNA in the absence of ATP using the ligase.

Abstract: The invention features methods of analyzing the kinetics properties of transfection reactions. Also featured are methods for creating structural promoters which are effectively unregulated by enhancers and repressors. The structural promoters are significantly more active than the native promoter sequences upon which they are based.

Abstract: Disclosed in certain embodiments is a method of inhibiting cell function comprising inducing the expression of a mRNA interferase that cleaves mRNA at GCU.

Abstract: The present invention relates to a method of generating eukaryotic cells suitable for the expression of transgenes in said cells comprising (a) introducing a nucleic acid encoding a selectable marker responsive to a selecting agent into the nucleus of cells, wherein the level of expression of said selectable marker is proportional to the level of phenotypic responsiveness to said selecting agent; (b) selecting, among the cells obtained in step (a), for cells with a detectable expression of said selectable marker; (c) optionally propagating the cells selected for in step (b); (d) mutagenizing the cells selected for in step (b) or propagated in step (c) or allowing for the appearance of spontaneous mutations in the cells selected for in step (b) or propagated in step (c); and (e) selecting for cells displaying an increased expression of said selectable marker compared to the expression obtained in step (b).

Abstract: Compositions and methods are provided for amplifying nucleic acid molecules. The nucleic acid molecules can be used in various research and diagnostic applications, such as gene expression studies involving nucleic acid microarrays.

Abstract: A polypeptide having a novel endoribonuclease activity; a nucleic acid encoding the polypeptide; recombinant DNA having the nucleic acid therein; a transformant transformed with the recombinant DNA; a process for producing the polypeptide comprising the steps of cultivating the transformant and collecting the polypeptide from the culture; a process for producing a digest of single-stranded RNA comprising the step of reacting the polypeptide with the single-stranded RNA; and a method for the digestion of single-stranded RNA.

Abstract: Based at least in part on an understanding of the mechanisms by which small RNAs (e.g., naturally-occurring miRNAs) mediate RNA silencing in plants, rules have been established for determining, for example, the degree of complementarity required between an RNAi-mediating agent and its target, i.e., whether mismatches are tolerated, the number of mismatches tolerated, the effect of the position of the mismatches, etc. Such rules are useful, in particular, in the design of improved RNAi-mediating agents which allow for more exact control of the efficacy of RNA silencing.

Abstract: Double-stranded RNA of about 19 to about 25 nucleotides in length capable of regulating gene expression by RNA interference is provided. Such double-stranded RNA are particularly useful for treating disease or conditions associated with a target mRNA or gene. Methods of manufacture and methods of use of the double-stranded RNA are also provided.

Abstract: Disclosed is a T7 RNA polymerase mutant having improved thermal stability and/or specific activity in comparison with wild-type T7-like bacteriophage RNA polymerase, wherein at least one amino acid residue corresponding to at least one of the amino acid residues selected from the group at least consisting of glutamine at position 768, lysine at position 179 and valine at position 685 of the amino acid sequence that composes wild-type T7 RNA polymerase shown in SEQ ID NO: 6, is substituted with another amino acid.

Abstract: A modified Dicer polypeptide is provided, which modified Dicer polypeptide exhibits enhanced catalytic activity. Also provided is a method for producing small regulatory RNAs from a dsRNA, involving contacting a dsRNA with a subject modified Dicer. Small regulatory RNAs produced by a subject method find use in a variety of applications, including research and therapeutic applications.

Abstract: Improved vector constructs useful in the expression of double-stranded RNA are provided. The constructs are particularly useful for expression of double-stranded RNA in vitro and in vivo.

Abstract: Dinucleotide cap analogs are disclosed, modified at different phosphate positions with a boranophosphate group or a phosphoroselenoate group. The analogs are useful as reagents in the preparation of capped mRNAs and have increased stability both in vitro and in vivo. They may be used as inhibitors of cap-dependent translation. Optionally, the boranophosphate or phosphoroselenoate group has a 2?-O or 3?-O-alkyl group, preferably a methyl group, producing analogs called BH3-ARCAs or Se-ARCAs. ARCAs may be modified with ?-, ?-, or ?-boranophosphate or phosphoroselenoate groups.

Abstract: Aspects of the disclosure are generally directed to probes and probe compositions for detecting or quantifying a target. One aspect provides a method for selectively hybridizing a probe to a polynucleotide by contacting a sample containing a first and second polynucleotide with a probe. The probe includes a number of nucleotides complementary to the first or second polynucleotide in the region of mismatch between the first and second polynucleotides. Another aspect provides arrays including the disclosed probes and methods of using the arrays and the probes.

Abstract: Double-stranded RNA (dsRNA) induces sequence-specific post-transcriptional gene silencing in many organisms by a process known as RNA interference (RNAi). Using a Drosophila in vitro system, we demonstrate that 19-23 nt short RNA fragments are the sequence-specific mediators of RNAi. The short interfering RNAs (siRNAs) are generated by an RNase III-like processing reaction from long dsRNA. Chemically synthesized siRNA duplexes with overhanging 3? ends mediate efficient target RNA cleavage in the lysate, and the cleavage site is located near the center of the region spanned by the guiding siRNA. Furthermore, we provide evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the produced siRNP complex.

Abstract: Double-stranded RNA (dsRNA) induces sequence-specific post-transcriptional gene silencing in many organisms by a process known as RNA interference (RNAi). Using a Drosophila in vitro system, we demonstrate that 19-23 nt short RNA fragments are the sequence-specific mediators of RNAi. The short interfering RNAs (siRNAs) are generated by an RNase III-like processing reaction from long dsRNA. Chemically synthesized siRNA duplexes with overhanging 3? ends mediate efficient target RNA cleavage in the lysate, and the cleavage site is located near the center of the region spanned by the guiding siRNA. Furthermore, we provide evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the produced siRNP complex.

Abstract: The present invention relates to a method for enzymatically synthesizing chemically modified RNA by using RNA-dependent RNA polymerases (RdRp), especially RdRps from viruses of the Caliciviridae family. The method of the present invention is particularly useful for preparing RNA molecules of increased stability especially with respect to RNA degradation, for example for in vivo applications. Further subject matter of the present invention relates to a kit for carrying out the enzymatic synthesis of the chemically modified RNA.

Abstract: The present invention is in the fields of biotechnology and molecular biology. More particularly, the present invention relates to cloning or subcloning one or more nucleic acid molecules comprising one or more type IIs restriction enzyme recognition sites. The present invention also embodies cloning such nucleic acid molecules using recombinational cloning methods such as those employing recombination sites and recombination proteins. The present invention also relates to nucleic acid molecules (including RNA and iRNA), as well as proteins, expressed from host cells produced using the methods of the present invention.

Abstract: The present invention relates to a method for the preparation of a labeling material (labeling agent) usable for non-radioactive selective labeling of proteins produced by in vitro translation with fluorophore or biotin; and a method for selective labeling of proteins produced by in vitro translation using the said labeling material. More specifically, the present invention provides a method for preparing a labeling material usable for selective labeling of a target protein produced only from the gene added to the cell-free protein synthesis reaction mixture by an experimenter without labeling pre-existing proteins in the reaction mixture, for which only one type of tRNA prepared by in vitro transcription is used instead of “total tRNA mixture”. The present invention also provides a method for labeling of the protein produced by in vitro translation by using the labeling material prepared by the above method.

Abstract: The invention features compositions and methods that are useful for reducing the expression or activity of a specified gene in a eukaryotic cell.

Abstract: The present invention provides a cell comprising a first heterologous nucleic acid construct and a second heterologous nucleic acid construct, wherein each of said first and second heterologous nucleic acid constructs comprises: A. a first nucleotide sequence encoding a nucleotide sequence of interest (NOI); and B.

Abstract: The present invention provides compositions, methods and kits for use in the detection of small RNA sequences, which allow for rapid and robust amplification and detection. The methods provide improved sensitivity and efficiency in the amplification-based detection of small RNA sequences by incorporating one or more base-modified duplex-stabilizing dNTPs during reverse transcription and/or amplification.

Abstract: Improved methods of studying RNA molecules are provided. In particular, methods of treating mixtures of RNA molecules so as to enrich the mixture for a desired type of RNA molecule are provided. For example, the methods permit depletion of mRNA from complex mixtures to facilitate study of microRNAs in the mixture.

Abstract: Translation of the hepatitis C virus (HCV) RNA is mediated by the interaction of ribosomes and cellular proteins with an internal ribosome entry site (IRES) located within the 5?untranslated region (5?UTR). We have investigated whether small RNA molecules corresponding to the different stem-loop (SL) domains of the HCV IRES, when introduced in trans, can bind to the cellular proteins and antagonize their binding to the viral IRES, thereby inhibiting HCV IRES-mediated translation. We have found that an RNA molecule corresponding to SL III of the HCV IRES could efficiently inhibit HCV IRES-mediated translation in a dose-dependent manner without affecting cap-dependent translation. The SL III RNA was also found to bind efficiently to most of the cellular proteins which interacted with the HCV 5?UTR. A smaller RNA corresponding to SL e+f of domain III also strongly and selectively inhibited HCV IRES-mediated translation.

Abstract: Novel cap analogs which are easily synthesized, resulting in high levels of capping efficiency and transcription and improved translation efficiencies are provided. Such caps are methylated at the N7 position of one or both guanosines of the dinucleotide cap as well as at the 3? position on the ribose ring. Substituent groups on the ribose ring also result in the cap being incorporated in the forward orientation. Also provided are methods useful for preparing capped analogs and using mRNA species containing such analogs are also contemplated herein, as well as kits containing the novel cap analogs.

Abstract: Provided herein are libraries of nucleic acid species each comprising a transcription unit having a promoter region operatively linked to a coding sequence. The coding sequence of each nucleic acid species encodes a RNA cleavage substrate comprising a unique compomer species and a cleavage site. Each compomer species has a molecular mass distinguishable from the molecular mass of other compomer species in the library, and cleavage at a cleavage site releases a polynucleotide comprising the compomer species from the RNA cleavage substrate.

Abstract: The present invention relates to newly identified mRNA stabilizing elements useful for the production of a target fermentation product, such as e.g. vitamins or enzymes, in particular riboflavin (vitamin B2), biotin, pantothenic acid (vitamin B5), folic acid, thiamin, pyridoxine (vitamin B6), vitamin B12, xylanase, amylase, protease, glucanase, amylomaltase or maltogenic amylase.

Abstract: Briefly described, embodiments of this disclosure include ligand-regulable transactivation systems, methods of producing ligand-regulable transactivation systems, methods of using ligand-regulable transactivation systems, reporter polynucleotides, method of producing reporter polynucleotides, activator fusion proteins, methods of producing activator fusion proteins, methods of regulating gene expression in vitro and in vivo for gene therapy, methods of screening estrogen receptor modulators with therapeutic treatments (e.g., anticancer, antiosteoporosis, and hormone replacement treatments), method of screening compounds (e.g., drugs and environmental pollutants) for the estrogenic effect, methods of evaluating the estrogen receptor pathway under different pathological conditions are provided, and the like.

Abstract: The present invention provides a composition and method for stabilizing ribonucleic acid (RNA) from biological samples such that the ribonucleic acid within the sample remains stable at room temperature. The composition comprises an anionic detergent and a buffering agent at a pH of about 5 to about 8.2 and is used in methods for extracting and storing ribonucleic acid from the biological sample.

Abstract: A polypeptide having a novel endoribonuclease activity; a nucleic acid encoding the polypeptide; recombinant DNA having the nucleic acid therein; a transformant transformed with the recombinant DNA; a process for producing the polypeptide comprising the steps of cultivating the transformant and collecting the polypeptide from the culture; a process for producing a digest of single-stranded RNA comprising the step of reacting the polypeptide with the single-stranded RNA; and a method for the digestion of single-stranded RNA.

Abstract: Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled substrate to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.

Abstract: Methods and means are provided to modulate gene silencing in eukaryotes through the alteration of the functional level of particular DICER or DICER like proteins. Also provided are methods and means to modulate post-transcriptional gene silencing in eukaryotes through the alteration of the functional level of proteins involved in transcriptional silencing of the silencing RNA encoding genes.

Abstract: The present invention provides a method of covalently joining a DNA strand to an RNA strand comprising (a) forming a topoisomerase-DNA intermediate by incubating a DNA cleavage substrate comprising a topoisomerase cleavage site with a topoisomerase specific for that site, wherein the topoisomerase-DNA intermediate has one or more 5? single-strand tails; and (b) adding to the topoisomerase-DNA intermediate an acceptor RNA strand complementary to the 5? single-strand tail under conditions permitting a ligation of the covalently bound DNA strand of the topoisomerase-DNA intermediate to the RNA acceptor strand and dissociation of the topoisomerase, thereby covalently joining the DNA strand to the RNA strand. The present invention also provides a method of tagging a 5? end of an RNA molecule. The present invention further provides a DNA-RNA molecule which has been joined in vitro by the use of a topoisomerase. The present invention also provides a method of tagging a 5? end of an mRNA.

Abstract: Methods and compositions for producing siRNAs, e.g., in the form of a d-siRNA composition, from dsRNAs are provided. In the subject methods, a dsRNA is contacted with a composition that includes an activity that cleaves dsRNA into siRNAs, where the composition efficiently cleaves dsRNA into siRNAs. siRNAs produced by the subject methods find use in a variety of applications, particularly in applications where the specific reduction or silencing of a gene is desired. Also provided are kits for use in practicing the subject invention.

Abstract: This invention provides RNA, oligoribonucleotide, and polyribonucleotide molecules comprising pseudouridine or a modified nucleoside, gene therapy vectors comprising same, methods of synthesizing same, and methods for gene replacement, gene therapy, gene transcription silencing, and the delivery of therapeutic proteins to tissue in vivo, comprising the molecules. The present invention also provides methods of reducing the immunogenicity of RNA, oligoribonucleotide, and polyribonucleotide molecules.

Abstract: The present invention relates generally to the field of screening or diagnostic applications in which a target is required to be displayed for binding to another molecule, or interaction or reaction with another molecule. In particular, the present invention relates to the use of DNA/protein interactions to immobilize or present one or more biomolecules for screening purposes.

Abstract: The present invention relates to novel double stranded RNA (dsRNA) structures and dsRNA expression constructs, methods for generating them, and methods of utilizing them for silencing genes. Desirably, these methods specifically inhibit the expression of one or more target genes in a cell or animal (e.g., a mammal such as a human) without inducing toxicity. These methods can be used to prevent or treat a disease or infection by silencing a gene associated with the disease or infection. The invention also provides methods for identifying nucleic acid sequences that modulate a detectable phenotype, such as the function of a cell, the expression of a gene, or the biological activity of a target polypeptide.

Abstract: Methods and reagents for effecting transgene expression in Hepatic Stellate Cells (HSC) comprising a 2.2 kb fragment of the promoter region of the Glial Fibrillary Acidic Protein (GFAP) gene, said construct being up-regulated by pro-fÊbronetic cytokines such as TGF-beta 1 in a dose and time dependent manner, and uses thereof.

Abstract: A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. The process may be practiced ex vivo or in vivo. The RNA has a region with double-stranded structure. Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods.

Abstract: Methods and compositions for producing siRNAs, e.g., in the form of a d-siRNA composition, from dsRNAs are provided. In the subject methods, a dsRNA is contacted with a composition that includes an activity that cleaves dsRNA into siRNAs, where the composition efficiently cleaves dsRNA into siRNAs. siRNAs produced by the subject methods find use in a variety of applications, particularly in applications where the specific reduction or silencing of a gene is desired. Also provided are kits for use in practicing the subject invention.

Abstract: Methods and kits are provided for performing multiple rounds of sense RNA synthesis. The sense RNA molecules can be used in various research and diagnostic applications, such as gene expression studies involving nucleic acid microarrays.

Abstract: A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. The process may be practiced ex vivo or in vivo. The RNA has a region with double-stranded structure. Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods.

Abstract: Based at least in part on an understanding of the mechanisms by which small RNAs (e.g., naturally-occurring miRNAs) mediate RNA silencing in plants, rules have been established for determining, for example, the degree of complementarity required between an RNAi-mediating agent and its target, i.e., whether mismatches are tolerated, the number of mismatches tolerated, the effect of the position of the mismatches, etc. Such rules are useful, in particular, in the design of improved RNAi-mediating agents which allow for more exact control of the efficacy of RNA silencing.

Abstract: Compositions and methods for the inducible expression of genes in eukaryotic cells. Expression of a nucleotide sequence of interest is controlled by a regulatory fusion protein that consists of a transcription blocking domain and a ligand-binding domain. When the cognate ligand for the ligand-binding domain is present, transcription of the nucleotide sequence of interest is blocked. Upon removal of the cognate ligand, the nucleotide sequence of interest is transcribed. The method is useful for large scale production of a desired product in eukaryotic cells.

Abstract: This invention relates generally to systems and methods for identifying and selecting, desired proteins or nucleic acid molecules by linking mRNA, with known or unknown sequences, to its translated protein to form a cognate pair. The cognate pair is selected based upon desired properties of the protein or the nucleic acid. This method also includes the evolution of a desired protein or nucleic acid molecule by amplifying the nucleic acid portion of the selected cognate pair, introducing variation into the nucleic acid, translating the nucleic acid, attaching the nucleic acid to its protein to form a second cognate pair, and re-selecting this cognate pair based upon desired properties. Modified mRNAs operable to crosslink to tRNAs are also provided. Methods of producing a psoralen monoadduct or a crosslink are also provided.

Abstract: Methods, apparatus, systems, computer programs and computing devices related to biologically assembling and/or synthesizing peptides and/or proteins are disclosed.

Abstract: Compositions and methods for the inducible expression of genes in eukaryotic cells. Expression of a nucleotide sequence of interest is controlled by a regulatory fusion protein that consists of a transcription blocking domain and a legends-binding domain. When the cognate ligand for the ligand-binding domain is present, transcription of the nucleotide sequence of interest is blocked. Upon removal of the cognate ligand, the nucleotide sequence of interest is transcribed. The method is useful for large scale production of a desired product in eukaryotic cells.

Abstract: Compositions and methods of treatments of cells are provided for altering the phenotype of a cell by administering an oligonucleotide complex to the cell, the complex having two strands and chemical modifications.

Abstract: Double-stranded RNA (dsRNA) induces sequence-specific post-transcriptional gene silencing in many organisms by a process known as RNA interference (RNAi). Using a Drosophila in vitro system, we demonstrate that 19-23nt short RNA fragments are the sequence-specific mediators of RNAi. The short interfering RNAs (siRNAs) are generated by an RNase III-like processing reaction from long dsRNA. Chemically synthesized siRNA duplexes with overhanging 3? ends mediate efficient target RNA cleavage in the lysate, and the cleavage site is located near the center of the region spanned by the guiding siRNA. Furthermore, we provide evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the produced siRNP complex.

Abstract: A circularly permuted chimeric pRNA molecule carrying a stabilized biologically active RNA, such as a ribozyme.