Abstract: The present invention relates to a novel method for detecting a target polynucleotide having a target sequence, comprising (a) exposing the target polynucleotide to an initiating oligonucleotide; (b) extending the initiating oligonucleotide with an extended sequence complementary to the target sequence; (c) ligating the initiating oligonucleotide sequence with the extended sequence to form a circular oligonucleotide having a nicking endonuclease (NE) recognition/cutting sequence; (d) exposing the circular oligonucleotide to a DNA polymerase and a DNA synthesis primer to synthesize DNA having a NE recognition sequence; (e) exposing the synthesized DNA to a probe having the NE recognition/cutting sequence to form a double stranded DNA having a full NE site; (f) exposing the double stranded DNA to a nicking endonuclease (NE) to cleave the probe; and (g) detecting the cleaved probe. The presence of the cleaved probe indicates the presence of the target polynucleotide.

Abstract: This invention relates to a quantitative method for determining whether a human subject has an impaired DNA mismatch repair function; providing a diagnostic sample taken from said human and producing a nuclear extract from said sample; providing MMR proficient and MMR deficient nuclear extracts as positive and negative controls, respectively; combining each nuclear extract with at least one mismatch bearing substrate DNA molecule; performing a mismatch repair assay; and determining whether said sample nuclear extract is capable of repairing said substrate DNA molecule; wherein said sample comprises normal, non-malignant constitutive cells, such as fibroblasts. The invention further relates to a kit providing necessary reagents for use in said method.

Abstract: A process of quantifying the extent of degradation present in a human DNA sample is described. The process makes use of a real time PCR system to separately quantitate within a sample a first retrotransposon interspersed element and a relatively longer second retrotransposon interspersed element, where the longer element is expected to be disrupted at a faster pace than is the shorter element as the sample degrades. In one embodiment, the process makes use of the appearance of the relatively young (on an evolutionary scale) Alu Yb-lineage subfamily sequences appearing in every human genome and their virtual absence in non-human samples. In a preferred embodiment, the process quantifies longer 290 bp sequences of “SVA” elements and shorter 80 bp sequences of Alu Yb8-lineage. Newly designed primers and TaqMan probes that are useful in the process are presented. A related process additionally quantifies male specific human DNA.

Abstract: A method of measuring the length of a G tail sequence, characterized by hybridizing the G tail of an nondenatured chromosomal DNA in a sample with a labeled DNA probe having a sequence complementary to the telomere repeat sequence, measuring chemiluminescence from the hybridized DNA probe, and determining the length of the G tail sequence from the measured value, and a kit used for use in such a method.

Abstract: An object of the invention is to provide a nucleic acid detection method which takes advantage of the high specificity of hybridization techniques, reduces the time length and the number of steps required for detection of PCR products, and allows for easy and highly accurate detection by visual observation without the need of special equipment; and a nucleic acid detection device or kit. The invention provides a method for detecting a target nucleic acid in a sample, which includes performing amplification of the target nucleic acid sequence to synthesize an amplification product having a partially double-stranded structure where a single-stranded region is added to each end of the target sequence, and hybridizing a nucleic acid sequence bound to a development medium and a nucleic acid sequence labeled with a labeling compound with the single-stranded regions of the amplification product to form a sandwich hybridization complex; and a detection device thereof.

Abstract: Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.

Abstract: A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.

Abstract: The invention relates to the use of signal processing methods in order to achieve higher signal to noise ratios, to increase the detection limits of target analytes. These techniques include the monitoring of the output signal at higher harmonic frequencies.

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: This invention relates to improved methods for sequencing and genotyping nucleic acid in a single molecule configuration. The method involves single molecule detection of fluorescent labeled PPi moieties released from NTPs as a polymerase extension product is created.

Abstract: In certain embodiments, the invention provides methods and devices for assaying single particles in a population of particles, wherein at least two parameters are measured for each particle. One or more parameters can be measured while the particles are in the separate reaction volumes. Alternatively or in addition, one or more parameters can be measured in a later analytic step, e.g., where reactions are carried out in the separate reaction volumes and the reaction products are recovered and analyzed. In particular embodiments, one or more parameter measurements are carried out “in parallel,” i.e., essentially simultaneously in the separate reaction volumes.

Abstract: The present invention relates to a method for detecting of a mutant DNA using a probe, comprising: (1) contacting a sample containing a single-stranded DNA which has a substituted nucleotide, a deleted nucleotide region, or an inserted nucleotide region (mutant-type DNA), or/and a wild-type single-stranded DNA (wild-type DNA) corresponding thereto with the probe which hybridizes with both single-stranded DNA, to form a hybrid with the mutant-type DNA (mutant-type hybrid) or/and a hybrid with a wild-type DNA (wild-type hybrid), wherein at least one of the obtained mutant-type hybrid and wild-type hybrid has the stem structure; (2) separating the obtained mutant-type hybrid or/and wild-type hybrid by electrophoresis on the basis of presence or absence of the stem structure or difference in the stem structure; and (3) detecting the presence or absence of the mutant-type DNA in the sample.

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

Abstract: A method for detecting a target nucleic acid comprising: forming a three-component association product by allowing the association of at least a nucleic acid molecule, a first nucleic acid probe having a first marker bound thereto, and a second nucleic acid probe having a second marker bound thereto; forming at least one covalent bond between the target nucleic acid molecule and the first nucleic acid probe and between the target nucleic acid molecule and the second nucleic acid probe; and binding the three-component association product to a solid phase carrier through the second marker; recovering the three-component association product bound to the solid phase carrier; releasing the first marker from the recovered three-component association product; and detecting the target nucleic acid molecule by detecting the free first marker.

Abstract: The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template.

Abstract: The present invention relates to a method for the determination of a nucleic acid sequence by physical manipulation. In particular, the said method comprises the steps of denaturing a double-stranded nucleic acid molecule corresponding to the said nucleic acid sequence by applying a physical force to the said molecule; and detecting a blockage of the renaturation of the double-stranded nucleic acid molecule. More specifically, the method comprises the steps of denaturing a double-stranded nucleic acid molecule corresponding to the said nucleic acid sequence by applying a physical force to the said molecule; providing a single-stranded nucleic acid molecule; renaturing the said double stranded nucleic acid molecule in the presence of the said single-stranded nucleic acid molecule; and detecting a blockage of the renaturation of the double-stranded nucleic acid.

Abstract: Methods and containers are provided for identifying a species, illustratively a bacterial species. Illustrative methods comprise amplifying various genes in the nucleic acid from the bacterial species in a single reaction mixture using pairs of outer first-stage primers designed to hybridize to generally conserved regions of the respective genes to generate a plurality of first-stage amplicons, dividing the reaction mixture into a plurality of second-stage reactions, each using a unique pair of second-stage primers, each pair of second-stage primers specific for a target bacterial species or subset of bacterial species, detecting which of the second-stage reactions amplified, and identifying the bacterial species based on second-stage amplification.

Abstract: The present invention relates to a method for the determination of a nucleic acid sequence by physical manipulation. The method is based on the precise determination of the localization of the replicating fork on the template by measuring the physical distance between one end of the molecule and the fork. This allows the determination of the physical location of the site where a pause or a blockage of the replication occurs, and deducing therefrom information on the sequence of the nucleic acid.

Abstract: The present invention relates to a fast method for the detection and the quantification of a nucleic acid, DNA or RNA. Specifically, the invention provides a method for detecting and quantifying the presence of a specific nucleic acid molecule which is based on physical and electronic treatments. The method of the invention is particularly useful for applications as diverse as detection of chromosomal abnormal distributions or gene expression analysis.

Abstract: The present invention relates to the sample preparation of nucleic acids for diagnostic purposes. More precisely, the invention provides a process for simultaneously isolating at least a first and a second target nucleic acid from a plurality of different types of fluid samples and optionally amplifying said isolated nucleic acids in a simultaneous manner.