Abstract: This invention provides for labeling reagents, labeled targets and processes for preparing labeling reagents. The labeling reagents can take the form of cyanine dyes, xanthene dyes, porphyrin dyes, coumarin dyes or composite dyes. These labeling reagents are useful for labeling probes or targets, including nucleic acids and proteins. These reagents can be usefully applied to protein and nucleic acid probe based assays. They are also applicable to real-time detection processes.

Abstract: The present invention relates to polymeric conjugates of adenine nucleoside analogs. In particular, the invention relates to multi-arm polyethylene glycol conjugates of adenine nucleoside analogs and use thereof. The present invention, more specifically, provides polymeric conjugates of toyocamycin and its derivatives. Furthermore, the present invention provides a method for preparing the polymeric conjugates of adenine nucleoside analogs and a method of using the same for treating a cancer, inhibiting the growth or proliferation of cancer cells, treating a viral infection, treating a disease or condition associated with abnormal expression of VEGF. Most polymeric conjugates of toyocamycin was stable in PBS but released toyocamycin in vivo to provided inhibition of cancer cell growth.

Abstract: A labeling agent comprising a plurality of nucleotide derivative units represented by Formula (1) below: (where, Z represents a nitrogen atom or CH, Y represents an uncondensed aromatic hydrocarbon group or condensed polycyclic hydrocarbon group, X1 represents O, S or Se, and X2 represents SH (or S?), Se?, a C1-4 alkyl or a morpholino group).

Abstract: Monumental adornments carrying an isolated genetic material of an organism, such as a human being, a non-human animal, a plant or a microorganism are described. Also described are methods of producing the monumental adornments.

Abstract: The present invention relates to a method for stereoselective synthesis of phosphorus compounds, whereby in the first reaction step a chiral auxiliary on the phosphorus atom of phosphoryl chloride, thiophosphoryl chloride or phosphorus trichloride is covalently bonded, the product from the first reaction step is reacted in the following step with an alcohol, thiol, or amine as the nucleophile in the presence of a base, and in the last step the chiral auxiliary is displaced from the product of the following step by a nucleophile.

Abstract: Disclosed is a composition comprising the nucleic acid and a chemical compound, said composition forming a star structure defining 3 or more stems extending from a reaction center. The stems are formed by a nucleic acid duplex and the chemical compound has been formed in the reaction center as the reaction product of 3 or more chemical groups. The advantage of the composition is that a close proximity is provided between the chemical groups in the reaction center, thereby promoting a reaction. The invention also relates to a method for preparation of the composition. The advantage of the method is that it does not require the pre-synthesis of a large number of templates and that it is not dependent upon codon/anti-codon recognition for an encoded molecule to be formed.

Abstract: The present invention is based on the in vivo demonstration that RSV can be inhibited through intranasal administration of iRNA agents as well as by parenteral administration of such agents. Further, it is shown that effective viral reduction can be achieved with more than one virus being treated concurrently. Based on these findings, the present invention provides general and specific compositions and methods that are useful in reducing RSV mRNA levels, RSV protein levels and viral titers in a subject, e.g., a mammal, such as a human. These findings can be applied to other respiratory viruses.

Abstract: Methods for the preparation of the ? isomer of a 9-deazapurine derivatives using benzyl protecting groups as the protecting groups for the 2 and 3 hydroxyl groups in ribose are provided.

Abstract: The synthesis of capped/tagged RNA, methods of use and kits providing same are contemplated. Tagged RNA permits isolation of RNA transcripts in vitro. The ability to isolate and purify capped RNA results in improved transcription and translation and provides a tool for identifying RNA-protein interactions. Such capped RNA finds use in therapeutic applications, diagnosis and prognosis and in the treatment of cancers and HIV.

Abstract: The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).

Abstract: The invention provides antisense antiviral compounds and methods of their use and production in inhibition of growth of viruses of the Flaviviridae, Picornoviridae, Caliciviridae, Togaviridae, Arteriviridae, Coronaviridae, Astroviridae and Hepeviridae families in the treatment of a viral infection. The antisense antiviral compounds are substantially uncharged morpholino oligonucleotides having a sequence of 12-40 subunits, including at least 12 subunits having a targeting sequence that is complementary to a region associated with stem-loop secondary structure within the 5?-terminal end 40 bases of the positive-sense RNA strand of the virus.

Abstract: The present invention provides methods of enhancing the efficacy and specificity of RNA silencing. The invention also provides compositions for mediating RNA silencing. In particular, the invention provides siRNAs, siRNA-like molecules, shRNAs, vectors and transgenes having improved specificity and efficacy in mediating silencing of a target gene. Therapeutic methods are also featured.

Abstract: A compound for use in the treatment or prophylaxis of viral infections such, for example as chicken pox or shingles caused by the Varicella Zoster virus, said compound having the general formula (II): wherein X is O, S, NH or CH2, Y is O, S or NH, Z is O, S or CH2, R1 is C1-6 alkyl, preferably n-alkyl, e.g., n-pentyl or n-hexyl, and one of R2 and R3 is OH, and the other of R3 and R2 is a neutral, non-polar amino acid moiety, or a pharmaceutically acceptable salt or hydrate thereof. Said neutral, non-polar amino acid moiety R2 or R3 may be (IV): in which R4, R5, R6 and R7 are each independently H or C1-2 alkyl. In preferred embodiments, one of R2 or R3 is valine, leucine, isoleucine or alanine, particularly valine.

Abstract: The invention employs an unlabeled signal primer comprising a 5? adapter sequence for detection of variations in nucleic acid target sequences. The detection system further comprises a reporter probe, the 3? end of which hybridizes to the complement of the 5? adapter sequence of the signal primer to produce a 5? overhang. Polymerase is used to fill in the overhang and synthesize the complement of the 5? overhang of the reporter probe. Synthesis of the reporter probe complement is detected, either directly or indirectly, as an indication of the presence of the target.

Abstract: Particles and conjugates for delivering nucleic acid agents. Compositions containing the particles, the conjugates, or both. Methods of using the particles, the conjugates, and the compositions.

Abstract: The invention relates to a method for the fluid-phase synthesis of a polymer formed from n monomers.

Abstract: Protective groups which may be cleaved with an activatable deprotecting reagents are employed to achieve a highly sensitive, high resolution, combinatorial synthesis of pattern arrays of diverse polymers. In preferred embodiments of the instant invention, the activatable deprotecting reagent is a photoacid generator and the protective groups are DMT for nucleic acids and tBOC for amino acids. This invention has a wide variety of applications and is particularly useful for the solid phase combinatorial synthesis of polymers.

Abstract: The present invention is concerned with the field of nucleic acid manipulation and particularly DNA manipulation, and uses thereof. Specifically, the invention pertains to methods involving the joining of nucleic acids and uses of such joined nucleic acids, for example for creating transformed microorganisms. Also, the invention pertains to materials useful in such methods.

Abstract: The invention herein disclosed provides for methods for the synthesis of polymers from monomers. In particular the method provides for the synthesis of polynucleotides from mononucleotides in the absence of catalytic enzymes. The method comprises providing an aqueous solution having a plurality of phospholipid molecules and monomer molecules; subjecting the aqueous solution to fluctuating temperature conditions; subjecting the aqueous solution to fluctuating cycles of drying and hydrating conditions; subjecting the aqueous solution to fluctuating [H+] conditions; the fluctuating conditions thereby allowing formation of a chemical bond between at least two monomers to create a polymer. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

Abstract: The present invention provides oligonucleotides including amplification primers and probes as well as pairs of said oligonucleotides that are useful in methods and uses for the determination of the sex of an avian subject. Similarly, these oligonucleotides can be used for the preparation of a kit for the determination of the sex of an avian subject. Also, the present invention provides a method for the identification of a pair of oligonucleotides for sexing of an avian subject and a kit comprising such oligonucleotides.

Abstract: An apparatus for forming a surface reservoir to hold a sample for a desirable period of time is described. The apparatus contains a platform, a solid surface disposed onto the platform, and an assembly of a bottomless vessel mounted on the solid surface. Also described is an apparatus that forms an array of surface reservoirs on a solid surface when multiple bottomless vessels are used, which can be used for high throughput applications. The apparatus can be used in applications on a solid surface, such as immunohistochemistry (IHC), oligo synthesis, peptide synthesis, ELISA, DNA array, peptide array, protein array, antibody array, tissue array, cell culturing, etc.

Abstract: Photoreactive DNA cleaving conjugate compounds are provided comprising a DNA cleaving moiety which comprises an aryl alkyne group and a polyfunctional pH-regulated DNA-binding moiety which comprises at least one or two amino groups.

Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.

Abstract: Methods, substrates, and systems for diagnostic sequencing are provided. Small circles of nucleic acids from about 10 bases to about 200 bases can be sequenced, for example using template dependent sequencing by synthesis. The use of small circles of nucleic acids allows for repeated sequencing of the same portions of the nucleic acid, providing for higher accuracy sequence determinations.

Abstract: The present invention provides methods of enhancing the efficacy and specificity of RNA silencing. The invention also provides compositions for mediating RNA silencing. In particular, the invention provides siRNAs, siRNA-like molecules, shRNAs, vectors and transgenes having improved specificity and efficacy in mediating silencing of a target gene. Therapeutic methods are also featured.

Abstract: A method and compositions for sulfurizing at least one phosphite or thiophosphite linkage in an oligonucleotide. The addition of N-alkyl imidazole to the acetyldisulfide sulfurization solution enables the use of industrially preferred solvents or solvents that are derived from renewable resources.

Abstract: The present invention provides methods of enhancing the efficacy and specificity of RNAi. The invention also provides compositions for mediating RNAi. In particular, the invention provides siRNAs, shRNAs, vectors and transgenes having improved specificity and efficacy in mediating silencing of a target gene. Therapeutic methods are also featured.

Abstract: The invention relates to modified siRNA compounds which down-regulate target gene expression, to pharmaceutical compositions comprising such compounds and to methods of treating and/or preventing the incidence or severity of various diseases or conditions associated with the genes and/or symptoms associated with such diseases or conditions.

Abstract: Disclosed are compounds of formula (I), a derivative, or a tautomer thereof, or a pharmaceutically acceptable salt of said compound or said tautomer. Also disclosed are methods of preparing compound of formula (I), a derivative, or a tautomer thereof, or a pharmaceutically acceptable salt of said compound or said tautomer. Further disclosed are methods of conducting drug discovery and research comprises applying the compound of formula (I), a derivative, or a tautomer thereof, or a pharmaceutically acceptable salt of said compound or said tautomer in an investigation.

Abstract: This disclosure relates to equipment utilized to manufacture chemical agents, particularly biopharmaceuticals. In some embodiments, reactor systems comprising a mobile carriage assembly; a disposable reaction container removably attached to the carriage assembly; and, a carriage holder into which the mobile carriage assembly may be removably inserted are provided.

Abstract: This invention relates to a process for the preparation of an (Rp)-8-substituted adenosine-3?,5?-cyclic phosphorothioic acid, or a salt or ester thereof, which comprises P-amidating 8-bromoadenosine-3?,5?-cyclic phosphoric acid, and reacting the P-amidate with a base and with carbon disulphide to yield (Rp)-8-bromoadenosine-3?,5?-cyclic phosphorothioic acid or a salt or ester thereof.

Abstract: The present invention provides methods of enhancing the efficacy and specificity of RNA silencing. The invention also provides compositions for mediating RNA silencing. In particular, the invention provides siRNAs, siRNA-like molecules, shRNAs, vectors and transgenes having improved specificity and efficacy in mediating silencing of a target gene. Therapeutic methods are also featured.

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: A method for preparing a therapeutic pegylated oligonucleotide is described. The method involves synthesis, cleavage and purification steps designed to improve the efficiency whereby the therapeutic oligonucleotide may be prepared. Also described are methods for large scale preparation at the improved efficiency.

Abstract: This disclosure provides novel reversibly terminated ribonucleotides which can be used as a reagent for DNA sequencing reactions. Methods of sequencing nucleic acids using the disclosed nucleotides are also provided.

Abstract: This invention provides a process for sequencing single-stranded DNA employing modified nucleotides.

Abstract: The invention is directed to polypeptides having any cellulolytic activity, e.g., a cellulase activity, e.g., endoglucanase, cellobiohydrolase, beta-glucosidase, xylanase, mannanse, ?-xylosidase, arabinofuranosidase, and/or oligomerase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts. The invention also provides compositions or products of manufacture comprising mixtures of enzymes comprising at least one enzyme of this invention.

Abstract: The instant invention provides polyvalent RNA nanoparticles comprising RNA motifs as building blocks that can form RNA nanotubes. The polyvalent RNA nanoparticles are suitable for therapeutic or diagnostic use in a number of diseases or disorders.

Abstract: The invention relates to 16S rRNA comprising a mutation at A1196, and to 16S rRNA further comprising a mutation at C1195 and/or A1197, and to 16S rRNA which comprises (i) C1195A and A1196G; or (ii) C1195T, A1196G and A1197G; or (iii) A1196G and A1197G. The invention also relates to ribosomes comprising such 16S rRNAs and to use of same.

Abstract: To provide a functional molecule including a modified nucleotide unit having a substituent introduced to a base thereof, wherein the substituent is removably introduced to the base; a functional molecule synthesizing amidite that has a substituent removably introduced to its base and that is used for the manufacture of the functional molecule; and a target substance analysis method including: preparing a random pool of functional molecules using a functional molecule synthesizing amidite; screening a functional molecule having affinity for a target substance from the random pool; amplifying the functional molecules having affinity for the target substance, wherein the method further comprises, prior to the amplification step, removing a substituent from the functional molecule having affinity for the target substance.

Abstract: The present invention relates to novel dendrimer compounds and methods of synthesizing the same. In particular, the present invention is directed to novel polyamidoamine (PAMAM) dendrimers, novel dendrimer branching units, methods for synthesizing such novel PAMAM dendrimers and functionalized dendrimers, as well as systems and methods utilizing the dendrimers (e.g., in diagnostic and/or therapeutic settings (e.g., for the delivery of therapeutics, imaging, and/or targeting agents (e.g., in disease diagnosis and/or therapy, etc.))).

Abstract: The present invention relates to an improved method for the bisulfite conversion of DNA. In certain time-temperature ranges the efficacy of the bisulfite conversion is clearly improved. By combination with denaturating solvents, new reaction conditions and new purification methods the efficacy can be further increased The converted DNA can subsequently be analysed by different methods. The present invention facilitates the analysis of cytosine methylation.

Abstract: A capture probe suitable for use with a method for isolating miRNAs. A method for isolating an miRNA of interest from a sample comprising the miRNA of interest comprising providing the capture probe. A method for identifying an miRNA of interest.

Abstract: A method comprising subjecting one or more sample portion(s) to a single amplification step, thereby amplifying a single molecule in the sample portion to a detectable level, and, in some embodiments, then determining whether the sample portion contains at least one molecule of the target nucleic acid. In some embodiments, the sample portion is in a porous sample structure, or in a sample chamber which comprises means for minimizing diffusion of the sample portion, or in a sample chamber which is inside a microcapillary device, or in a sample retaining means.

Abstract: Method of identifying a microRNA-recognition element and of generating microRNAs are disclosed. System and computer programs for performing such methods are disclosed. Recombinant nucleic acid molecule comprising a heterologous coding sequences and one or more MREs are also disclosed as are isolated nucleic acid molecule comprising one or more MRE sequences and being free of a coding sequence operably linked to regulatory elements. MicroRNA generated by a methods of the invention and the usr of the microRNAs to downregulate gene expression are disclosed.

Abstract: 3-alkynyl inosine analogs and their uses as universal bases are provided. The inosine analogues can be incorporated into nucleic acid primers and probes. They do not significantly destabilize nucleic acid duplexes. As a result, the novel nucleic acid primers and probes incorporating the inosine analogues can be used in a variety of methods. The analogs function unexpectedly well as universal bases. Not only do they stabilize duplexes substantially more than hypoxanthine opposite A, C, T, and G but they are also recognized in primers by polymerases, allowing efficient amplification.

Abstract: A particulate body having a hollow particle and a surface polymer disposed on the outside of the hollow particle and suitable for use in solid phase synthesis, especially production of peptides and oligonucleotides. The particulate body may be used as a chromatography stationary phase column and the buoyancy of the body allows the column to be packed efficiently from the bottom reducing the risk of damage to the stationary phase. The buoyancy of the particulate body may also allow species for example a catalyst to be suspended in a liquid phase to allow reactions, for example hydrolysis of vegetable oil and esterification to produce biodiesel to be carried out with a reduced risk of catalyst loss from a reaction zone.

Abstract: Regulatory regions are shown which regulate expression of an operably linked heterologous nucleic acid molecule in plants. Promoters are described which express at lower levels in pollen cells that in other plant cells. Methods of using such promoter to regulate expression of an operably linked nucleic acid molecule are described. A polyadenylation nucleotide sequence from soybean is further shown.

Abstract: The present invention provides novel algorithms for designing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts. Such oligonucleotides are particularly useful as primers for reverse transcription. The invention also provides compositions containing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts.

Abstract: A method for synthesizing a nucleic acid having a desired sequence and length comprises providing a solid support having an immobilized nucleic acid, performing a nucleic acid addition reaction to elongate the immobilized nucleic acid by adding a nucleotide or an oligonucleotide to the nucleic acid, determining whether the nucleotide or the oligonucleotide is added to the nucleic acid by detecting whether there is an increase in electrophoretic force applied to the solid support when an electric field and a magnetic field gradient are applied to the support, wherein the increase in electrophoretic force applied to the support is caused by adding the nucleotide or the oligonucleotide to the nucleic acid, repeating the addition reaction and determination steps if the nucleotide or the oligonucleotide is not added to the nucleic acid, and continuing until the immobilized nucleic acid has a desired sequence and length.