Abstract: This invention pertains to the field of combination oligomers, including the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries and other compositions.

Abstract: The present invention relates to oligoribonucleotide derivatives which have a 2?5?-linked oligoribonucleotide residue without a 5?-phosphate residue on the 3? end and to the use thereof for specific inhibition of gene expression.

Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.

Abstract: The invention concerns a method for analyzing nucleic acids using a small-size probe array comprising deoxyinostines (dI) instead of deoxyguanogines (dG). The invention also concerns such probe arrays and their use in methods for detecting and/or quantifying target oilgonucleotides present in DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) molecules in a sample, in particular mRNA editing rate of the serotonin 5-HT2C receptor (5-HT2C-R). The invention further concerns a biochip or a reactor in liquid medium comprising such probe arrays as well as their uses, in particular for detecting and/or identifying genetic polymorphisms or for determining an mRNA editing rate, whether it is that of a 5-HT2C-R mRNA or any other RNA capable of being edited.

Abstract: A method is provided for efficiently removing the silicon substituent which protects the 3?-hydroxyl group and the 5?-hydroxyl group of a ribose of a ribonucleic acid derivative in which the 2?-hydroxyl group of the ribose is protected with the following substituent (I) where WG1 represents an electron withdrawing group, and the 3?-hydroxyl group and the 5?-hydroxyl group of the ribose are protected with a silyl protecting group.

Abstract: The present invention relates to a process for the production, by a prokaryotic host cell, of an active, stable transposase of a Mariner mobile genetic element belonging to the mauritiana subfamily. The invention also relates to an active, stable transposase that can be produced using such a process, and to the molecular biology tools, such as the prokaryotic host cells, the expression vectors or the kits, which make it possible to produce an active, stable transposase, or which use it. In addition, the present invention relates to the uses of the active, stable transposases.

Abstract: The present invention relates to a method of preparing a primer used for determining the IVS7-2A?G site mutation involved in the large vestibular aqueduct syndrome. The method comprises the steps of: designing a primer pair which may introduce any base substitutive mutation in the region of 1-13 bases between upstream and downstream including the IVS7-2 mutation site (A?G) based upon the IVS7-2 A?G mutation site in the PDS gene, so as to obtain a new restriction site which may be used for distinguishing IVS7-2 wild type A site and mutant G site in the amplification products. The present invention further relates to the primers prepared according to this method, the kit or reagent or identical product comprising the primers, and a method for determining the IVS7-2A?G site mutation of large vestibular aqueduct syndrome with said primers in vitro.

Abstract: The invention relates to a novel process for the preparation of 4?-azido-cytidine (I) or a pharmaceutically accepted salt thereof. The compound of formula I is useful for treating virus mediated diseases, particularly for treating HCV mediated diseases.

Abstract: Methods are provided for making a circular duplex polynucleotide. Such methods can include providing a mixture of sequence specific linear duplex polynucleotides and denaturing and reannealing the polynucleotide mixture under conditions such that some of the polynucleotides form circular duplexes that comprise the desired polynucleotide.

Abstract: The present invention provides methods, compositions, and kits for polynucleotide assembly.

Abstract: A method and oligonucleotides for targeted nucleotide exchange of a duplex DNA sequence, wherein the donor oligonucleotide contains at least one modified nucleotide having a higher binding affinity compared to naturally occurring A, C, T or G and/or binds stronger to a nucleotide in an opposite position in the first DNA sequence as compared to a naturally occurring nucleotide complementary to the nucleotide in the opposite position in the first DNA sequence.

Abstract: The present invention relates to transcription regulating sequences from Solanaceae triose-phosphate translocator (TPT) genes and their use in plant expression cassettes. Preferably, the transcription regulating sequence is from the Solanum tuberosum triose-phosphate translocator gene. The transcription regulating sequences preferably exhibit strong expression activity in all tissues beside the reproductive organs (e.g., flowers, seed) and are especially useful for expression in potato tubers.

Abstract: The invention provides a method for producing a cytosine nucleoside compound from pentose-1-phosphate and cytosine or a derivative thereof using a nucleoside phosphorylase reactive to cytosine or a bacterium having the enzyme activity. The invention also provides a method for specifically reducing an activity to degrade the substrates or the product, resulting in efficient production of the cytosine nucleoside compound. According to the invention, little by-product is produced in producing cytonucleocide compounds.

Abstract: The present invention relates to a modified L-nucleic acid, comprising a L-nucleic acid part and a non-L-nucleic acid part, whereby the L-nucleic acid part is conjugated to the non-L-nucleic acid part and the conjugation of the L-nucleic acid part with the non-L-nucleic acid past leads to a slowed elimination out of the organism, in comparison with a L-nucleic acid which only comprises the L-nucleic acid part, said L-nucleic acid part being a spiegelmer.

Abstract: The present invention relates to a novel thermostable N-acylamino acid racemase (NAAAR) isolated from Deinococcus radiodurans NCHU1003, the coding sequence and the preparation thereof. The present invention also discloses the process for preparing highly optically pure L-amino acids, such as L-homophenylalanine (L-HPA) and the derivatives thereof, from N-protected amino acid by using the novel NAAAR combined with L-N-carbamoylase.

Abstract: A composition comprising individual single-stranded oligonucleotides capable of self assembling to form a pair of complementary, substantially contiguous single strands of a double-stranded nucleic acid filament, and a method for forming such filaments are disclosed.

Abstract: Small interfering ribonucleic acid duplexes that inhibit gene expression containing at least one arabinose modified nucleotide are provided. Preferably, the duplexes contain ribonucleotides at least one arabinose modified nucleotide is 2?-deoxy-2?-fluoroarabinonucleotide (FANA) nucleotide.

Abstract: The present invention provides a substrate having a plurality of immobilised furanone moieties associated with at least part of a surface of the substrate. The invention also relates to articles consisting of or comprising such a substrate.

Abstract: The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charged-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.

Abstract: This invention provides a method for determining the sequence of a DNA or an RNA, wherein (i) about 1000 or fewer copies of the DNA or RNA are bound to a solid substrate via 1,3-dipolar azide-alkyne cycloaddition chemistry and (ii) each copy of the DNA or RNA comprises a self-priming moiety.

Abstract: The invention is directed to nucleic acid sequences having decreased thermodynamic stability to complementary sequence as well as a method for producing these sequences.

Abstract: The present invention relates to a simple, economical method for introducing substituent (I) at the 2?-hydroxyl group of the ribose of a ribonucleic acid derivative whose 3?-hydroxyl group and 5?-hydroxyl group are protected with a silicon protecting group, wherein WG1 represents an electron-withdrawing group: The invention also relates to a method for producing a ribonucleic acid derivative of formula (3), comprising the reaction of a ribonucleic acid derivative of formula (1) with a monothioacetal compound of formula (2) to produce the ribonucleic acid derivative of formula (3), using iodine as the reagent for halogenating the sulfur atom of the monothioacetal compound of formula (2) in the presence of an acid: In formulae (1), (2), and (3), Bz represents a nucleobase which may or may not have a protecting group; WG1 represents an electron-withdrawing group; R3 represents alkyl or aryl; and A represents a silicon substituent.

Abstract: A novel artificial nucleic acid base pair which is obtained by forming a selective base pair by introducing a group having steric hindrance (preferably a group having steric hindrance and static repulsion and a stacking effect) and can be recognized by a polymerase such as DNA polymerase; a novel artificial gene; and a method of designing nucleic acid bases so as to form a selective base pair with the use of steric hindrance, static repulsion and stacking effect at the base moiety of the nucleic acid. An artificial nucleic acid comprising these bases; a process for producing the same; a codon containing the same; a nucleic acid molecule containing the same; a process for producing a non-natural gene by using the same; a process for producing a novel protein by using the above nucleic acid molecule or non-natural gene, and the like.

Abstract: An object of the present invention is to provide novel ribozyme systems capable of catalyzing tRNA acylation using various carboxylic acids as acyl donors and uses thereof. Disclosed is a ribozyme catalyzing tRNA acylation having a structure consisting of the RNA sequence represented by (formula 1): P1-Z1Z2Z3Z4(N1)1(N1)2 . . . (N1)p—P2-(N2)1(N2)2 . . . (N2)qY1Y2Y3(N3)1(N3)2N4GGN wherein (N1)1-(N1)p each independently represent any monoribonucleotide of U, C, A and G; p represents 3 or 4; (N2)1-(N2)q each independently represent any monoribonucleotide of U, C, A and G; q represents 5 or 6; (N3)1-(N3)2 each independently represent any monoribonucleotide of U, C, A and G; N4 represents any monoribonucleotide of U, C, A and G; Z1-Z4 each independently represent C or G; Y1-Y3 each independently represent C or G; N represents a monoribonucleotide complementary to A or G; and P1 and P2 represent a domain consisting of any RNA sequence capable of having a stem-loop structure.

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 a nucleic acid-lipophilic conjugates and methods for modulating an immune response using the conjugates. The lipophilic moiety associated with an immunostimulatory nucleic acid.

Abstract: Methods for measuring environmental parameters using chemical recording are provided. In some embodiments, the methods include generating a polymer comprising an ordered series of chemical units, wherein the position and number of each chemical unit in the polymer is indicative of a reading of the environmental state variable at a given point in time. The presently disclosed subject matter also provides compositions that can be employed in and/or that employ the disclosed methods for recording environmental state variables.

Abstract: Within oligonucleotides 2-azapurine and especially 2-azaadenine bases form specifically base pairs with guanine. This base pair is of analogous stability as an adenine-thymine but less stable than a guanine-cytosine base pair. Therefore, the incorporation of 2-azaadenine residues into oligonucleotides instead of cytosine leads specifically to hybridization complexes with nucleic acids with homogenous stability. This is useful for the adaptation of the stabilities of different oligonucleotide sequences in all kinds of hybridization techniques, for example in oligomer chip technology.

Abstract: The present invention is directed to sensitive and accurate multiplexed assays for target analyte detection and detection of methylation in nucleic acid samples.

Abstract: Provided is a hydroxyl-protected alcohol comprising a thermolabile hydroxyl-protecting group comprising a 2-pyridyl substituent and a precursor of the thermolabile hydroxyl-protected alcohol. An exemplary thermolabile hydroxyl-protected alcohol is represented by the formula Pg-O—R, wherein Pg is a protecting group of the formula: (Formula) wherein: A is a 2-pyridyl; Z is CH2 or NR1; R1, R2, R2?, R3 and R3? are the same or different and each can be, e.g., H, alkyl, or alkyl comprising an aryl substituent; W is CO, CS, or SO; and R is the organic residue of the hydroxyl-protected alcohol. Also provided is a method of producing an alcohol, which method comprises heating the hydroxyl-protected alcohol, which optionally may be obtained from a precursor, at a temperature effective to cleave the hydroxyl-protecting group. The method can be used to produce oligonucleotides.

Abstract: The present invention relates to a crosslinked hyaluronic acid that can be obtained according to a process comprising: (a) activation of a hyaluronic acid, (b) reaction of the activated hyaluronic acid with an oligopeptide- or polypeptide-based crosslinking agent, in a reaction medium adjusted to a pH of from 8 to 12, so as to obtain a crosslinked hyaluronic acid, (c) adjustment of the pH of the reaction medium to a value ranging from 5 to 7, and (d) precipitation of the crosslinked hyaluronic acid from an organic solvent. It also relates to the above process, to a hydrogel obtained from the crosslinked hyaluronic acid and to the use of the crosslinked hyaluronic acid for the manufacture of implants that can be used in particular in plastic surgery.

Abstract: The present invention concerns a system for isolating, depleting, and/or preventing the amplification of a targeted nucleic acid, such as mRNA or rRNA, from a sample comprising targeted and nontargeted nucleic acids.

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 invention provides an immunostimulatory nucleic acid comprising CpG motifs, and methods of use thereof in stimulating immunity.

Abstract: This invention pertains to the field of combination oligomers, including the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries and other compositions.

Abstract: The invention provides a method for constructing a high resolution physical map of a polynucleotide. In accordance with the invention, nucleotide sequences are determined at the ends of restriction fragments produced by a plurality of digestions with a plurality of combinations of restriction endonucleases so that a pair of nucleotide sequences is obtained for each restriction fragment. A physical map of the polynucleotide is constructed by ordering the pairs of sequences by matching the identical sequences among the pairs.

Abstract: Robust nucleic acid arrays and lattices are assembled based on double crossover cohesion of polygonal units whose edges are composed of nucleic acid multi-crossover domains.

Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.

Abstract: The invention relates to double-stranded nucleic acid fragments comprising a chemically modified backbone and at least 4-1000 bp, preferably 8-500 bp, and most preferably 16-200 bp. The disclosed molecules (DRIL molecules) may interfere with DNA damage signaling and repair pathways, in particular the non homologous NHEJ pathway of double-stranded break repair. The invention discloses the application of the DRIL molecules as adjuvant compositions to be used in association with a DNA breaking treatment, particularly radiotherapy or chemotherapy, in combination with a pharmaceutically acceptable carrier, in an efficient amount to be introduced in the tumoral cell nuclei in order to trigger DNA repair induced lethality (DRIL in short) of tumoral cells/tissues.

Abstract: Methods for obtaining antisense oligonucleotides with activity against a desired target are provided. Methods of identifying oligonucleotide sequence motifs which are predictive of antisense oligonucleotide activity are provided, as are motifs identified according to this method. Methods of selecting effective antisense oligonucleotide sequences and effective antisense target sequences are provided, as are sequences selected according to these methods. In other methods of the invention, oligonucleotides are designed to hybridize to target sequences containing one or more activity-enhancing motifs. Antisense oligonucleotides designed according to these methods are also provided.

Abstract: The present invention relates to a method and compounds for hydrolysing nucleic acids. In particular it relates to compounds that can be used for the preferential cleavage of a phosphodiester bond at a specific position in RNA.

Abstract: The present invention relates to polyamide compositions and therapies for treating cells infected with human papilloma virus (HPV).

Abstract: Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

Abstract: The invention is a process for the preparation of at least one nucleic acid duplex by the steps of: (a) synthesizing a first single strand oligonucleotide to produce a crude solution of the first single strand oligonucleotide; (b) purifying the first single strand oligonucleotide from the crude solution by first liquid chromatography to produce a solution of purified first single strand oligonucleotide in a first liquid chromatography eluant; (c) synthesizing a second single strand oligonucleotide to produce a crude solution of the second single strand oligonucleotide; (d) purifying the second single strand oligonucleotide from the crude solution by second liquid chromatography to produce a solution of purified second single strand oligonucleotide in a second liquid chromatography eluant; (e) mixing the solution of purified first single strand oligonucleotide in the first liquid chromatography eluant with the solution of purified second single strand oligonucleotide in the second liquid chromatography eluant

Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.

Abstract: This application includes methods for detecting single nucleotide polymorphisms (SNPs) in a sample using an electronically addressable microchip having a plurality of test sites. A sample nucleic acid is electronically biased, concentrated at, and immobilized to a test site on the microchip. A mixture comprising a first labeled probe and a second labeled probe is electronically hybridized to the sample nucleic acid to form first or second hybridized complexes. The first labeled probe is perfectly complementary to the first sample nucleic acid and the second labeled probe is complementary to the sample nucleic acid and contains a nucleotide that forms a mismatch with the nucleotide at the site of the polymorphism. The first or second hybridized complexes are detected by determining a signal intensity of the label of the first or second probe.

Abstract: The present invention relates to improved methods for the preparation of nucleic acids. More particularly, conventional solid supports used for nucleic acid synthesis are derivatized with activators having pKas within the 4 to 7 range. Preferentially, CPG-based solid supports are reacted with trialkoxysilanes containing an activator moiety such as pyridine. During each deblocking step of the nucleic acid synthesis cycle, bound pyridiniums are generated, yielding a weak acidic medium spreads throughout the solid support. The bound activators efficiently activate the phosphoramidite reagents towards coupling with 5?-hydroxynucleosides bound to the solid supports, thus eliminating or supplementing external deliveries of activator during the coupling steps.

Abstract: An organic compound synthesizer for synthesizing organic compounds contains at least one type of polymerizable repeat unit and includes a substrate for organic compound synthesis. A liquid supply unit is configured to supply a reaction liquid containing compounds necessary for the synthesis of organic compounds and a reaction liquid containing a thermal acid generator for generating protons by heating. A substrate heater is configured to selectively heat a specific portion of said substrate for organic compound synthesis to thereby heat the reaction liquid containing a thermal acid generator.

Abstract: Novel compositions comprised of at least one bead conjugated to a solid support and further conjugated to at least one nucleic acid and preferred methods for making the novel compositions are described. As compared to “flat” surfaces, beads linked to a solid support provide an increased surface area for immobilization of nucleic acids. Furthermore, by selecting a bead with the desired functionality, a practitioner can select a functionalization chemistry for immobilizing nucleic acids, which is different from the chemistry of the solid support.