Abstract: It has been discovered that certain natural mRNAs serve as metabolite-sensitive genetic switches wherein the RNA directly binds a small organic molecule. This binding process changes the conformation of the mRNA, which causes a change in gene expression by a variety of different mechanisms. Modified versions of these natural “riboswitches” (created by using various nucleic acid engineering strategies) can be employed as designer genetic switches that are controlled by specific effector compounds. Such effector compounds that activate a riboswitch are referred to herein as trigger molecules. The natural switches are targets for antibiotics and other small molecule therapies.

Abstract: The present invention relates to a method for the targeted selection of a double-stranded ribonucleic acid (dsRNA) consisting of two single strands that exhibits increased effectiveness in inhibiting the expression of a target gene by means of RNA interference, wherein at least end of the dsRNA comprises a nucleotide overhang of 1 to 4 unpaired nucleotides in length; wherein the unpaired nucleotide adjacent to the terminal nucleotide pair comprises a purine base; and wherein the terminal nucleotide pair on both ends of the dsRNA is a G-C pair, or at least two of the last four consecutive terminal nucleotide pairs are G-C pairs.

Abstract: The invention provides short interfering nucleic acids, either single-stranded or double-stranded, that cause RNAi-induced degradation of mRNA from the Nav1.8 sodium channel gene; to pharmaceutical compositions comprising such short interfering nucleic acids; recombinant vectors comprising such short interfering nucleic acids; a method for inhibiting translation of an mRNA; a method for inhibiting expression of a polypeptide; a method for blocking the membrane potential in a cell; a method for blocking the sodium current in a cell; and a method for inhibiting chronic pain.

Abstract: Described are compositions and methods relating to gene therapy, particularly as applied to hematopoietic progenitor (HP) cells, to transduced cells and methods of obtaining them, and to methods of using them to provide prolonged engraftment of modified hematopoietic cells in human subjects. The invention particularly relates to ex vivo gene therapy of HP cells for treatment or prevention of HIV infection.

Abstract: Naturally occurring miRNAs that regulate human oncogenes and methods of use thereof are described. Suitable nucleic acids for use in the methods and compositions described herein include, but are not limited to, pri-miRNA, pre-miRNA, mature miRNA ,or fragments of variants thereof that retain the biological activity of the mature miRNA and DNA encoding a pri-miRNA, pre-miRNA, mature miRNA, fragments or variants thereof, or regulatory elements of the miRNA. The compositions are administered to a subject prior to administration of a cytotoxic therapy in an amount effective to sensitize cells or tissues to be treated to the effects of the cytotoxic therapy.

Abstract: In one aspect, the invention provides methods and compositions for the expression of small RNA molecules within a cell using a retroviral vector (FIG. 1A). Small interfering RNA (siRNA) can be expressed using the methods of the invention within a cell. In a further aspect, the invention provides methods for producing siRNA encoding lentivirus where the siRNA activity may interfere with the lentiviral life cycle. In yet a further aspect, the invention provides methods for expression of a small RNA molecule within a cell, such as an siRNA capable of downregulating CCR5, wherein expression of the small RNA molecule is relatively non-cytotoxic to the cell. The invention also includes small RNA molecules, such as an siRNA capable of downregulating CCR5, that are relatively non-cytotoxic to cells.

Abstract: The invention provides methods and compositions for the expression of small RNA molecules within a cell using a lentiviral vector. The methods can be used to express doubles stranded RNA complexes. Small interfering RNA (siRNA) can be expressed using the methods of the invention within a cell, which are capable of down regulating the expression of a target gene through RNA interference. A variety of cells can be treated according to the methods of the invention including embryos, embryogenic stem cells, allowing for the generation of transgenic animals or animals constituted partly by the transduced cells that have a specific gene or a group of genes down regulated.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of siRNAs are disclosed including those directed to nucleotide sequences for DGAT2.

Abstract: The present invention relates to compounds, small interfering RNAs and compositions and methods of inhibiting tumorigenesis and methods of inhibiting tumor cell growth and proliferation using agents that inhibit the hedgehog and Gli signaling pathway, including agents that inhibit GLI synthesis and/or function. The present invention also relates to particular biomarkers that can be used in the diagnosis and prognosis of melanomas. Methods of treating cancer, including melanoma are also provided using small organic compounds, siRNAs and blocking antibodies that inhibit or block the SHH/GLI pathway. In addition, the use of agents that inhibit other signaling pathways is contemplated for use as second agents to be used in conjunction with the inhibitors of the GLI pathway.

Abstract: The present invention relates to a novel LPS-responsive and Beige-like Anchor gene (lrba), variants of the lrba gene, fragments of the lrba gene, and polypeptides encoded thereby. The subject invention also pertains to lrba interfering RNA, and uses thereof. In another aspect, the present invention also includes methods of inhibiting tumor growth in a patient by suppressing lrba function.

Abstract: The present invention provides short antisense oligonucleotide compositions and methods for their use in the treatment of Bcl-2-associated diseases like cancer, such as follicular lymphoma (FL). The antisense oligonucleotides contain sequences that hybridize to Bcl-2 nucleic acids, the gene products of which are known to interact with the tumorigenic protein Bcl-2. The use of novel short antisense oligonucleotides, from 7 bases to 9 bases in length, is described in this invention. The invention also describes certain specific sequences which are longer than 9 bases and are 11 or 15 bases long. Used alone, or in conjunction with other antisense oligonucleotides, these antisense oligonucleotide compositions inhibit the proliferation of cancer cells.

Abstract: This invention provides methods for increasing the susceptibility of cells to DNA-damaging agents, and for treating tumors in a subject, comprising introducing antisense that prevent expression of DNA dependent protein kinase catalytic subunit Ku70 or Ku80, wherein the antisense is in an amount sufficient to increase the sensitivity of the cells and tumors to heat, chemical, or radiation-induced DNA damage.

Abstract: The present invention provides novel methods and compositions for the diagnosis, prognosis and treatment of pancreatic cancer. The invention also provides methods of identifying anti-pancreatic cancer agent.

Abstract: The present invention relates to the use of a nucleic acid encoding a chimeric transfer RNA (tRNA), which chimeric tRNA originates from the modification of a tRNA by insertion of an RNA into the stem-loop of the anticodon of the tRNA and/or by substitution of all or part of the stem-loop of the anticodon of the tRNA with an RNA, for the production of the RNA or of a part of the RNA, in a cell.

Abstract: A method and antisense compound for inhibiting the growth of pathogenic bacterial cells are disclosed. The compound contains no more than 12 nucleotide bases and has a targeting nucleic acid sequence of no fewer than 10 bases in length that is complementary to a target sequence containing or within 10 bases, in a downstream direction, of the translational start codon of a bacterial mRNA that encodes a bacterial protein essential for bacterial replication. The compound binds to a target mRNA with a Tm of between 50° to 60° C. The relatively short antisense compounds are substantially more active than conventional antisense compounds having a targeting base sequence of 15 or more bases.

Abstract: The present invention provides catalytic RNA molecules having cis or trans aminoacylation activity. The catalytic RNA molecules having cis aminoacylation activity comprise a catalytic domain and an aminoacylation domain. The catalytic RNA molecules having trans aminoacylation activity only have the catalytic domain. A method is provided for constructing and screening of these molecules. These molecules are suitable for aminoacylating with specific amino acids.

Abstract: The present invention provides improved oligomeric compound, in particular oligonucleotide compounds, and methods for modulating the expression of the Bcl-2 gene in humans. In particular, this invention relates to oligomeric compounds of 10-30 nucleobases in length which comprise a target binding domain that is specifically hybridizable to a region ranging from base position No. 1459 (5?) to No. 1476 (3?) of the human Bcl-2 mRNA, said target binding domain having the formula: 5?-[(DNA/RNA)0-1-(LNA/LNA*)2-7-(DNA/RNA/LNA*)4-14-(LNA/LNA*)2-7-(DNA/RNA)0-1]-3? and said target binding domain comprising at least two LNA nucleotides or LNA analogue nucleotides linked by a phosphorothioate group (—O—P(O,S)—O—). In particular the oligo is predominantly or fully thiolated. The invention also provides the use of such oligomers or conjugates or chimera for the treatment of various diseases associated with the expression of the Bcl-2 gene, such as cancer.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of siRNAs are disclosed.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of siRNAs are disclosed including those directed to RRM 2.

Abstract: The present disclosure relates to an LNA oligonucleotide consisting of a sequence selected from the group consisting of 5?-(Tx)GxGxcsasasgscsastscscsTxGxT-3? and 5?-(Gx)TxTxascstsgscscststscsTxTxA-3?, wherein capital letters designate a beta-D-oxy-LNA nucleotide analogue, small letters designate a 2-deoxynucleotide, underline designates either a beta-D-oxy-LNA nucleotide analogue or a 2-deoxynucleotide, subscript “s” designates a phosphorothioate link between neighbouring nucleotides/LNA nucleotide analogues, and subscript “x” designates either a phosphorothioate link or a phosphorodiester link between neighbouring nucleotides/LNA nucleotide analogues, and wherein the sequence is optionally extended by up to five 2-deoxynucleotide units. The LNA oligonucleotides are useful for modulating the expression of hypoxia-inducible factor-1a (HIF-1a), e.g. in the treatment of cancer diseases, inhibiting angiogenesis, inducing apoptosis, preventing cellular proliferation, or treating an angiogenic disease, e.g.

Abstract: The present invention relates to riboswitches that have been engineered to regulate pre-mRNA splicing. In particular, the insertion of a high affinity theophylline binding aptamer into the 3? splice site region, 5? splice site region, or branchpoint sequence (BPS) of a pre-mRNA modulates RNA splicing in the presence of theophylline. Accordingly, the aspects of the present invention include, but are not limited to, theophylline-dependent riboswitches which modulate RNA splicing, methods of modulating RNA splicing using theophylline and its corresponding riboswitches, methods of improving/identifying theophylline-dependent riboswitches, methods of treating diseases associated with or caused by abnormal RNA splicing.

Abstract: Compounds, compositions and methods are provided for modulating the expression of PTP1B. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding PTP1B. Methods of using these compounds for modulation of PTP1B expression and for treatment of diseases associated with expression of PTP1B are provided.

Abstract: A method for the preparation of an antisense oligonucleotide or derivative thereof comprising the steps of: selecting a target nucleic acid, if necessary elucidating its sequence; generating the antisense oligonucleotide with the proviso that: the oligonucleotide comprises at least 8 residues; the oligonucleotide comprises at maximum twelve elements, which are capable of forming three hydrogen bonds each to cytosine bases; the oligonucleotide does not contain four or more consecutive elements, capable of forming three hydrogen bonds each with four consecutive cytosine bases (CCCC) within the target molecule or alternatively four or more consecutive elements of GGGG; the oligonucleotide does also not contain 2 or more series of three consecutive elements, capable of forming three hydrogen bonds each with three consecutive cytosine bases (CCC) within the target molecule, or alternatively 2 or more series of three consecutive elements of GGG; and the ratio between residues forming two hydrogen bonds per residue

Abstract: The present invention utilizes three families of bacterial enzymes, which play a key role in mycothiol biosynthesis. The three families are bacterial cysteine:glucosaminyl inositol ligases (MshC) with catalytic ligase activity for ligation of glucosaminyl inositol and cysteine, bacterial acetyl-CoA:Cys-GlcN-Ins acetyltransferases (MshD) with catalytic activity for addition of an acetyl group to Cys-GlcN-Ins and bacterial MshA glycosyltransferase with catalytic activity for production of GlcNAc-Ins. The invention provides methods for using the mycothiol biosynthesis ligases, acetyltransferases or glycosyltransferases in drug screening assays to determine compounds that inhibit activity. The invention provides for treatment of actinomycete infections in mammals using antibiotics that inhibit production or activity of the enzymes of mycothiol biosynthesis, in particular MshC, MshD or MshA, and thereby reduce the production of mycothiol and the virulence of the infecting bacteria.

Abstract: The present invention discloses antisense poly-2?-O-(2,4-dinitrophenyl) oligoribonucleotides which are capable of down regulating the expression of the RI? subunit of protein kinase A. An example is 5?-GGCUGCGUGCCUCCUCACUGG (named antisense poly-DNP RNA-21) or a sequence which has a one-base mismatch therewith. The antisense oligoribonucleotide can be synthesized by in vitro transcription followed by chemical derivatization. The base sequence of the oligoribonucleotides is complementary to that of nt 110 to 130 in RI?/PKA mRNA. The antisense poly-DNP RNA-21 was found to inhibit cell growth with IC50 values in the nanomolar range. These oligonucleotides can be used as effective anti-cancer agents.

Abstract: The application discloses methods for identifying and using compounds that inhibit extra-cellular matrix (ECM) degradation and inflammation, using a polypeptide sequence including SEQ ID NO: 17-127 (hereinafter “TARGETS”) and fragments thereof, expression inhibitory agents such as antisense polynucleotide, a ribozyme, and a small interfering RNA (siRNA), comprising a nucleic acid sequence complementary to, or engineered from, a naturally occurring polynucleotide sequence encoding a polypeptide of SEQ ID NO: 17-127, useful in pharmaceutical compositions comprising said agent, for the treatment, or prevention, of chronic joint degenerative and/or inflammatory diseases such as rheumatoid arthritis.

Abstract: The present invention relates to the significant functional role of several C. elegans genes and of their corresponding gene products in spindle formation or microtubule function during cell division that could be identified by means of RNA-mediated interference (RNAi) and to the identification and isolation of functional orthologs of said genes including all biologically functional derivatives thereof The invention further relates to the use of said genes and gene products (including said orthologs) in the development or isolation of anti-proliferative agents, particularly their use in appropriate screening assays, and their use for diagnosis and treatment of proliferative and other diseases. In particular, the invention relates to the use of small interfering RNAs derived from said genes for the treatment of proliferative diseases.

Abstract: Methods and compositions for treating scarring conditions associated with increased expression of connective tissue growth factor (CTGF). Aspects of the invention include ribozymes that cleave mRNA targets required for CTGF expression, cells containing anti-CTGF ribozymes and vectored anti-CTGF ribozymes suitable for delivery to cellular targets capable of CTGF expression.

Abstract: The present invention provides methods and combinations of compositions for the modulation of diseases caused by a subject possessing a disease-specific nucleic acid sequence. Included are methods for the treatment, prevention and/or inhibition of the diseases by administering a combination of a prodrug component, drug and catalytic component such that the drug is catalytically released when contacting the combination to the disease-specific nucleic acid sequence.

Abstract: Novel lipid-nucleic acid particulate complexes which are useful for in vitro or in vivo gene transfer are described. The particles can be formed using either detergent dialysis methods or methods which utilize organic solvents. Upon removal of a solubilizing component (i.e., detergent or an organic solvent) the lipid-nucleic acid complexes form particles wherein the nucleic acid is serum-stable and is protected from degradation. The particles thus formed have access to extravascular sites and target cell populations and are suitable for the therapeutic delivery of nucleic acids.

Abstract: This invention relates to new polypeptides which exhibit kinase activity or, more specifically, which show phosphoinositide (PI) 3-kinase activity. Such polypeptides are involved in pathways responsible for cellular growth and differentiation. An isolated polypeptide which possesses PI3-kinase activity when produced by recombinant production in insect cells is disclosed.

Abstract: Compounds and methods for modulating cell proliferation, preferably inhibiting the proliferation of tumor cells are described. Compounds that may be used to modulate cell proliferation include antisense oligonucleotides complementary to regions of the mammalian ribonucleotide reductase genes.

Abstract: Compositions and methods relating to small interfering RNA (siRNA) polynucleotides are provided as pertains to modulation of biological signal transduction. Shown are siRNA polynucleotides that interfere with expression of members of the protein tyrosine phosphatase (PTP) class of enzymes that mediate signal transduction, and with certain MAP kinase kinases (MKK). In certain preferred embodiments siRNA modulate signal transduction pathways comprising SHP2, cdc14a/b, cdc25A/B/C, KAP, PTP-?, PRL-3, CD45, dual specificity phosphatase-3 (DSP-3), MKK-4, and/or MKK-7. Modulation of PTP-mediated biological signal transduction has uses in diseases associated with defects in cell proliferation, cell differentiation and/or cell survival, such as metabolic disorders (including diabetes and obesity), cancer, autoimmune disease, infectious and inflammatory disorders and other conditions.

Abstract: The present invention provides methods for preventing retinal ganglion cell death in the glaucomatous eye and methods for suppressing apoptosis-specific eIF5A1 expression through the use of antisense oligonucleotides targeted to human apoptosis-specific eIF5A1.

Abstract: Described are compositions and methods relating to gene therapy, particularly as applied to hematopoietic progenitor (HP) cells, to transduced cells and methods of obtaining them, and to methods of using them to provide prolonged engraftment of modified hematopoietic cells in human subjects. The invention particularly relates to ex vivo gene therapy of HP cells for treatment or prevention of HIV infection.

Abstract: The invention provides a method of increasing expression of p21WAF1/Cip 1 in cells to decrease proliferation of the cells, the method comprising decreasing levels of PP5 protein in the cells. The invention further provides a method of treating or preventing an abnormal condition resulting from a defect in a tumor suppressor gene in a subject that results in decreased induction of p21WAF1/Cip 1 in the cells of the subject, the method comprising administering to the subject an amount of a compound effective to decrease levels of PP5 protein in the cells of the subject.

Abstract: This disclosure provides TRT antisense oligonucleotides, methods of detecting TRT, methods of diagnosing telomerase-related conditions, methods of diagnosing and providing a prognosis for cancer, and methods of treating telomerase-related conditions, including cancer.

Abstract: The present invention feature antisense IAP oligonucleotides and other negative regulators of the IAP anti-apoptotic pathway, and methods for using them to enhance apoptosis.

Abstract: Compounds, compositions and methods are provided for modulating the expression of HIF1? and/or HIF2?. The compositions comprise oligonucleotides, targeted to nucleic acid encoding HIF1? and HIF2?. Methods of using these compounds for modulation of HIF1? and/or HIF2? expression and for diagnosis and treatment of disease associated with expression of HIF1? and/or HIF2? are provided.

Abstract: A stress-phosphorylated endoplasmic reticulum protein, Nogo B, is provided. The protein is hyperphosphorylated as a result of exposure of cells to stress. Two transcripts of Nogo B are identified in human tissues, and the longer transcript is predominant in human brain tumor samples.

Abstract: Highly specific hammerhead ribozymes are provided that human target estrogen receptor mRNA. These ribozymes, designated RZ1 through RZ7 provide predictable mRNA cleavage products. Methods for inhibiting estrogen-dependent tumor growth, such as that characteristic of breast cancer, are also provided employing these ribozymes. One or both of the ribozymes may be used together or separately with equal efficiency. The ribozymes possess a sequence region with a catalytic core that provides the attributed catalytic activity to these ribozymes.

Abstract: Compounds, compositions and methods are provided for modulating the expression of PTP1B. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding PTP1B. Methods of using these compounds for modulation of PTP1B expression and for treatment of diseases associated with expression of PTP1B are provided.

Abstract: A method is described for cleaving a nucleic acid substrate with a nucleic acid enzyme at a cleavage site comprising mixing the substrate with the enzyme, wherein the substrate includes a 7 nucleotide sequence with at least 6 nucleotides 3? to the cleavage site and at least 1 nucleotide 5? to the cleavage site and of formula: 5?-H?GNNHNN-3? wherein each N is a nucleotide which may be the same or different, H is a nucleotide selected from the group consisting of A, U, C, and T, and is the site of cleavage, and H? is a ribonucleotide selected from the group consisting of A, U, and C, wherein (i) the first nucleotide 3? to the cleavage site is capable of forming a wobble pair with the enzyme, (ii) the second, third, fifth, and sixth nucleotides 3? to the cleavage site are capable of forming conventional Watson-Crick base pairs with the enzyme, (iii) the fourth nucleotide 3? to the cleavage site is capable of forming a non-conventional Watson-Crick base pair with the enzyme, and (iv) the first nucleotide 5? to

Abstract: Compounds, compositions and methods are provided for modulating the expression of hypoxia-inducible factor 1 alpha. The compositions comprise oligonucleotides, targeted to nucleic acid encoding hypoxia-inducible factor 1 alpha. Methods of using these compounds for modulation of hypoxia-inducible factor 1 alpha expression and for diagnosis and treatment of disease associated with expression of hypoxia-inducible factor 1 alpha are provided.

Abstract: The present invention discloses deoxyribonucleic acid enzymes—catalytic or enzymatic DNA molecules—capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

Abstract: A strategy for suppressing specifically or partially specifically an endogenous gene and introducing a replacement gene, said strategy comprising the steps of: 1. providing suppressing nucleic acids or other suppression effectors able to bind to an endogenous gene, gene transcript or gene product to be suppressed and 2. providing genomic DNA or cDNA (complete or partial) encoding a replacement gene wherein the suppressing nucleic acids are unable to bind to equivalent regions in the genomic DNA or cDNA to prevent expression of the replacement gene. The replacement nucleic acids have modifications in one or more third base (wobble) positions such that replacement nucleic acids still code for the wild type or equivalent amino acids.

Abstract: The present invention provides methods for synthesis and therapeutic use of DNA and RNA oligonucleotides and analogs. RNA oligonucleotides are synthesized using a small, circular DNA template which lacks an RNA polymerase promoter sequence. The RNA synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective RNA polymerase and at least two types of ribonucleotide triphosphate to form an RNA oligonucleotide multimer comprising multiple copies of the desired RNA oligonucleotide sequence. Preferably, the RNA oligonucleotide multimer is cleaved to produce RNA oligonucleotides having well-defined ends. Preferred RNA oligonucleotide multimers contain ribozymes capable of both cis (autolytic) and trans cleavage.

Abstract: Nucleozymes containing ribonucleotides and deoxyribonucleotides or nucleic acid analogues are described herein. The nucleozymes have catalytic activity and are significantly more resistant to degradation than their all-RNA ribozyme counterparts. Also described are methods for preparing the nucleozymes along with methods of using nucleozymes, e.g., as therapeutic agents.

Abstract: Method for purification and synthesis of RNA molecules and enzymatic RNA molecules in enzymatically active form.

Abstract: A vector system which can be incorporated in liposomes, comprising at least one DNA vector, the vector or vectors containing a target-cleaving hammerhead ribozymal DNA sequence under control of a promoter effective in human cells and which, upon transcription to RNA will cleave the mRNA transcribed from a target gene encoding the CCR5 or CXCR4 protein. Preferably the ribozymal DNA contains a first recognition sequence (5? to 3?): tagattg or ctcact, respectively for CCR5 or CXCR4 and downstream thereof a second recognition sequence acttg or acgttgt respectively for CCR5 or CXCR4.