Abstract: The present invention relates to the use of cross-linking probes to covalently bind probes to nucleic acid targets. In some embodiments, the probe comprises an initiator region that is able to bind to a first portion of a target nucleic acid, a probe region linked too the initiator region that is able to bind to a second region of the target nucleic acid and that comprises one or more cross-linkers, and a blocking region hybridized to the probe region.

Abstract: Methods of isolating target double-stranded polynucleotides with internal single-stranded regions are provided.

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: A method is disclosed for isolating both free and protein-associated DNA from bodily fluids, such as urine, saliva, serum, tears, sweat, cerebral spinal fluid, and plasma. The method comprises as a first step concentrating and isolating both the free DNA and the proteins present in the bodily fluid. The proteins are then digested in order to release the formerly protein-associated DNA from the isolated proteins. Lastly, the free and formerly protein-associated DNA can be isolated and purified.

Abstract: The present invention provides aptamer- and nucleic acid enzyme-based systems for simultaneously determining the presence and optionally the concentration of multiple analytes in a sample. Methods of utilizing the system and kits that include the sensor components are also provided. The system includes a first reactive polynucleotide that reacts to a first analyte; a second reactive polynucleotide that reacts to a second analyte; a third polynucleotide; a fourth polynucleotide; a first particle, coupled to the third polynucleotide; a second particle, coupled to the fourth polynucleotide; and at least one quencher, for quenching emissions of the first and second quantum dots, coupled to the first and second reactive polynucleotides. The first particle includes a quantum dot having a first emission wavelength. The second particle includes a second quantum dot having a second emission wavelength different from the first emission wavelength. The third polynucleotide and the fourth polynucleotide are different.

Abstract: The present invention relates to processes and reagents for oligonucleotide synthesis and purification. One aspect of the present invention relates to compounds useful for activating phosphoramidites in oligonucleotide synthesis. Another aspect of the present invention relates to a method of preparing oligonucleotides via the phosphoramidite method using an activator of the invention. Another aspect of the present invention relates to sulfur-transfer agents. In a preferred embodiment, the sulfur-transfer agent is a 3-amino-1,2,4-dithiazolidine-5-one. Another aspect of the present invention relates to a method of preparing a phosphorothioate by treating a phosphite with a sulfur-transfer reagent of the invention. In a preferred embodiment, the sulfur-transfer agent is a 3-amino-1,2,4-dithiazolidine-5-one. Another aspect of the present invention relates to compounds that scavenge acrylonitrile produced during the deprotection of phosphate groups bearing ethylnitrile protecting groups.

Abstract: The invention relates to a method for the chemical synthesis of RNA, comprising the following steps: a) bonding to a solid support of a monomer having formula (II) in which—X1 is a dimethoxytrityl group,—X6 is H or an OAc group or OX3, in which X3 is a group having formula (A), in which X is O or S, R? is H or CH3 and R is selected from a linear or branched alkyl group at C1 to C4 and a R1—O—R2 group in which R1 is an alkyl group at C1 to C2 and R2 is a CH3 group or CH2CH2—O—CH3 or aryl; b) assembly with the monomer having formula (II) bound to the support thereof obtained in step (a) of at least one monomer having formula (III) in which X1, Bp, X3 are as defined for formula (II) and X5 is a hydrogen phosphonate monoester or phosphoramidite group, preferably a 2-cyanoethyl-N,N-diisopropylphosphoramidite group, which is used to obtain a protected single-strand RNA bound to a support.

Abstract: This invention relates to a method of modulating the expression of a target gene in an organism comprising administering an iRNA agent, wherein the iRNA comprises at least one 2?-deoxy-2?-fluoro (2?-F) nucleotide in the antisense strand and at least one modified nucleotide in the sense strand. The invention also relates to compositions comprising a single-stranded oligonucleotide that contains at least one 2?-deoxy-2?-fluoro (2?-F) nucleotide. siRNA molecule containing these oligonucleotides have decreased immunogenicity.

Abstract: The present invention relates to systems and methods for sequencing nucleic acids, including sequencing nucleic acids in fluidic droplets. In one set of embodiments, the method employs sequencing by hybridization using droplets such as microfluidic droplets. In some embodiments, droplets are formed which include a target nucleic acid, a nucleic acid probe, and at least one identification element, such as a fluorescent particle. The nucleic acid probes that hybridize to the target nucleic acid are determined, in some instances, by determining the at least one identification element. The nucleic acid probes that hybridize to the target nucleic acid may be used to determine the sequence of the target nucleic acid. In certain instances, the microfluidic droplets are provided with reagents that modify the nucleic acid probe. In some cases, a droplet, such as those described above, is deformed such that the components of the droplets individually pass a target area.

Abstract: Compositions and methods for preparing nucleic acid nanotubes using DNA origami techniques are described, which provide for nanotubes of predictable and uniform length. The nucleic acid nanotubes thus formed are suitable as liquid crystal preparations enabling liquid-crystal NMR spectroscopy of proteins solubilized in detergent.

Abstract: single-stranded extension having a desired length and sequence composition. Methods for forming single-stranded extensions include: the use of a cassette containing at least one nicking site and at least one restriction site at a predetermined distance from each other and in a predetermined orientation; or primer-dependent amplification which introduces into a polynucleotide molecule, a modified nucleotide which is excised to create a nick using a nicking agent. The methods and compositions provided can be used to manipulate a DNA sequence including introducing site specific mutations into a polynucleotide molecule and for cloning any polynucleotide molecule or set of joined polynucleotide molecules in a recipient molecule such as a vector of choice.

Abstract: The invention provides methods, reagents and kits for using extracellular RNA in bodily fluids including plasma and serum to detect, infer, or monitor diseases such as cancer and other neoplasia.

Abstract: The invention includes RNA complexes comprising at least three monomeric units of an RNA molecule, each monomeric unit comprising an RNA polymer having first and second helical domains that have respective first and second binding sites, wherein the first binding sites are adapted to binding to one another and are not adapted to bind to the second binding sites, and the second binding sites are adapted to binding to one another and are not adapted to bind to the first binding sites; such that the at least three monomeric units are adapted to self-assemble by forming pairs of cognate interactions and so as to form the RNA complex in a circular closed complex. The invention also includes derivatives of these complexes including aptamers, and analytical methods and devices using same.

Abstract: Described herein are oligonucleotides useful for screening, detecting, isolating, quantitating, monitoring and sequencing of viruses and host biomarkers associated with prostate cancer and methods and kits of using the described oligonucleotides.

Abstract: Provided is a ribonucleoside derivative represented by General Formula (I): (wherein R1 represents a hydrogen atom or the like, R2 represents a hydrogen atom or the like, R3 represents a methyl group or the like, and B represents a nucleic acid base residue optionally having a protecting group or a modifying group). An RNA containing this ribonucleoside derivative shows excellent hybridization ability and resistance to nuclease.

Abstract: The present invention features methods for enhancing the ability of a genotype 2b NS5B sequence to function in a replicon, for producing replicons containing a functional genotype 2b NS5B, and for using replicons to measure the ability of a compound to affect HCV replication that is sustained with the genotype 2b polymerase. Also featured is a genotype 1b NS4B adaptive mutation. The ability to produce replicons containing a functional genotype 2b NS5B is illustrated by the production of chimeric replicons based on HCV genotype 1b where substantially all the NS5B sequence is replaced with a genotype 2b NS5B.

Abstract: The present invention provides an improved method for the bisulfite conversion of DNA, and facilitates the analysis of cytosine methylation of genomic DNA. Novel combinations of denaturing solvents, new reaction conditions and new purification methods provide surprisingly efficacious methods for bisulfite conversion of DNA relative to prior art methods. The converted DNA may subsequently be analyzed by many different methods.

Abstract: The present invention provides a TLR7 ligand and its use in therapeutic applications. Specifically, the present application provides a RNA oligonucleotide comprising a G:U wobble base pair in the context of a fully double-stranded structure and its use in treating disease such as viral infections, immune disorders and cancer.

Abstract: Provided herein are methods and kits for the specific and ubiquitous detection of Streptococcus agalactiae.

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: Crystals of a purine nucleoside compound, particularly crystals of 2?,3?-dideoxyinosine, which have excellent storage stability and have a concentration of phosphate attached to the crystal of 25 ppm or more, may be produce by: (1) preparing an aqueous solution containing phosphate ion (PO43?) and a purine nucleoside compound; and (2) crystallizing the purine nucleoside compound from the aqueous solution.

Abstract: The present invention relates to novel bicyclic and tricyclic nucleoside and nucleotide analogues as well as to oligonucleotides comprising such elements. The nucleotide analogues, LNAs (Locked Nucleoside Analogues), are able to provide valuable improvements to oligonucleotides with respect to affinity and specificity towards complementary RNA and DNA oligomers. The novel type of LNA modified oligonucleotides, as well as the LNAs as such, are useful in a wide range of diagnostic applications as well as therapeutic applications. Among these can be mentioned antisense applications, PCR applications, strand displacement oligomers, as substrates for nucleic acid polymerases, as nucleotide based drugs, etc. The present invention also relates to such applications.

Abstract: Processes are disclosed that use 3?-reversibly terminated nucleoside triphosphates to analyze DNA for purposes other than sequencing using cyclic reversible termination. These processes are based on the unexpected ability of terminal transferase to accept these triphosphates as substrates, the unexpected ability of polymerases to add reversibly and irreversibly terminated triphosphates in competition with each other, the development of cleavage conditions to remove the terminating group rapidly, in high yield, and without substantial damage to the terminated oligonucleotide product, and the ability of reversibly terminated primer extension products to capture groups. The presently preferred embodiments of the disclosed processes use a triphosphate having its 3?-OH group blocked as a 3?-ONH2 group, which can be removed in buffered NaNO2 and use variants of Taq DNA polymerase, including one that has a replacement (L616A).

Abstract: According to the present invention, there is provided a process for the preparation of a first compound selected from peptides, oligonucleotides and peptide nucleic acids. The process comprises synthesising the first compound and then separating the first compound formed in step (i) from a second compound, which is a reaction by-product of the synthesis of the first compound and/or an excess of a reagent used for the synthesis of a first compound by a process of diafiltration. The membrane used for the diafiltration process is stable in organic solvents and provides a rejection for the first compound which is greater than the rejection for the second compound.

Abstract: The present invention relates to a method for nucleic acid replication and novel artificial base pairs. The method of the present invention for nucleic acid replication is characterized in that a deoxyribonucleoside 5?-triphosphate, in which the hydroxyl group of phosphoric acid at the ?-position is substituted with a group selected from the group consisting of an amino group, a methylamino group, a dimethylamino group, a mercapto group and a fluoro group, is used as a substrate during replication reaction. The novel artificial base pairs of the present invention are characterized in that 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) or an analog thereof forms a base pair with pyrrole-2-carbaldehyde (Pa) or an analog thereof.

Abstract: The present invention relates to a DNA sequencing method using a nucleoside triphosphate with a fluorescent blocking group on its 3?-OH end as a reversible terminator. Further, the present invention relates to sequencing-by-synthesis method using the mono-modified reversible terminator (MRT), the novel nucleotide monomer having a reversible fluorescent blocking group removable chemically or enzymatically at its 3?-OH end. The sequencing method of the present invention facilitates sequencing of bases inserted by terminating extension of a nucleotide chain by the nucleotide monomer and then detecting fluorescence signal from 3?-OH end. At this time, after analyzing the fluorescence signal, the blocking group conjugated to the 3?-OH end can be effectively removed, indicating that a free 3?-OH functional group can be successfully restored, so that the next monomer insertion is possible, making continuous sequencing possible.

Abstract: Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.

Abstract: The synthesis of arrays of DNA probes sequences, polypeptides, and the like is carried out using a patterning process on an active surface of a substrate. An image is projected onto the active surface of the substrate utilizing reflective projection optics. The projection optics project a light image onto the active surface of the substrate to deprotect linker molecules thereon. A first level of bases may then be applied to the substrate, followed by development steps, and subsequent exposure of the substrate utilizing a different light image, with further repeats until the elements of a two dimensional array on the substrate surface have an appropriate base bound thereto.

Abstract: The present invention provides novel, water-soluble, red-emitting fluorescent rhodamine dyes and red-emitting fluorescent energy-transfer dye pairs, as well as labeled conjugates comprising the same and methods for their use. The dyes, energy-transfer dye pairs and labeled conjugates are useful in a variety of aqueous-based applications, particularly in assays involving staining of cells, protein binding, and/or analysis of nucleic acids, such as hybridization assays and nucleic acid sequencing.

Abstract: The present disclosure relates to isolated polynucleotides with two polynucleotide sequences linked within one open reading frame, in which the first polynucleotide sequence encodes a peptide that binds to a carbohydrate. The present disclosure also relates to vectors and genetically modified host cells containing such isolated polynucleotides and polypeptides encoded by such isolated polynucleotides. The present disclosure further relates to methods of increasing the ability of a recombinant protein to bind to a carbohydrate and methods of identifying a protein having an ability to bind to a carbohydrate.

Abstract: Compositions and methods of preparing carboranes and metallacarboranes, which can be used as a new type of electrochemically active label for biological compounds, are disclosed. Nucleic acid derivatives labelled with carborane or metallacarborane can be detected by electrochemical methods and can find several practical applications, such as materials for nanoconstruction, in DNA array technology or for the construction of biosensors, especially electrochemical biosensors. Other applications can include use as modified primers in amplification of RNA and DNA, antisense drugs, boron carriers for BNCT, radiopharmaceuticals bearing a range of isotopes useful in different types of radiotherapy, molecular probes, elements of biosensors, materials for nanotechnology and others.

Abstract: Methods and compositions for making nucleoside phosphoramidites and nucleic acids, including mono-, di-, and polynucleotides, comprising a linker covalently attached to a levulinyl moiety are provided. A levulinyl-protected linking moiety affords an orthogonal approach to modifying a polynucleotide during or after solid phase synthesis with a molecule of interest, for example, a conjugate or a dye.

Abstract: The invention provides methods and compositions for hybridizing at least one molecule to a target. The invention may, for example, eliminate the use of or reduce the dependence on formamide in hybridization. Compositions for use in the invention include an aqueous composition comprising at least one nucleic acid sequence and at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.

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: According to the present invention, there is provided a process for synthesis of a first compound selected from peptides, oligonucleotides, and peptide nucleic acids, which comprises synthesis of the first compound linked to a soluble support, wherein the soluble support is degraded following the synthesis so that it can be separated from the first compound.

Abstract: One aspect of the present invention relates to a ribonucleoside substituted with a phosphonamidite group at the 3?-position. In certain embodiments, the phosphonamidite is an alkyl phosphonamidite. Another aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-phosphate linkage. Representative non-phosphate linkages include phosphonate, hydroxylamine, hydroxylhydrazinyl, amide, and carbamate linkages. In certain embodiments, the non-phosphate linkage is a phosphonate linkage. In certain embodiments, a non-phosphate linkage occurs in only one strand. In certain embodiments, a non-phosphate linkage occurs in both strands. In certain embodiments, a ligand is bound to one of the oligonucleotide strands comprising the double-stranded oligonucleotide. In certain embodiments, a ligand is bound to both of the oligonucleotide strands comprising the double-stranded oligonucleotide.

Abstract: The invention relates to [NiFe]-hydrogenases having an improved resistance to dioxygen, said [NiFe]-hydrogenases may be obtained by:—providing an initial polynucleotide comprising a sequence encoding a large subunit of a [NiFe]-hydrogenase, said large subunit comprising the following peptide motifs: L1: RGXE, wherein X=L, I, F, V or M L2: [R/K]X1C[G/R]X2C, wherein Xi is any amino acid residue, X2=L, V, I or M; L1 and L2 being separated by 16 any amino acid residues; L3: X1X2X3X4X5X6X7X8X9X10X11X12[D/S/E], wherein X1=D, S, N or E, X2=H, D, S, N or L, X5=H, S, A, Q or W, X6=F, T, Y or G, X9=L, F, M or Y, the other Xn being any amino acid residue; L4: D[P/I/S]CX1X2CX3X4[H/R], wherein X2=A.S.V.G or T, X1, X3 and X4 are any amino acid residue and optionally comprising a motif LO: R[I/V/A]EG[H/D/A].—modifying said initial polynucleotide in order to substitute at least one of the residues X2 of motif L2 and Z or X4 of motif L3 and Z or X9 of motif L3 of said large subunit by a methionine.

Abstract: 5-bromo-2?-deoxy-uridine (BrdU) labeled nucleotide triphosphates and nucleic acid probes are described herein. The BrdU labeled nucleotide triphosphates include a linker between the nucleotide triphosphate and the BrdU moiety. The linker can be cleavable or non-cleavable. The nucleotide triphosphates can be a ribonucleotide triphosphates, 2?-deoxyribonucleotide triphosphates or 2?,3?-dideoxyribonucleotide triphosphates. The nucleic acid probes can be used for in situ hybridization.

Abstract: DNA dendrimers for targeted delivery of radiation absorbing nanoparticles and thermal ablation of cells and tissues are provided. Also provided are methods of making and methods of using the DNA dendrimers.

Abstract: The present invention relates to compositions useful as probes and in other applications and methods of their use. In some embodiments, nucleotides are prepared and functionalized with dyes. In some embodiments a first molecule is functionalized with an alkynyl group, a second molecule is functionalized with an azide group, and said first and second molecules are mixed under conditions to form a conjugate with a 1,2,3-triazol group. In further embodiments, a nucleotide is functionalized with an alkynyl group, a dye is functionalized with an azide group, and mixing the nucleotide and the dye forms a conjugate capable of emitting light.

Abstract: Hydrazino, oxyamino and carbonyl-based monomers and methods for incorporation into oligonucleotides during enzymatic synthesis are provided. Modified oligonucleotides are provided that incorporate the monomers provided herein. Immobilized oligonucleotides and oligonucleotide conjugates that contain covalent hydrazone or oxime linkages are provided. Methods for preparation of surface bound oligonucleotides are provided. Methods for the preparation of oligonucleotide conjugates are also provided.

Abstract: Nucleoside monomers, nucleic acids, e.g., oligonucleotides and polynucleotides, methods of making each, methods of deprotecting each, and the like are disclosed herein. Aspects of the invention include 2? silyl containing thiocarbonate protecting groups. Corresponding compositions and methods are provided.

Abstract: Elongated molecules are stretched across a substrate by controlled fluid flow.

Abstract: The present invention relates to processes and reagents for oligonucleotide synthesis and purification. One aspect of the present invention relates to compounds useful for activating phosphoramidites in oligonucleotide synthesis. Another aspect of the present invention relates to a method of preparing oligonucleotides via the phosphoramidite method using an activator of the invention. Another aspect of the present invention relates to sulfur-transfer agents. In a preferred embodiment, the sulfur-transfer agent is a 3-amino-1,2,4-dithiazolidine-5-one. Another aspect of the present invention relates to a method of preparing a phosphorothioate by treating a phosphite with a sulfur-transfer reagent of the invention. In a preferred embodiment, the sulfur-transfer agent is a 3-amino-1,2,4-dithiazolidine-5-one. Another aspect of the present invention relates to compounds that scavenge acrylonitrile produced during the deprotection of phosphate groups bearing ethylnitrile protecting groups.

Abstract: An improved method of preparing a sugar modified nucleoside analog includes a protocol in which a hydroxy group of a sugar is selectively deprotected and oxidized prior to nucleophilic modification of the corresponding carbonyl group. The modified sugar is then coupled to a heterocyclic base that is modified with a dual nucleophilic reagent in a further step that provides N6-modified adenosine analogs with high stereoselectivity.

Abstract: The invention provides a family of tethered nucleotide analogs useful in sequencing nucleic acids containing a homopolymer region comprising, for example, two or more base repeats, and to sequencing methods using such tethered nucleotide analogs.

Abstract: The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the above amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.

Abstract: The invention provides compounds of formula (I) and salts thereof: R1-L-R2—B wherein R1, L, R2, and B have any of the values defined herein, as well as compositions comprising such compounds, and therapeutic methods comprising the administration of such compounds or salts. The compounds block siderophore production in bacteria and are useful as antibacterial agents.

Abstract: A method for diagnosing the presence of hereditary spastic paraplegia (HSP) or predicting the risk of developing HSP in a human subject, comprising detecting the presence or absence of a defect in a gene encoding a polypeptide comprising the sequence of FIG. 9 (SEQ ID NO: 19), in a nucleic acid sample of the subject, whereby the detection of the defect is indicative that the subject has or is at risk of developing HSP.

Abstract: A protective group represented by the following general formula (I) (the oxygen atom attached with * represents oxygen atom of 2?-hydroxyl group of a ribonucleoside, a ribonucleotide or a derivative thereof; R1 and R2 both represent hydrogen atom, or represent a halogen atom, a C1-6 alkyl group, or a C1-6 halo-substituted alkyl group; R3 and R4 represent hydrogen atom, a halogen atom, a C1-6 alkyl group, or a C1-6 halo-substituted alkyl group; and R5 and R6 represent a halogen atom, a C1-6 halo-substituted alkyl group, cyano group, nitro group, or the like), which is stable under the reaction conditions of the nucleic acid synthetic cycles and has little steric hindrance, and can be removed under mild conditions using fluoride ions as a base.