Abstract: Methods, compositions, and kits that include small hairpin RNA (shRNA) useful for inhibition of gene expression, such as viral-mediated gene expression, are described.

Abstract: Methods, compositions, and kits that include small hairpin RNA (shRNA) useful for inhibition of gene expression, such as viral-mediated gene expression, are described.

Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.

Abstract: Methods, compositions, and kits that include small hairpin RNA (shRNA) useful for inhibition of gene expression, such as viral-mediated gene expression, are described.

Abstract: We describe new hybridization probes and methods for their use in detection, identification, and quantitation of polynucleotides such as RNA and DNA. Ordinary short oligonucleotide probes usually provide higher sequence-specificity but lower efficacy of hybridization than longer ordinary polynucleotide probes where both are fully complementary to the target polynucleotide. Our new polynucleotide probes combine the hybridization efficacy of long probes with the sequence-specificity of short probes. The polynucleotide probes contain a target binding domain and a binding enhancer domain, where the binding enhancer domain does not for stable structures under hybridizing conditions with the target binding domain or its corresponding target. These binding enhancer domains are able to improve the hybridization features of the target binding domain as well as the signal-to-noise ratio for target detection.

Abstract: The invention provides allosterically regulatable polynucleotides capable of target-dependent circularization and topological linkage to a target nucleic acid molecule. Polynucleotides of the invention include a target binding sequence and a regulatory element which prevents circularization in the absence of the target binding. Polynucleotides may include a catalytic domain, allowing circularization to proceed via catalysis when the target binding sequence of the polynucleotide is bound to the target. Topologically linked polynucleotides may be used for detection of target molecules or to inhibit transcription or translation of the target.

Abstract: The present invention is directed to novel nucleic acid molecules and methods for their use. More specifically, the novel nucleic acid molecules of the present invention are capable of tightly and specifically interacting with a target molecule of interest not only through standard Watson-Crick base pairing, but also through additional features which allow the antisense molecules to become topologically “locked” onto the target nucleic acid, thereby imparting improved transcription and translation inhibitory properties.

Abstract: Methods of preparing gene-specific oligonucleotide libraries are disclosed. In one embodiment a double-stranded RNA corresponding to both sense and antisense strands of mRNA is digested by ribonuclease to produce short RNA fragments. In subsequent ligation steps, flanking oligoribonucleotides of defined sequences may be attached to the 3- and 5-ends of each fragment by RNA ligase (such as T4 RNA ligase). The products of ligation can be reverse transcribed and PCR amplified (RT-PCR) using the oligonucleotides attached to the gene-derived sequences as primer-binding sites. Various methods for incorporating libraries into expression vectors allowing expression of either siRNAs or shRNAs are also disclosed.