Abstract: Disclosed herein are methods of extracting genetic material from a diverse population of one or more types of microbes in a sample. Microbes can be prokaryotes or eukaryotes and may include bacteria, archaea, fungi, protozoa, helminths, parasites, viruses, phages, and others. Extraction may be from a single sample and subsequent identification may be through a molecular method such as qPCR, PCR, RFLP, SSCP, allele specific PCR, targeted sequencing, pull down sequencing, whole shotgun sequencing, or other methods. Also provided are methods that include extracting nucleic acid molecules from a variety of organisms such as fungi (i.e., Saccharomyces spp.), animal cells (Bos taurus), plants (e.g., Hordeum vulgare) from the gut of a human subject, performing a metagenomics analysis therefrom, and determining a probiotic treatment or dietary guidance for the subject based on the metagenomics analysis.

Abstract: Provided herein are compositions, kits, and methods for detecting methicillin-resistant Staphylococcus aureus (MRSA) nucleic acids. In some embodiments, the compositions, kits, and methods can be used to detect one or more of type i, ii, iii, iv, v, vi, vii, viii, ix, xii, xiii, xiv, xv, or xxi SCCmec right extremity junction (MREJ) MRSA nucleic acids and one or more of mecA, mecC, and/or an additional S. aureus-specific gene.

Abstract: Data storage is provided using double-stranded nucleic acid molecules provided on a thermal control device comprising a plurality of sites and temperature control circuitry to independently control a temperature of each of the plurality of sites. The temperature control circuitry, controls the site temperatures to provide a different temperature at a target site compared to other sites of the plurality of sites. The different temperatures at the target site and the other sites provide a greater probability of a read or write operation acting on the target site compared to the other sites. The temperature-based addressing helps to increase physical storage density.

Abstract: The invention relates to methods of synthesizing polymers, biopolymers, and nucleic acids, to immobilised dNTP/NTPs and kits comprising said immobilised dNTP/NTPs for use in said methods of nucleic acid synthesis.

Abstract: The present disclosure, among other things, provides technologies for preparing and purifying phosphoramidites for oligonucleotide synthesis.

Abstract: Automated methods for extracting nucleic acid from one or more tissue samples disposed on slides are disclosed. The methods utilize an automated slide staining apparatus that dispenses a plurality of nucleic acid extraction reagents onto the tissue sample, thus creating an extracted nucleic acid sample. The extracted nucleic acid sample may be used directly in downstream applications such as nucleic acid amplification or sequencing procedures, or may be further purified.

Abstract: The present invention relates to compositions and methods (reagents and protocols) for the post-synthetic modification of nucleic acids obtained from solid-phase oligonucleotide synthesis with a label (such as fluorescent dyes). The coupling reagent is the triazine-based salt 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMT-MM) in the presence of a counteranion.

Abstract: The present disclosure relates to solid phase synthesis of organic molecules and particularly to highly efficient methods for synthesizing polymers, such as peptides, nucleotides or saccharides, employing solid phase synthesis.

Abstract: This disclosure provides, among other things, a 5? adapter of the formula 3?*—X—(5?5?)—Y—3?, where: 3?* is a blocked 3? end, X is a synthetic sequence, (5?5?) is an internal 5?-5? linkage, Y is an adapter sequence, and 3? is a hydroxylated 3? end. In use, sequence X hybridizes to sequence X? in a population of RNA molecules of formula R—X?, which increases the efficiency of ligation of the 5? adapter to the nucleic acid molecules.

Abstract: The present invention provides, among other things, methods of purifying messenger RNA (mRNA) including the steps of (a) precipitating mRNA from an impure preparation; (b) subjecting the impure preparation comprising precipitated mRNA to a purification process involving membrane filtration such that the precipitated mRNA is captured by a membrane; and (c) eluting the captured precipitated mRNA from the membrane by re-solubilizing the mRNA, thereby resulting in a purified mRNA solution. In some embodiments, a purification process involving membrane filtration suitable for the present invention is tangential flow filtration.

Abstract: Disclosed herein is a method for preparing a multilayer of nanocrystals. The method comprises the steps of (i) coating nanocrystals surface-coordinated by a photosensitive compound, or a mixed solution of a photosensitive compound and nanocrystals surface-coordinated by a material miscible with the photosensitive compound, on a substrate, drying the coated substrate, and exposing the dried substrate to UV light to form a first monolayer of nanocrystals, and (ii) repeating the procedure of step (i) to form one or more monolayers of nanocrystals on the first monolayer of nanocrystals.

Abstract: The invention relates to a method for synthesising long nucleic acids, including at least one cycle of elongating initial fragments of nucleic acids, including a) a phase comprising the enzymatic addition of nucleotides to said fragments, b) a phase comprising the purification of the fragments having a correct sequence, c) an optional phase of enzymatic amplification, each cycle being performed in a reaction medium which is compatible with enzymatic addition and amplification, such as an aqueous medium, the synthesis method also comprising, at the end of all the elongation cycles, a last step of final amplification. The invention also relates to the use of the method for the production of genes, or sequences of synthetic nucleic acids, DNA or RNA. The invention further relates to a kit for implementing said method.

Abstract: The invention consists of an assembly of a light (e.g., UV, visible, IR) source, a reaction vial holder and a photochemistry device that allows for conducting arrays of photochemical reaction conditions at room temperature with magnetic stirring. The photochemistry assembly is compatible with multiple reaction vial size holder.

Abstract: Provided is a method of isolating biochemical molecules on a microarray substrate, the method including providing a microarray substrate to which clusters of different kinds of biochemical molecules being classified by individual spot units are attached, the individual spots being regularly arranged thereon; obtaining location information of the individual spot in which a desired cluster among clusters of the biochemical molecules locates; locating an extraction tool for applying energy to isolate the desired cluster according to the location information; and isolating the desired cluster from the microarray substrate by applying energy in a contact or non-contact manner using the extraction tool.

Abstract: The present invention is directed to treatment of nucleic acid molecules that are attached or associated with solid supports for biochemical analysis, including nucleic acid sequencing. After loading on the solid support, the nucleic acid molecules are treated with a composition comprising a condensing agent, a volume excluding agent, or both, then treated with a composition comprising a protein.

Abstract: The invention relates to a method for synthesising long nucleic acids, including at least one cycle of elongating initial fragments of nucleic acids, including a) a phase comprising the enzymatic addition of nucleotides to said fragments, b) a phase comprising the purification of the fragments having a correct sequence, c) an optional phase of enzymatic amplification, each cycle being performed in a reaction medium which is compatible with enzymatic addition and amplification, such as an aqueous medium, the synthesis method also comprising, at the end of all the elongation cycles, a last step of final amplification. The invention also relates to the use of the method for the production of genes, or sequences of synthetic nucleic acids, DNA or RNA. The invention further relates to a kit for implementing said method.

Abstract: Provided are compositions, kits, and methods for the identification of Salmonella. In certain aspects and embodiments, the compositions, kits, and methods may provide improvements in relation to specificity, sensitivity, and speed of detection.

Abstract: The present invention concerns the use of methods and compositions for the isolation of small RNA molecules (100 nucleotides or fewer), such as microRNA and siRNA molecules. Such molecules are routinely lost in commonly used isolation procedures and therefore the present invention allows for a much higher level of enrichment or isolation of these small RNA molecules.

Abstract: The present disclosure provides a solid phase method of making oligonucleotides via sequential coupling cycles including at least one coupling of a dinucleotide dimer subunit to a free 3?-terminal group of a growing chain. The oligonucleotides include at least two nucleoside subunits joined by a N3??P5? phosphoramidate linkage. The method may include the steps of (a) deprotecting the protected 3? amino group of a terminal nucleoside attached to a solid phase support, said deprotecting forming a free 3? amino group; (b) contacting the free 3? amino group with a 3?-protected amino-dinucleotide-5?-phosphoramidite dimer in the presence of a nucleophilic catalyst to form an internucleoside N3??P5? phosphoramidite linkage; and (c) oxidizing (e.g., sulfurizing) the linkage. The compositions produced by the subject methods may include a reduced amount of one or more (N?x) oligonucleotide products. Also provided are pharmaceutical compositions including the subject oligonucleotide compositions.

Abstract: The invention provides compositions of oligonucleotides targeted at influenza genes and at host animal genes involved in response to influenza infection. In some embodiments, the oligonucleotides are modified. In some embodiments, the compositions contain one, or more than one, oligonucleotide. The invention also provides methods and kits using the compositions of the invention for the treatment and prevention of influenza.

Abstract: The subject innovation relates to a RNA binding buffer comprising (a) at least one chaotropic agent; and (b) an organic solvent selected from the group consisting of ethylene carbonate, ethylene glycol diacetate and 2-pyrrolidone or combinations thereof. The subject innovation further relates to a method of binding RNA to a solid support and to a method of isolating RNA both making use of the binding buffer of the subject innovation. The subject innovation finally relates to a kit comprising the RNA binding buffer or the organic solvent as relevant substance therein.

Abstract: The present invention relates to chirally controlled oligonucleotides of select designs, chirally controlled oligonucleotide compositions, and methods of making and using the same. In some embodiments, a provided chirally controlled oligonucleotide composition provides different cleavage patterns of a nucleic acid polymer than a reference oligonucleotide composition. In some embodiments, a provided chirally controlled oligonucleotide composition provides single site cleavage within a complementary sequence of a nucleic acid polymer.

Abstract: The invention provides a cut-out method capable of suppressing production of a byproduct, wherein the object RNA oligonucleotide is not cleaved from a universal linker, which is produced in cutting out the object RNA oligonucleotide from the universal support, and capable of increasing the yield of the object RNA oligonucleotide. The RNA oligonucleotide cut-out method includes a step of bringing a universal support supporting an RNA oligonucleotide in contact with an aqueous solution containing alkylamine and a monovalent inorganic salt.

Abstract: The invention relates to improved RNAi constructs and uses thereof. The construct has a double stranded region of 19-49 nucleotides, preferably 25, 26, or 27 nucleotides, and preferably blunt-ended. The construct has selective minimal modifications to confer an optimal balance of biological activity, toxicity, stability, and target gene specificity. For example, the sense strand may be modified (e.g., one or both ends of the sense strand is/are modified by four 2?-O-methyl groups), such that the construct is not cleaved by Dicer or other RNAse III, and the entire length of the antisense strand is loaded into RISC. In addition, the antisense strand may also be modified by 2?-O-methyl group at the 2nd 5?-end nucleotide to greatly reduce off-target silencing. The constructs of the invention largely avoids the interferon response and sequence-independent apoptosis in mammalian cells, exhibits better serum stability, and enhanced target specificity.

Abstract: Aspects of the present disclosure include methods for double coupling a nucleoside phosphoramidite during synthesis of an oligonucleotide. The method can include coupling a free hydroxyl group of a nucleoside residue with a first sample of a protected nucleoside phosphoramidite via an internucleoside P(III) linkage, followed by exposure to an oxidizing agent prior to a second coupling step with a second sample of the protected nucleoside phosphoramidite, and further exposure to an oxidizing agent. The method finds use in synthesizing an oligonucleotide on a solid phase support, such as a planar surface. The double coupling method can be utilized at one or more nucleotide positions during oligonucleotide synthesis thereby reducing single base deletion rates. Oligonucleotide containing compositions synthesized according to the disclosed methods are also provided.

Abstract: The present invention relates to methods and kits for the detection of 5-hydroxymethylcytosine (5hmC) and/or 5-methylcytosine (5meC). In some embodiments, the present invention relates to methods and kits for detection of 5hmC and/or 5meC in nucleic acid (e.g., DNA, RNA). In some embodiments, the present invention relates to detection of 5hmC in genomic DNA, e.g., mammalian genomic DNA.

Abstract: The present invention provides novel compositions, kits and methods employing RNA 5? polyphosphatases, RNA 5? monophosphatases, capping enzymes, decapping enzymes, nucleic acid pyrophosphatases and RNA ligases, as well as other enzymes, for selective 5? ligation tagging of desired classes of RNA molecules that differ with respect to particular chemical moieties on their 5? ends. The 5? tagged RNA molecules can be used for synthesis of tagged first-stand cDNA, double-stranded cDNA, and sense or antisense RNA for a variety of uses.

Abstract: De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.

Abstract: Disclosed herein are methods for detecting a fungal pathogen in a patient sample, involving isolating the sample, carrying out a PCR reaction on the sample to generate an amplicon that includes a region of the fungal 28S ribosomal RNA gene, and detecting the PCR amplicon. Also disclosed are sequences of primers for specifically detecting a broad range of fungal pathogens in the presence of human ribosomal DNA. In certain embodiments, the amplicon is detected by sequencing or by two-dimensional melt-curve analysis. In yet other embodiments, more than one fungal pathogen is detected in a sample using the methods disclosed herein.

Abstract: A method of analyzing molecules using a nanopore array including a plurality of cells included on a chip is disclosed. Nanopores are caused to be formed in at least a portion of the plurality of the cells. A first physical measurement of the nanopores is evaluated. It is determined whether to cause the molecules to interact with the nanopores. At least a portion of the nanopores is caused to interact with the molecules. A second physical measurement of the nanopores that indicates a property of the molecules is evaluated. It is determined whether to cause the nanopores to be reformed so that the cells may be reused to interact with additional molecules.

Abstract: The invention provides compounds that bind to deoxycytidine kinase (dCK) and compositions including pharmaceutically acceptable compositions containing the compounds. The compounds are useful in treating diseases and disorders where dCK activity is implicated such as cancer and immune disorders. The compounds also find use in clinical methodologies including positron emission tomography (PET) imaging.

Abstract: Assays using non-natural bases are described. In one embodiment, the method involves contacting a sample suspected of containing the target nucleic acid with a polymerase and first and second primers; amplifying the target nucleic acid by PCR using the first and second primers to generate an amplification product having a double-stranded region and a single-stranded region that comprises the non-natural base; contacting the sample with a reporter comprising a label and a non-natural base that is complementary to the non-natural base of the single-stranded region; annealing at least a portion of the reporter to the single-stranded region of the amplification product; and correlating a signal of the label with the presence of the target nucleic acid in the sample. The invention also provides corresponding kits for use in detecting target nucleic acids in a sample.

Abstract: Nucleotide and/or oligonucleotide represented by formula (1) and the liquid phase synthesis process thereof. The present invention provides a liquid phase synthesis process for preparing a nucleotide and/or an oligonucleotide, comprising a process for combining the nucleotide and/or oligonucleotide protective groups, in which, under the condition that the 2?-hydroxyl group is protected by a group with a sterically hindered silane structure, the 3? phosphate group(s) of the nucleotide and/or oligonucleotide is/are directly protected by (a)?-cyanoethyl group(s), and after the ?-cyanoethyl group(s) is/are removed, the resulting product can directly participate in the next cycle of synthesis, wherein the synthesis reaction is carried out in a reaction flask or reaction kettle, without being limited by a solid carrier or synthesizer, so that the large scale preparation of oligonucleotides can be achieved.

Abstract: The invention provides compositions and methods for making closed nucleic acid structures in which one or both strands are continuous. The closed nucleic acid structures can be used as sequencing templates among other applications.

Abstract: This invention concerns non-standard nucleotides that can form non-standard Watson-Crick nucleobase pairs having geometries similar to the geometries of standard nucleotide pairs, but that are joined by a non-standard hydrogen bonding schemes. Disclosed are processes that yield oligonucleotides that are semi-complementary to a standard oligonucleotide, where the region of semi-complementarity pairs one or more standard nucleotides with a non-standard nucleotide, or vice versa. Duplexes formed from two semi-complementary oligonucleotides are also inventions disclosed.

Abstract: A method is provided for detecting a bacterial pathogen in a sample. One step of the method includes obtaining a sample and then subjecting the sample to nested PCR. The nested PCR is conducted in the presence of at least two outer oligonucleotide primers complementary to a target nucleotide sequence of the bacterial pathogen so that a first amplified product is produced. The target nucleotide sequence includes at least a portion of a 16S-23S ribosomal RNA sequence. The first amplified product is subjected to the nested PCR in the presence of at least two inner oligonucleotide primers complementary to the nucleotide sequence of the first amplified product so that a second amplified product is obtained. Detection of the second amplified product indicates the presence of the bacterial pathogen in the sample.

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: Disclosed is a method for lowering the detection limit in a method of detecting a nucleic acid comprising (i) contacting a solution comprising a first PNA with a substrate having a second PNA affixed thereto, the second PNA comprising at least one trans-cyclopentane residue, wherein the first PNA has two linker-attached biotins attached thereto and the first and second PNAs being complementary to different portions of a target DNA; (ii) contacting a sample suspected of containing the nucleic acid with the first and second PNAs; and (iii) determining the presence of the reporter molecule on the substrate. Also disclosed are a detection assay and a kit for detecting a target nucleic acid.

Abstract: The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to a solid support at the 5? end, cleaving one or both strands of the double-stranded nucleic acid molecule, and subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the solid support, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Brain derived neurotrophic factor (BDNF), in particular, by targeting natural antisense polynucleotides of Brain derived neurotrophic factor (BDNF). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of BDNF.

Abstract: Described herein are techniques for assembling a polynucleotide encoding a transcription activator-like effector nucleases (TALEN). The techniques ligate and digest necessary modules for a TALEN assembly in one reactor or system. Methods and Kits for generating a TALEN are also described.

Abstract: DNA oligomers comprising sequences that are absent from the genome of one or more organisms of interest are used as reference markers (RMs). The RMs are added to biological samples to “tag” and subsequently identify the samples as authentic and to distinguish tagged samples from samples obtained without said markers, for example, in forensic, medical, legal and other applications.

Abstract: Methods and compositions for the amplification of nucleic acids and generation of concatemers are disclosed. Amplification methods provided herein may be performed under isothermal conditions. Methods and compositions may include reagents such as nucleic acid polymerases and primers.

Abstract: A method for preparing a crosslinked polymer coated controlled porosity glass (CPG) particle is provided. The method involves mixing CPG particles in a solution comprising polyvinylbenzylchloride and a first solvent at a temperature below 10° C. A second solvent is added and a crosslinking agent is added to the mixture. The first solvent is removed rapidly within hours of addition of the crosslinking agent. The crosslinking reaction is permitted to proceed and the mixture is then cooled and treated to remove any remaining solvent. The resulting coated CPG particles are washed and dried. Also provided a polymer coated CPG particles using for loading ligand thereon.

Abstract: An oligonucleotide derivative having the structure of formula (A) and methods for preparing the oligonucleotide derivative are disclosed. wherein R3 is a first oligonucleotide; R1 is selected from the group consisting of alkyl, cycloalkyl, aryl, heterocyclyl, heteroaryl, a polyethylene glycol, a peptide, a protein, a polysaccharide, and a second oligonucleotide; R2 is a linker or a direct bond; Z1 is NR4, S, or O, and Z2 is NR4 or S, wherein R4 is selected from H, alkyl, aryl, heterocyclyl, or heteroaryl. A method includes: synthesizing an oligonucleotide derivative comprising an amino or thiol group; and reacting a 3,4-dialkoxycyclobutene-1,2-dione with the oligonucleotide derivative to produce an oligonucleotide-squarate mono-conjugate.

Abstract: Disclosed herein are compositions and methods for sequencing, analyzing, and utilizing samples such as single samples. Also disclosed herein are compositions and methods for matching together two or more sequences from a sample. Also disclosed herein are compositions and methods for expressing and screening molecules of interest.

Abstract: Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.

Abstract: The invention provides improved methods for investigating nucleic acid sequences, wherein at least one additional probe is used which is specific for a (pseudo)gene variant of a target nucleic acid.

Abstract: Disclosed are lipophilic polynucleotide conjugates including polynucleotide-cholesterol conjugates and methods of delivering therapeutic polynucleotides to a mammalian cell or patient in need of treatment using said conjugates. The disclosure further provides methods of synthesizing the lipophilic polynucleotide conjugates. The conjugates are designed to mimic or target cellular miRNAs. The lipophilic moiety, such as cholesterol or cholesterol derivative, is spaced from the polynucleotide by a substantially linear hydrocarbon group. Due to an absence of significantly polar groups and/or exchangeable protons in the vicinity of the lipophilic moiety, the interaction between the lipophilic moiety and cell membranes is enhanced to provide for efficient entry into cells.

Abstract: The present invention relates to methods and reagents for detecting analytes, e.g. nucleic acids. The new methods and reagents allow a simple and sensitive detection even in complex biological samples.