Abstract: The invention concerns methods for detecting a nucleic acid of interest in a solution comprising (a) contacting a solution suspected of containing the nucleic acid of interest with a PNA capture probe and a PNA reporter probe; wherein (i) the PNA capture probe comprises at least two trans-cyclopentanes; (ii) the PNA reporter probe comprises at least six biotin groups; (iii) the PNA capture probe bound to a surface; and (iv) the PNA capture probe and the PNA reporter probe each comprise a nucleobase sequence that is complementary to different non-overlapping portions of the nucleic acid of interest; (b) detecting the presence of the PNA capture probe and the PNA reporter probe bound to the surface; wherein the nucleic acid of interest is detected when 1-1000 molecules of the nucleic acid of interest are present in the solution being tested.

Abstract: The present invention relates to a method of designing DNA probe chip for room-temperature hybridization in order to solve the solvent evaporation problem occurring when carrying out said hybridization at a high temperature of 40° C.˜50° C. or higher, wherein the method is designed to allow genotyping through hybridizing at a room temperature of 20° C.˜30° C. The method of designing DNA probe chip comprises designing DNA probe to start at ?10˜+5 position that is between ?10 position which is overlapped 10 sequences with primer and +5 position which is 5 sequences far from the 3?-terminal of primer, based on 0 position which is 3?-terminal of primer.

Abstract: Disclosed is a method for detecting a nucleic acid using a substance that suppresses, in the labeling step of the post-staining method, detachment of a target nucleic acid that has once hybridized with a capture probe immobilized on a support, which method enables detection of the target nucleic acid with a sensitivity equivalent to or higher than that achieved by a method using sodium ion even in cases where the substance is used at a lower concentration. The method for detecting a nucleic acid comprises the steps of: (1) hybridizing a capture probe with a target nucleic acid to form a double-stranded nucleic acid; bringing the formed double-stranded nucleic acid into contact with a solution containing a labeling substance and a divalent metal cation at a concentration of not less than 10 mM to introduce the labeling substance into the double-stranded nucleic acid; and detecting the labeling substance introduced into the double-stranded nucleic acid.

Abstract: This disclosure provides, among other things, a method of combining nucleic acid fragments, comprising: (a) providing two double-stranded DNA molecules with a common sequence, wherein the common sequence is at the end of each molecule; (b) nicking one strand in the common sequence of both molecules at a respective nicked site; (c) moderately denaturing both molecules to remove a single-stranded fragment from the nicked site to one end of each molecule, wherein the single-stranded fragment includes the common sequence in part or in whole, resulting in an overhanging sequence in each molecule, and the overhanging sequences in both molecules are complementary to each other; (d) allowing the overhanging sequences of both molecules to anneal to each other, and ligating the molecules. Alternative ways for performing the method are also provided.

Abstract: The invention relates to a new method of characterizing a target polynucleotide. The method uses a pore and a RecD helicase. The helicase controls the movement of the target polynucleotide through the pore.

Abstract: Plasmonics-active nanoprobes are provided for detection of target biomolecules including nucleic acids, proteins, and small molecules. The nucleic acids that can be detected include RNA, DNA, mRNA, microRNA, and small nucleotide polymorphisms (SNPs). The nanoproprobes can be used in vito in sensitive detection methods for diagnosis of diseases and disorders including cancer. Multiplexing can be performed using the nanoprobes such that multiple targets can be detected simultaneously in a single sample. The methods of use of the nanoprobes include detection by a visible color change. The nanoprobes can be used in vivo for treatment of undesireable cells in a subject.

Abstract: This disclosure relates to a method for increasing the hybridization efficiency of a probe and a target RNA in a sample, for example to identify a particular RNA present in the sample. The method includes heating a lysate sample comprising at least one target RNA, such as a tRNA, mRNA or rRNA, at a temperature of about 95° C. for a time sufficient to interfere with secondary structure of the RNA, wherein the time is short enough, such that the RNA in the cell lysate sample are not significantly degraded, and wherein the lysate comprises a cell lysis buffer comprising a chemical denaturant. To detect a target RNA in the lysate, the lysate is contacted with at least one detectable probe, such as a labeled probe, designed to specifically hybridize to the target RNA in the lysate.

Abstract: The present application provides polynucleotides comprising 5?-tails with sequence segments useful for the detection of target nucleic acid sequences, and methods for their use in detecting target nucleic acids. The polynucleotides are used to amplify a subsequence of a target nucleic acid in the presence of one or more ribonucleotides. The ribonucleotides are incorporated into amplification products at regular intervals complementary to the 5?-tail sequence segments. Cleavage of amplification products at the bond immediately 3? to incorporated ribonucleotides produces detectably distinct fragments indicative of the presence or absence of a target nucleic acid.

Abstract: Provided herein is a method for enriching a target nucleic acid molecule. In one embodiment, the method may involve hybridizing a C-probe to a strand of a target nucleic acid to produce a complex, enzymatically removing any 3? overhanging end from the target nucleic acid of the complex to produce a 3? hydroxyl group at the 3? end; extending the 3? end of the first sequence using the oligonucleotide sequence of the C-probe as a template; enzymatically removing any 5? overhanging end from the target nucleic acid, either before or after the extending step, to produce an 5? phosphate group at the end of the second sequence; and ligating the 5? phosphate group at the end of the second sequence to the 3? hydroxyl group at the end of the first sequence to produce a circular DNA molecule that contains the target sequence and the complement of the oligonucleotide sequence.

Abstract: The present invention provides compositions, apparatuses and methods for detecting one or more nucleic acid targets present in a sample. Methods of the invention include utilizing two or more ligation probes that reversibly bind a target nucleic acid in close proximity to each other and possess complementary reactive ligation moieties. When such probes have bound to the target in the proper orientation, they are able to undergo a spontaneous chemical ligation reaction that yields a ligation product that is directly detected or that is amplified to produce amplicons that are then detected. The present invention also provides methods to stabilize sample RNA so that degradation does not significantly affect the results of the analysis.

Abstract: A method of determining the sequence of a target nucleic acid is provided. The method can include the steps of (a) performing a defined number of incremental extension cycles to produce a population of nucleic acid fragments having different portions of the target nucleic acid wherein the individual nucleic acid fragments in the population have a defined length that is correlated with the number of incremental extension cycles; (b) determining the sequence of the first end of individual nucleic acid fragments in the population, thereby providing first end sequences; (c) determining the sequence of the second end of individual nucleic acid fragments in the population, thereby providing second end sequences; and (d) determining the sequence of the target nucleic acid based on the first end sequences, the second end sequences and the defined length.

Abstract: The present invention provides compositions, apparatuses and methods for detecting one or more nucleic acid targets present in a sample. Methods of the invention include utilizing two or more oligonucleotide probes that reversibly bind a target nucleic acid in close proximity to each other and possess complementary reactive ligation moieties. When such probes have bound to the target in the proper orientation, they are able to undergo a spontaneous chemical ligation reaction that yields a ligated oligonucleotide product. In one aspect, the ligation product is of variable length that correlates with a particular target. Following chemical ligation, the probes may be amplified and detected by capillary electrophoresis or microarray analysis.

Abstract: Methods and compositions for the detection and quantification of nucleic acids are provided. In one embodiment, a sample is contacted with a primer complementary to a first region of a target nucleic acid and a probe complementary to a second region of the target nucleic acid downstream of the first region under conditions suitable for hybridization of the target nucleic acid with the primer and the probe. The probe in this embodiment comprises a fluorophore and is attached to a solid support. The hybridized probe is cleaved with a nucleic acid polymerase having exonuclease activity to release the reporter from the solid support. The presence of the target nucleic acid is then detected and optionally quantified by detecting a decrease in signal from the reporter on the solid support.

Abstract: The present invention relates to a single-stranded nucleic acid molecule for use in a method for the production of a nucleic acid, whereby the nucleic acid molecule comprises a part A and a part B, whereby part A comprises a sequence, which corresponds at least to a partial sequence of the recognition site of a type IIS restriction enzyme, and part B comprises an arbitrary but defined sequence of nucleotides. By using such nucleic acid molecules it is possible to assemble different fragments in a sequence-independent manner and thus conduct the synthesis of a nucleic acid with recourse to standardized elements.

Abstract: An array chip design is provided where the chip includes a field region arranged with sites according to a first pitch and at least one track region having a one-dimensional site pattern arranged according to a second pitch that is less dense and is an integer multiple of the first pitch so that observation through pixel-based sensors using one-dimensional quad-cell averaging can be applied in the track region, thereby to attain alignment of the chip to pixel-based optical instrumentation with a higher density of sites.

Abstract: The present invention provides compositions, apparatuses and methods for detecting one or more nucleic acid targets present in a sample. Methods of the invention include utilizing two or more ligation probes that reversibly bind a target nucleic acid in close proximity to each other and possess complementary reactive ligation moieties. When such probes have bound to the target in the proper orientation, they are able to undergo a spontaneous chemical ligation reaction that yields a ligation product that is directly detected or that is amplified to produce amplicons that are then detected. The present invention also provides methods to stabilize sample RNA so that degradation does not significantly affect the results of the analysis.

Abstract: In alternative embodiments, the invention provides compositions such as devices, pills, beads, capsules, products of manufacture, particles, microparticles, nanoparticles, gels, liquid gels, liquid gel capsules, capsules, tablets, geltabs, liquids, sprays, emulsions, suspensions, pastes or yogurts, for the detection and isolation of biomarkers, nucleic acids, proteins or peptides, proteoglycans, lipids, fats, sugars or polysaccharides in the gastrointestinal tract for e.g., detecting the presence of particular exogenous or endogenous nucleic acids, e.g., DNA or RNA, or proteins, in the gastrointestinal tract, for example, to diagnose the presence of an infectious or exogenous agent such as a virus, a fungus, a parasite, a bacteria, intestinal helminths and protozoan parasites, and the like, or a biomarker such as a cancer-causing or cancer-predisposing allele, e.g., mutations of the KRAS2 oncogene in pancreatic cancer.

Abstract: The present invention relates to a device for interfacing nanofluidic and microfluidic components suitable for use in performing high throughput macromolecular analysis. Diffraction gradient lithography (DGL) is used to form a gradient interface between a microfluidic area and a nanofluidic area. The gradient interface area reduces the local entropic barrier to nanochannels formed in the nanofluidic area. In one embodiment, the gradient interface area is formed of lateral spatial gradient structures for narrowing the cross section of a value from the micron to the nanometer length scale. In another embodiment, the gradient interface area is formed of a vertical sloped gradient structure. Additionally, the gradient structure can provide both a lateral and vertical gradient.

Abstract: A composition suitable for formulation of an enzymatic reaction mixture, the composition comprising a reaction component essential for an ex-vivo non-polymerase enzymatic reaction in which a substrate is catalyzed by an enzyme in a reaction mixture to form a product, and a tracer compatible with the enzyme, the composition being substantially free of the substrate.

Abstract: Described herein are nucleic acid based probes and methods for discriminating and detecting single nucleotide variants in nucleic acid molecules (e.g., DNA). The methods include use of a pair of probes can be used to detect and identify polymorphisms, for example single nucleotide polymorphism in DNA. The pair of probes emit a different fluorescent wavelength of light depending on the association and alignment of the probes when hybridized to a target nucleic acid molecule. Each pair of probes is capable of discriminating at least two different nucleic acid molecules that differ by at least a single nucleotide difference. The methods can probes can be used, for example, for detection of DNA polymorphisms that are indicative of a particular disease or condition.