Abstract: The present invention relate to a method of detecting a genetic recombinant by using the PCR method. A method of quantitatively detecting method is provided whereby the total content ratio of the genetic recombinants and the individual content ratio of the genetic recombinant in a population containing plural genetic recombinant lines can be quantified. The method of the present invention comprises performing PCR for the DNA sequence specific to the recombinant and the endogenous DNA sequence shared by the species corresponding to the recombinant using, as a standard molecule, a molecule containing the DNA sequence specific to the recombinant and the endogenous DNA sequence shared by the species on the single molecule, and determining the content ratio of the number of molecules thereof.

Abstract: Provided are compositions and processes that utilize genomic regions differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuplodies.

Abstract: This invention provides a new method of obtaining a high density, reproducible and uniform coverage of a solid surface, compounds suitable for such a method and methods of preparing such compounds. This invention further relates to methods of the chemical modification (carboxylation) of solid surfaces and their subsequent use for the attachment of amine-containing molecules including DNA, proteins and other polymers.

Abstract: New modifiers were synthesized for incorporation of a methacrylic function in 3?-, 5?- and internal positions of oligonucleotides during solid phase synthesis. A modifier was used for synthesis of 5?-methacrylated oligonucleotides for preparation of microarrays by a co-polymerization method.

Abstract: The invention relates to a method for the design and/or the preparation of a polynucleotide capture molecule for detecting an amplicon having one strand serving as target to be detected and/or quantified after hybridization on said capture molecule, comprising the steps of: (a) selecting a primer pair defining the amplicon; (b) selecting a specific sequence of 10 to 100 nucleotides within the amplicon, such that said specific sequence defines two non-complementary ends of the amplicon; (c) defining the capture molecule having a capture portion that is complementary to the specific sequence selected in step b), and a spacer portion comprising at least 20 nucleotides; and (d) identifying among the two non-complementary ends of the amplicon a spacer end and a non-spacer end, respectively, such that the spacer end is non-complementary to the spacer portion of the capture molecule, and said spacer end exceeds said non-spacer end by at least 50 bases.

Abstract: The present invention provides solid support media for use in oligomer synthesis, methods of producing the media, and methods of using the media. In some embodiments, the processes of the invention comprise (a) providing an organic phase comprising an olefin monomer, a cross-linker, a functionalizing reagent and an initiator; and (b) contacting the organic phase with an aqueous phase under conditions of time and temperature effective to form the polymeric bead.

Abstract: The present invention provides a method for identifying a methylated CpG containing nucleic acid by contacting a nucleic acid with a methylation sensitive restriction endonuclease that cleaves unmethylated CpG sites and contacting the sample with an isoschizomer of the methylation sensitive restriction endonuclease, which cleaves both methylated and unmethylated CpG sites. The method also includes amplification of the CpG-containing nucleic acid using CpG-specific oligonucleotide primers A method is also provided for detecting an age associated disorder by identification of a methylated CpG containing nucleic acid. A method is further provided for evaluation the response of a cell to an agent A kit useful for detection of a CpG containing nucleic acid is also provided. Nucleic acid sequences encoding novel methylated clones.

Abstract: A process of forming a double strand cleavage in DNA includes providing a reaction mixture containing double stranded DNA having a break in a first strand defining a target site in a second strand. The method continues by adding to the reaction mixture a photoreactive lysine conjugate selected from a lysine-enediyne conjugate, a lysine-acetylene conjugate or a combination thereof, for a time sufficient for the lysine conjugate to bind to the DNA adjacent the target site. The reaction mixture is then irradiated with electromagnetic radiation sufficient to photoactivate the lysine conjugate to cleave the second strand adjacent the target site.

Abstract: A method of specifically amplifying desired regions of nucleic acid from a sample is provided. The method uses a plurality of first and second PCR primers, each having a region of fixed nucleotide sequence identical or complementary to a consensus sequence of interest and a region of randomized nucleotide sequence located 5? to, 3? to, anywhere within, or flanking the region of fixed nucleotide sequence; and then amplifying the nucleic acid present in the sample via PCR using the plurality of first and second PCR primers; whereby a subset of the first primers binds to the consensus sequence of interest wherever it occurs in the sample, and a subset of the second primers binds to the sample at locations removed from the first primers such that DNA regions flanked by the first primer and the second primer are specifically amplified.

Abstract: Linkers and methods for determining a nucleotide sequence of a reference oligonucleotide are provided.

Abstract: The present invention relates to a method for the manufacture of labeled oligonucleotide conjugates comprising the reaction of (a) an oligonucleotide having a labile protecting group bound to a terminal hydroxy group, and (b) a labeling compound, wherein said labile protecting group is partially or completely substituted by said labeling compound in a nucleophilic substitution reaction.

Abstract: The present invention is an apparatus, system and method for forming nanoscale architectures having nanoparticles bound thereto. The present invention provides a photon beam crosslinked polymer matrix, wherein the crosslinked matrix includes one or more polymers crosslinked to one or more crosslinking agents and one or more protein-coated metal nanoparticles.

Abstract: A nucleoside monomer that is protected by a thionocarbamate protecting group is provided, as well as a method for making a polynucleotide that uses the same. Also provided is a polynucleotide synthesis method that employs a diamine to deprotect a protected polynucleotide.

Abstract: A solution phase synthesis method for preparing an oligonucleotide, wherein at least some of the reagents are solid supported. The method suitable for large-scale synthesis comprises coupling a protected compound with a nucleotide derivative having a protection group in the presence of a solid supported activator to give an elongated oligonucleotide with a P(III)-internucleotide bond; optionally processing the elongated oligonucleotide by capping by reaction with a solid supported capping agent and/or by oxidizing or sulfurizing by reaction of the oligonucleotide with a solid supported oxidizing or sulfurization reagent; and removing the protection group. The coupling may include reacting a 3?-protected compound of formula: with a nucleotide derivative having a 5?-protection group, or reacting a 5?-protected compound of formula with a nucleotide derivative having a 3?-protection group.

Abstract: The present invention relates to novel phosphoramidites, including positive and neutrally charged compounds. The present invention also provides charge tags for attachment to materials including solid supports and nucleic acids, wherein the charge tags increase or decrease the net charge of the material. The present invention further provides methods for separating and characterizing molecules based on the charge differentials between modified and unmodified materials.

Abstract: The disclosure provides nucleotide analogs and methods of their use. Analogs of the invention comprise a reporter molecule (label) attached via the N4, N6, O4, or O6 position of the nitrogenous base portion of the analog. In a preferred embodiment, nucleotide analogs of the invention comprise a label attached to the nitrogenous base portion of the analog via a cleavable linker at the N4, O4, N6 or O6 position.

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 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: It has been discovered that the uptake of anionic charged species into cells can be enhanced by noncovalently associating such species with specifically modified forms of cyclodextrin. The invention modified forms of cyclodextrin form well defined stoichiometric complexes with anionic charged molecules. This discovery enables one to produce various compositions containing anionic charged molecules and facilitates methods for enhancing the cellular uptake of double-stranded or hairpin nucleic acid.

Abstract: The invention relates to a molecular beacon in the form of a hairpin oligonucleotide or oligonucleotide analogue comprising a first nucleotide sequence containing two or more aromatic or heteroaromatic ring systems P able to form an excimer or exciplex; a second sequence (the loop) consisting of an oligonucleotide probe able to hybridise with a target polynucleotide; and a third sequence containing one or more aromatic or heteroaromatic ring systems X, wherein at least one aromatic ring system X interacts with two aromatic ring systems P of the first sequence inhibiting excimer or exciplex formation. The invention further relates to a method for detecting the presence of a target polynucleotide using such a molecular beacon, and to a kit comprising a molecular beacon of the invention for use in this method.

Abstract: Disclosed are methods for preparing 2-alkynyladenosine derivatives of formula A: or a stereoisomer, pharmaceutically acceptable salt, hydrate, solvate, acid salt hydrate or isomorphic crystalline form thereof, the method comprising the step of: contacting 2-iodoadenosine-5?-N-ethyluronamide with a compound of formula B: wherein Z is —C(?O)OR or —CH2C(?O)R, where R is a C1 to C5 alkyl, preferably The methods are useful for preparing 2-alkynyladenosine derivatives that are, in certain embodiments, adenosine receptor agonists.

Abstract: This invention relates to the field of nucleic acid chemistry, more specifically to the field of compositions and processes that are nucleic acid analogs. More specifically, it relates to purine analogs that contain three rings, where the third ring bridges the exocyclic substituent at position 6 to position 7, using the purine numbering system. Still more specifically it relates to analogs having this structure that are able to form nucleobase pairs having the Watson-Crick geometry with a pyrimidine or pyrimidine analog, where the nucleobase pair is joined by hydrogen bonding patterns that either present a standard hydrogen bonding pattern, or a non-standard hydrogen bonding pattern. Most specifically, it to nucleoside analogs that are analogs of isoguanosine, but where the 5-6 ring system of the purine ring in isoguanosine is fused to another five- or six-membered ring, where the fused ring joins the exocyclic amino group with an atom that is, by analogy, at position 7 of the isoguanine ring system.

Abstract: Methods of nucleic acid preparation are described, including preparation of MnRNA, using FMOC derivatives to synthesize oligonucleotides in addition to applying FMOC protocols to various therapeutic and diagnostic methods. In some embodiments a single stranded oligonucleotide is synthesized bound to a polymer support (such as optic fiber glass filters) using said FMOC derivatives.

Abstract: A method of manufacturing a microarray includes providing a substrate having a surface that is immobilized with a functional group protected with an acid-labile protecting group and capable of coupling with an oligomer probe, providing a photoacid generator onto the substrate, disposing on the substrate an imprint template comprising a convex region and a plurality of concave regions surrounding the convex region so that the convex region contacts with or is adjacent to an upper surface of the substrate to define a plurality of reaction zones by the upper surface of the substrate and the convex region and the concave regions of the imprint template, exposing one or more of the reaction zones to light so that an acid is generated by the photoacid generator in the one or more exposed reaction zones and a functional group in the one or more exposed reaction zones is deprotected by the acid, and providing an oligomer probe onto the substrate so that the oligomer probe couples with the deprotected functional group

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: The present invention relates to ionic liquids for use in chemical applications and capable of serving the dual function of solvent and liquid support. The ionic liquid lends itself to a method of synthesizing oligomers selected from the group consisting of oligopeptides, oligosaccharides and oligonucleotides, comprising contacting a first monomer unit with an ionic liquid at reaction conditions to provide an ionic liquid bound monomer unit; and contacting the ionic liquid bound monomer unit with at least one further monomer unit at reaction conditions to provide an ionic liquid bound oligomer comprising from 2 to 30 monomer units. The method lends itself to large scale manufacture of oligopeptides, oligosaccharides and oligonucleotides.

Abstract: Oligonucleotide probes containing two labels are provided and are useful in hybridization assays. The probes can also contain a minor groove binding group.

Abstract: A class of 2?-fluoro-nucleoside compounds are disclosed which are useful in the treatment of hepatitis B infection, hepatitis C infection, HIV and abnormal cellular proliferation, including tumors and cancer.

Abstract: The present invention provides artificial universal base capable of base pairing nonspecifically with any of four kinds of natural nucleic acid bases (A, T, G, and C) without the function to specifically recognize pairing natural nucleic acid bases for base pair formation. Universal base capable of base paring nonspecifically with four kinds of natural nucleic acid bases, wherein the universal base has a structure represented by the following chemical formula: wherein R represents a monovalent group other than a hydrogen atom.

Abstract: The present invention relates to solid supports functionalized with phosphorus-containing dendrimers, to a process for preparing them, to their use for preparing biochips and to the uses of these biochips, in particular for immobilizing molecules of interest, especially biological molecules of interest such as nucleic acids, polypeptides, lipids and proteins.

Abstract: The present invention relates to the field of synthesis of short double-stranded RNAs. An in vitro transcription method using bacteriophage polymerases and target sequence-specific single-stranded DNA oligonucleotides as templates is disclosed. The present invention finds particularly advantageous use in the synthesis of short interfering RNAs (siRNAs) that have been shown to function as key intermediates in triggering sequence-specific RNA degradation during posttranscriptional gene silencing in plants and RNA interference in invertebrates and vertebrate systems.

Abstract: The present invention concerns methods of polymerase independent template directed elongation of polynucleotides, nucleotide building blocks used in these methods as well as the use of the methods and building blocks for the determination of nucleotide sequences, in particular for the determination of SNPs, base modifications, mutations, rearrangements and methylation patterns.

Abstract: An isolated protein comprising a VP1 amino acid sequence wherein one or more exposed loops within said VP1 has an insertion of an amino acid sequence from a virus protein other than VP1, and encoding nucleic acid, are provided. Typically, the virus protein other than VP1 is derived from an influenza virus and in particular, avian influenza virus. The isolated protein may have an insertion of amino acid sequence from a single protein or a plurality of proteins. Also provided are expression constructs, VLPs, pharmaceutical compositions, vaccines and methods of treatment that may be useful in the prophylactic and/or therapeutic treatment of any disease of viral origin, and in particular, influenza virus.

Abstract: A process for the preparation of a poly(alkoxylated) oligonucleotide is provided. The process comprises reacting an oligonucleotide which has been purified by ultrafiltration with a poly(alkoxide) thereby to form a poly(alkoxylated) oligonucleotide. The poly(alkoxyalted) oligonucleotide may be separated from non-poly(alkoxyalted) oligonucleotide by ultrafiltration under denaturing conditions, such as the presence of organic solvents, for example, ethanol; the presence of urea; the addition of chaotropic salts, for example perchlorate and guanidinium salts; the presence of formamide; and the application of heat, for example a temperature of up to about 70° C.

Abstract: The present invention relates to the use of nucleic acid probes to bind to targets. In some embodiments, the probe comprises a shielded cross-linking probe.

Abstract: The present invention relates to a method for synthesising templated molecules. In one aspect of the invention, the templated molecules are linked to the template which templated the synthesis thereof. The intion allows the generation of libraries which can be screened for e.g. therapeutic activity.

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 invention relates to methods and devices for preparing synthetic nucleic acids.

Abstract: The present invention relates to methods and reagents for modifying the emission of light from labeled nucleic acids for the purpose of real time detection, analysis, and quantitation of nucleic acid sequences, e.g., using singly labeled probes. These methods and reagents exploit advantageous properties of thiazine dyes and diazine dyes. Furthermore, the use of these light emission modifiers in background reduction, nucleic acid duplex stabilization and other uses is also described. Related kits, reaction mixtures and integrated systems are described.

Abstract: The present invention provides a novel method for solid-phase phosphoramidite based synthesis of borane phosphonate DNA. Also provided are novel phosphoramidite molecules, novel extended length borane phosphonate nucleic acid compounds, and methods of use thereof.

Abstract: The invention relates to a method for stripping undesired nucleic acid components from double-stranded DNA, in particular, super-coiled plasmid DNA. The method according to the invention is characterised by the steps: (a) provision of a mixture containing completely and/or partly double-stranded nucleic acids and optionally single-stranded nucleic acids; (b) resuspension of the mixture from step (a) in an aqueous, low-molarity buffer system with low ionic strength and low buffer effect; (c) adjusting conditions in the mixture from step (b), under which the completely and/or partly double-stranded nucleic acids are denatured; (d) further addition of buffer and a polymer component to the mixture from step (c); (e) incubation of the mixture from step (d) for a time which is sufficient for the formation of an aqueous two-phase system with an upper and lower phase; and (f) removal of the upper phase containing the single-strand nucleic acid and collection of the double-strand nucleic acid from the lower phase.

Abstract: This invention relates to molecular and cellular biology and biochemistry. In one aspect, the invention provides polypeptides having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or ?-glucosidase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or ?-glucosidase 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.

Abstract: Nucleic acid (e.g., DNA) hybridization probes are described which comprise a labeled, single copy nucleic acid which hybridizes to a deduced single copy sequence interval in target nucleic acid of known sequence. The probes, which are essentially free of repetitive sequences, can be used in hybridization analyses without adding repetitive sequence-blocking nucleic acids. This allows rapid and accurate detection of chromosomal abnormalities. The probes are preferably designed by first determining the sequence of at least one single copy interval in a target nucleic acid sequence, and developing corresponding hybridization probes which hybridize to at least a part of the deduced single copy sequence. In practice, the sequences of the target and of known genomic repetitive sequence representatives are compared in order to deduce locations of the single copy sequence intervals.

Abstract: The invention provides compositions and methods for selectively reducing the expression of a gene product from a desired target gene, as well as treating diseases caused by expression of the gene. The method involves introducing into the environment of a cell an amount of a double-stranded RNA (dsRNA) such that a sufficient portion of the dsRNA can enter the cytoplasm of the cell to cause a reduction in the expression of the target gene. The dsRNA has a first oligonucleotide sequence that is between 26 and about 30 nucleotides in length and a second oligonucleotide sequence that anneals to the first sequence under biological conditions. In addition, a region of one of the sequences of the dsRNA having a sequence length of from about 19 to about 23 nucleotides is complementary to a nucleotide sequence of the RNA produced from the target gene.

Abstract: Methods and compounds, including compositions therefrom, are provided for determining the sequence of nucleic acid molecules. The methods permit the determination of multiple nucleic acid sequences simultaneously. The compounds are used as tags to generate tagged nucleic acid fragments which are complementary to a selected target nucleic acid molecule. Each tag is correlative with a particular nucleotide and, in a preferred embodiment, is detectable by mass spectrometry. Following separation of the tagged fragments by sequential length, the tags are cleaved from the tagged fragments. In a preferred embodiment, the tags are detected by mass spectrometry and the sequence of the nucleic acid molecule is determined therefrom. The individual steps of the methods can be used in automated format, e.g., by the incorporation into systems.

Abstract: A novel method for detecting chromosome aberrations is disclosed. More specifically, chromosome aberrations are detected by in situ hybridisation using at least two sets of hybridisation probes, at least one set comprising one or more peptide nucleic acid probes capable of hybridising to specific nucleic acid sequences related to a potential aberration in a chromosome, and at least one set comprising two or more peptide nucleic acid probes capable of hybridising to specific nucleic acid sequences related to another potential aberration in a chromosome. In particular, the method may be used for detecting chromosome aberrations in the form of breakpoints.

Abstract: An isolated DNA sequence capable of serving as regulatory element in a chimeric gene which can be used for the transformation of plants is disclosed. A chimeric gene containing the DNA sequence as a regulatory element for the transformation of plants is also disclosed. The gene comprises at least, in the direction of transcription, a promoter sequence, a transgene and a regulatory element, characterized in that the regulatory element comprises an intron from the noncoding 5? region of a plant histone gene, allowing the expression of the protein in the zones undergoing rapid growth. The production of transgenic plants is also disclosed.

Abstract: The invention provides hydrolases, polynucleotides encoding them, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides, e.g., enzymes, having a hydrolase activity, e.g., an esterase, acylase, lipase, phospholipase (e.g., phosphplipase A, B, C and D activity, patatin activity, lipid acyl hydrolase (LAH) activity) or protease activity, including thermostable and thermotolerant hydrolase activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The hydrolase activities of the polypeptides and peptides of the invention include esterase activity, lipase activity (hydrolysis of lipids), acidolysis reactions (to replace an esterified fatty acid with a free fatty acid), transesterification reactions (exchange of fatty acids between triglycerides), ester synthesis, ester interchange reactions, phospholipase activity and protease activity (hydrolysis of peptide bonds).

Abstract: The present invention provides porous resin beads containing an aromatic monovinyl compound-divinyl compound-(meth)acrylamide derivative copolymer. Preferably, the copolymer further contains as a structural unit a second aromatic monovinyl compound having a functional group capable of binding to a carboxyl group by a dehydrating condensation reaction.

Abstract: A method of generating a double stranded (ds) recombinant nucleic acid molecule covalently linked in both strands by contacting two or more ds nucleotide sequences with a topoisomerase under conditions such that both termini of at least one end of a first ds nucleotide sequence are covalently linked by the topoisomerase to both termini of at least one end of a second ds nucleotide sequence is provided. Also provided is a method for generating a ds recombinant nucleic acid molecule covalently linked in one strand, by contacting two or more ds nucleotide sequences with a type IA topoisomerase under conditions such that one strand, but not both strands, of one or both ends of a first ds nucleotide sequence are covalently linked by the topoisomerase. Compositions for performing such methods, and compositions generated from such methods also are provided, as are kits containing components useful for conveniently practicing the methods.