Abstract: The present invention provides a novel method for detection of liver cancer. This method detects high-sensitively, high-specifically, simply and accurately liver cancer, especially that in early stage by identifying and/or quantifying methylation on particular genes and/or their DNA fragments in clinical specimens, and by combining said methylated DNA values with existing tumor marker values and/or DNA amounts in blood. This invention also detects a precancerous lesion, detects a risk of recurrence after treatment of liver cancer, detects malignancy of liver cancer and monitors progression of liver cancer with time by the same method. As for particular genes, BASP1 gene, SPINT2 gene, APC gene, CCND2 gene, CFTR gene, RASSF1 gene and SRD5A2 gene are mentioned.

Abstract: The invention relates to a method for linking at least two target nucleic acid molecules from a single biological compartment, comprising the steps of isolating a fraction from a sample, wherein the fraction comprises the compartment comprising at least two nucleic acid molecules; diluting said fraction and aliquoting the dilution in multiple separate reaction vessels such that each reaction vessel comprises preferably one compartment, or encapsulating said compartment in emulsion droplets such that each droplet comprises preferably one compartment; linking said at least two target nucleic acid molecules, preferably by overlap extension PCR. The method may be employed in the analysis of mutations present in a single cell and in the production of antibodies which are present in a single hybridoma.

Abstract: A DNA amplification device utilizing a polydimethylsiloxane (PDMS) and silicon substrate coated with spin-on glass (SOG) is provided. This PDMS layer is irreversibly bonded to the SOG layer of the silicon substrate using oxygen plasma. The amplification device is an inexpensive, microfluidic device, which can be utilized as a portable thermo-cycler to perform PCR amplification of DNA in the field.

Abstract: A method of manufacturing a nanoparticle chain is disclosed. The method comprises the steps of: providing a single-stranded circular primer with a determined length, and amplifying the single-stranded circular primer into single-stranded DNA nanotemplate by an isothermal nucleotide amplification reaction such that an end of the single-stranded DNA nanotemplate is fixed to a surface of a substrate; and adding a single-stranded DNA probe conjugated with nanoparticle at one end of which, and attaching the single-stranded DNA probe to the corresponding sequence on the single-stranded DNA nanotemplate to form a nanoparticles chain. The method of manufacturing a nanoparticle chain further comprises providing a fluid, and the flowing direction of the fluid controls the aligning direction of the nanoparticle chain. Wherein, the inter-nanoparticle distance of the nanoparticle chain can be adjusted by adjusting a reaction temperature or adding the single-stranded DNA probe without conjugating with nanoparticles.

Abstract: Compositions and methods are described to modify Family B DNA polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo?” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic DNA polymerase.

Abstract: The present invention provides a novel method for identifying an olfactory receptor included in one olfactory cell. In the present invention, amplified is the cDNA derived from the mRNA of the one olfactory cell by a PCR method using a forward primer represented by SEQ ID: 01 and a reverse primer represented by SEQ ID: 02. Subsequently, determined is whether or not a gene sequence of the amplified cDNA is identical to one gene sequence included in gene sequences coding for olfactory receptors included in the mouse olfactory receptor group A. Finally, determined is that the olfactory receptor included in the one olfactory cell is the olfactory receptor corresponding to the one gene sequence which is identical to the gene sequence of the cDNA in the previous step, if the gene sequence of the cDNA is identical to the one gene sequence in the previous step.

Abstract: Compositions and methods are described to modify Family B DNA polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo?” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic DNA polymerase.

Abstract: A method of determining a probability that a human test subject has colorectal cancer as opposed to not having colorectal cancer is disclosed.

Abstract: The present invention provides for determining relative copy number difference for one or more target nucleic acid sequences between a test sample and a reference sample or reference value derived therefrom. The methods facilitate the detection of copy number differences less than 1.5-fold.

Abstract: Methods and kits for generating circular nucleic acids in a cell-free system, and uses for the generated circular nucleic acids are provided. The methods comprise in vitro amplification of a nucleic acid template comprising a recombination site to produce tandem repeat nucleic acid sequence, and employ a recombination protein to generate the circular nucleic acids from the tandem repeat nucleic acid sequence.

Abstract: Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.

Abstract: The present invention comprises systems and devices for isothermal amplification of polynucleotide sequences to produce DNA cluster arrays.

Abstract: The present invention provides methods to produce a reduced representation of a genome for sequencing and DNA polymorphism detection. In particular, the invention provides PCR-based methods, with normalization of the amplified products using a duplex-specific nuclease, in order to reduce over-representation of PCR products. Oligonucleotides for use in the disclosed method are also provided.

Abstract: The present invention relates to amplification primers with a universal tag and sequencing primers comprising at least one non-natural nucleobase capable of hybridizing to a complementary non-natural nucleobase. The present invention further relates to amplification methods of nucleic acid amplification and sequencing using an amplification primer with a universal tag and sequencing primers, as well as kits and solid supports comprising such primers and tags.

Abstract: A chemically-enhanced primer is provided comprising a negatively charged moiety (NCM), an oligonucleotide sequence having a) non-nuclease resistant inter-nucleotide linkages or b) at least one nuclease resistance inter-nucleotide linkage. The chemically-enhanced primer can be used for sequencing and fragment analysis. Methods for synthesizing the chemically-enhanced primer as well as a method of preparing DNA for sequencing, a method of sequencing DNA, and kits containing the chemically-enhanced primer are also provided. The method of sequencing DNA can comprise contacting amplification reaction products with the composition wherein excess amplification primer is degraded by the nuclease and the chemically-enhanced primer is essentially non-degraded.

Abstract: The present invention provides methods and compositions for improving the efficiency of nucleic acid amplification reactions. The invention encompasses hybrid polymerases that show increased processivity over wild type polymerases as well as decreased exonucleases activity. The invention also encompasses methods, compositions and kits for conducting nucleic acid synthesis and amplification reactions in which non-specific amplification of primers is reduced.

Abstract: The invention provides an apparatus of treating water to obtain small water cluster, which comprises one or more illumination devices and one or more holders holding metal particles. The invention also provides a method of preparing the small water cluster and the small water cluster prepared from the apparatus or the method.

Abstract: A method for the amplification of nucleic acids (1), in which nanoparticles (8) in a reaction volume (2) transfer heat to their environment through excitation.

Abstract: Disclosed are methods for amplifying a nucleic acid target region using an amplification oligomer comprising a target-binding segment and a heterologous displacer tag situated 5? to the target-binding segment. Initiation of an amplification reaction from the tagged amplification oligomer produces an amplicon comprising the displacer tag, such that once the complement of the displacer tag has been incorporated into a second amplicon, a displacer oligonucleotide having a sequence substantially corresponding to the displacer tag sequence is used to participate in subsequent rounds of amplification for displacement of an extension product primed from a site within the second amplicon 5? to the displacer priming site. Also disclosed are related kits and reaction mixtures comprising the displacer-tagged amplification oligomer and corresponding displacer oligonucleotide.

Abstract: The present invention provides a microfluidic biochip, which comprises: a fluid transportation unit having a fluid transportation reservoir and a fluid transportation air chamber; a first fluid storage reservoir; a second fluid storage reservoir; a first valve unit having a first valve and a first valve control air chamber; and a second valve unit having a second valve and a second valve control air chamber; wherein the first valve unit is located between the first fluid storage reservoir and the fluid transportation unit, the second valve unit is located between the second fluid storage reservoir and the fluid transportation unit, and the top portion of the fluid transportation reservoir and the valves are made of a flexible material. The structure of the present microfluidic biochip allows fluids to be transported and/or mixed therein.

Abstract: A reliable and highly sensitive method is provided for detecting methylation status of CpG-containing nucleic acids by nucleic acid amplification and melting curve analysis of amplification products. The methods and compositions employs a novel design of primers, CpG-containing methylation-independent oligonucleotide primers, wherein both unmethylated and methylated alleles of a CpG-containing nucleic acid can be detected by use of only one set of primers after the CpG-containing nucleic acid has been subjected to cytosine to thymine conversion of unmethylated Cytosine. The method is useful for detection of methylation status in for example cancer genes and other disease related genes, wherein methylation influences gene expression.

Abstract: The present invention pertains to novel oligonucleotide compounds for use in various biological assays, such as nucleic acid amplification, ligation and sequencing reactions. The novel oligonucleotides comprise a ribonucleic acid domain and a blocking group at or near the 3? end of the oligonucleotide. These compounds offer an added level of specificity previously unseen. Methods for performing nucleic acid amplification, ligation and sequencing are also provided. Additionally, kits containing the oligonucleotides are also disclosed herein.

Abstract: The present invention provides methods, compositions, and kits comprising snap-back primers used for forming 3? hairpin structures, 5? hairpin structures, and double hairpin structures. The hairpin structures may be used for detecting target sequences (e.g., such as small RNA target sequence), for detecting polymorphisms in target sequences (e.g., such as polymorphisms located near the 5? or 3? ends of the target sequence), or other nucleic acid characterization methods. In certain embodiments, the hairpin structures form invasive cleavage structures (e.g., in combination with a probe or upstream oligonucleotide) which may be cleaved by structure-specific enzymes in order to detect the presence or absence of a particular nucleotide or nucleotide sequence.

Abstract: Systems and methods are provided for single-molecule sequencing of template nucleic acids in which the signal from a label attached to a polymerase enzyme is used to monitor conformational changes in the polymerase which occur while labeled nucleotides or nucleotide analogs are added to a growing nucleic acid chain which is complementary to the template nucleic acid. The signal indicative of the conformational state of the enzyme is used to determine with higher confidence when true nucleotide or nucleotide analog incorporation events occur, allowing for the improved quality of base calls and sequence determination.

Abstract: Disclosed are preloaded analysis modules comprising reagents disposed within a barrier material capable of liberating the reagents, at a time advantageous to a reaction scheme, when exposed to certain activation conditions or reagents. Also disclosed are related methods for analyzing samples with such modules.

Abstract: Embodiments of the present disclosure generally pertain to systems and methods for performing amplicon rescue multiplex polymerase chain reaction (arm-PCR). In one embodiment, the system comprises a processor and a reader coupled to a control element. The control element is configured to control the operation of the processor and the reader based on a variety of settings. The processor is configured to receive a self-contained cassette for performing PCR amplification of DNA and/or RNA obtained from an organic specimen. The processor engages with the cassette and manipulates reagents within the cassette in order to amplify and detect the DNA from the specimen. The processor also causes the cassette to deposit the DNA on a microarray within the cassette. The reader is configured to receive the cassette after it has been processed by the processor and to capture an image of the microarray for transmission to the control element as test data.

Abstract: The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-)dominant genotypes of the genetic markers.

Abstract: Methods and apparatus are provided for point-of-care nucleic acid amplification and detection. One embodiment of the invention comprises a fully integrated, sample-to-answer molecular diagnostic instrument that optionally may be used in a multiplexed fashion to detect multiple target nucleic acid sequences of interest and that optionally may be configured for disposal after one-time use. Optionally, sample preparation is fully or partially achieved via heat treatment and/or using a filter paper, such as a chemically treated filter paper, e.g., an FTA card. The instrument preferable utilizes an isothermal nucleic acid amplification technique, such as loop-mediated isothermal amplification (LAMP), to reduce the instrumentation requirements associated with nucleic acid amplification. Detection of target amplification may be achieved, for example, via detection of a color shift or fluorescence in a dye added to the amplification reaction.

Abstract: Method of detecting methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) in a nucleic acid coamplification assay. The invention advantageously reduces the incidence of false-positive MRSA determinations in real-time assays by requiring satisfaction of a threshold criterion that excludes certain co-infections from the MRSA determination. The invention further provides for determination of MSSA, even when the MSSA is present in combination with methicillin-resistant coagulase-negative (MR-CoNS) bacteria at high or low levels.

Abstract: Methods and kits that use miRNA expression to predict the development of brain metastases in non-small cell lung cancer patients are disclosed.

Abstract: Provided is aptamers screening method based on graphene without target immobilization and the aptamers obtained from the method, and more particularly, a new GO-SELEX method without target immobilization in which a single-stranded nucleic acid pool may react with a non-bound target material or a counter-target material, after which a single-stranded nucleic acid which has not been bound to the target or counter-target may be separated by using the graphene. Also, the specific aptamer obtained through the above-described method may be used for diagnosing target related diseases.

Abstract: The present invention provides, among other things, chimeric DNA polymerases containing heterologous domains having sequences derived from at least two DNA polymerases that have at least one distinct functional characteristics (e.g., elongation rate, processivity, error rate or fidelity, salt tolerance or resistance) and methods of making and using the same. In some embodiments, the present invention can combine desired functional characteristics (e.g., high processivity; high elongation rate; thermostability; resistance to salt, PCR additives (e.g., PCR enhancers) and other impurities; and high fidelity) of different DNA polymerases in a chimeric polymerase.

Abstract: The invention provides improved mutagenic plasmids and a method for making and using them. In one embodiment a cyclic mutagenic nucleic acid is replicated to form interlocking, digestibly separable duplex or simplex rings; and then one or more of the interlocked rings are cleaved selectively by means of a restriction enzyme to liberate an intact duplex or simplex ring. The mutagenic plasmids show substantially improved efficiencies in transforming cellular microorganism that are exposed to them.

Abstract: Provided are the following: a method, for improving reactivity of a nucleic acid synthesis reaction, comprising a step for adding an ?-amino acid to a reaction solution; a composition, for a nucleic acid synthesis reaction, comprising DNA polymerase, reaction buffer, at least one primer, at least one deoxyribonucleotide triphosphate, and an ?-amino acid; and a reaction buffer, for a nucleic acid synthesis reaction, comprising an ?-amino acid.

Abstract: The present invention relates to systems and methods for performing isothermal amplification reactions, in particular, denaturation methods for use in isothermal amplification reactions. An exemplary method may comprise: a) contacting a target nucleic acid with an electrode, wherein the electrode surface has a plurality of first and optionally second nucleic acid primers immobilized thereon, and wherein a target nucleic acid hybridizes to at least one of said first and second nucleic acid primers; b) extending at least one of the first and second primers using a DNA polymerase to form extended target nucleic acids; c) applying positive electrical bias to the electrode such that the extended target nucleic acids anneal to one of the first and second primers; d) extending the target nucleic acid with a DNA polymerase to form amplified target nucleic acid; e) reversing the electrical bias such that the amplified target nucleic acid is denatured from the surface.

Abstract: Success or failure of unmethylated cytosine conversion treatment is determined by using a first primer set comprising plural primers that hybridize with a nucleic acid comprising a nucleotide sequence not containing cytosine in the nucleotide sequence of biological DNA that is subject to an unmethylated cytosine conversion treatment and a second primer set comprising plural primers that hybridize with a nucleic acid comprising a nucleotide sequence in which cytosine in a nucleotide sequence containing cytosine and not containing a CpG site is converted into a base other than cytosine, in the nucleotide sequence of biological DNA.

Abstract: The present invention provides a fluid transfer control method, the method based on measurements of intensities of dyes within the fluid to be transferred. In more detail, the present invention makes use of control dyes and quencher molecules for the fluid transfer controls.

Abstract: Disclosed herein are apparatuses and methods for conducting multiple simultaneous micro-volume chemical and biochemical reactions in an array format. In one embodiment, the format comprises an array of microholes in a substrate. Besides serving as an ordered array of sample chambers allowing the performance of multiple parallel reactions, the arrays can be used for reagent storage and transfer, library display, reagent synthesis, assembly of multiple identical reactions, dilution and desalting. Use of the arrays facilitates optical analysis of reactions, and allows optical analysis to be conducted in real time. Included within the invention are kits comprising a microhole apparatus and a reaction component of the method(s) to be carried out in the apparatus.

Abstract: Disclosed are methods and kits for the specific detection of E. coli O157:H7 and not E. coli O55:H7 from samples such as: complex food matrices, water, beverages, fermentation broths, forensic & biological samples, and environmental samples including food processing and manufacturing surfaces. In some embodiments, a method of the disclosure comprises: hybridizing at least a first pair of polynucleotide primers to at least a first target polynucleotide sequence, hybridizing at least a second pair of polynucleotide primers to at least a second target polynucleotide sequence, amplifying the at least first and at least second target polynucleotide sequences, and detecting the first and second amplified target polynucleotide sequence products, wherein the detection of both the first amplified target polynucleotide sequence product and the second amplified target polynucleotide sequence product is indicative of the presence of E. coli O157:H7 in a sample and not E. coli O55:H7.

Abstract: Methods and devices for performing chemical reactions under controlled temperature are described. In one embodiment, the devices provided by the invention comprise a housing dimensioned to hold a reaction chamber disposed within an interior volume of the housing. The reaction chamber has thermally conductive interior and exterior surfaces defining an internal volume therein at a first temperature. The device also includes at least one temperature-control substance at a second temperature received into said bladder and expels said temperature-control substance, the bladder expands to about substantially at least a portion of said exterior surfaces of said reaction chamber to enable thermal exchange between said temperature-control substance and the said internal volume of reaction chamber.

Abstract: A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.

Abstract: A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided.

Abstract: A method of transcriptional amplification includes: (a) obtaining a mixture by combining (i) a biological sample comprising nucleic acids, (ii) amplification primers, (iii) amplification reagents including enzymes required for amplification, and (iv) at least one polyol capable of stabilizing the enzymes required for amplification; (b) denaturing the nucleic acids by heating the mixture at a temperature above 41° C.; and (c) transcriptionally amplifying at least one target nucleic acid at a temperature above 41° C. when present in the mixture.

Abstract: Methods and compositions for detection of HIV nucleic acids in a sample, such as a biological sample obtained from a human subject, are provided according to embodiments of the present invention which include providing a reaction mixture including at least one LAMP, accelerated LAMP, RT-LAMP or RT-accelerated LAMP assay primer set specific for HIV-I or HIV-2 nucleic acids and the biological sample to be tested for presence of HIV-I and/or HIV-2 nucleic acids; incubating the reaction mixture under conditions suitable to produce a LAMP assay reaction product; and detecting the reaction product. Primers and primer sets for use in LAMP assays of HIV-I or HIV-2 nucleic acids are provided.

Abstract: Aspects of the invention provide methods, nucleic acids and kits for detecting, or for detecting and distinguishing between or among liver cell proliferative disorders or for detecting, or for detecting and distinguishing between or among colorectal cell proliferative disorders. Particular aspects disclose and provide genomic sequences the methylation patterns of which have substantial utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients.

Abstract: A thermocycling device includes a sample holder, a thermal reference and a heating and cooling device which is arranged between the sample holder and thermal reference. The heating and cooling device is in thermally conductive contact with the sample holder and with the thermal reference. The thermocycling device further includes a reference heating and cooling device for maintaining the temperature of the thermal reference at a predetermined temperature level during cycling, and a heat sink which is in thermally conductive contact with the reference heating and/or cooling device.

Abstract: The invention provides methods and apparatus for carrying out multiple amplification reactions in a single reaction chamber by successive cycles of loading reaction mixture, amplifying, and removing spent reaction mixture in a fluidly closed reaction system. In particular, the present invention allows amplification of a plurality of target polynucleotides from a single sample by carrying out under closed-loop control successive amplifications of different target polynucleotides from different portions of the sample.

Abstract: The present invention relates to compositions, methods and systems for analyzing the methylation state of nucleic acids. Some embodiments relate to a compositions, methods and systems for analyzing the methylation state of DNA with a gene array.

Abstract: This invention relates to a method, kit and system for collecting and processing of samples to release and treat DNA and RNA for gene sequence detection. The method described here in provides for rapid and convenient release, and recovery of DNA and RNA from tissues and cellular materials.

Abstract: This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.