Abstract: A method for providing defined mixtures of nucleic acids is described. In certain embodiments, the method uses oligonucleotide probes attached to a solid support as a sequence-specific affinity agent to isolate and facilitate the amplification of defined nucleic acid fragment mixtures.

Abstract: A method for providing defined mixtures of nucleic acids is described. In certain embodiments, the method uses oligonucleotide probes attached to a solid support as a sequence-specific affinity agent to isolate and facilitate the amplification of defined nucleic acid fragment mixtures.

Abstract: Systems and methods for analysis of polymers, e.g., polynucleotides, are provided. The systems are capable of analyzing a polymer at a specified rate. One such analysis system includes a structure having a nanopore aperture and a molecular motor, e.g., a polymerase, adjacent the nanopore aperture.

Abstract: Embodiments of labeled nucleotide compositions are described. Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled nucleotide composition to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.

Abstract: A method for sequencing a nucleic acid is provided. In certain embodiments, the method includes contacting a nucleic acid duplex comprising a nucleic acid template and a primer annealed to the template with a reagent mix under primer extension conditions to produce an extended primer and ATP. The reagent mix may contain an adenosine-2?-deoxynucleoside tetraphosphate moiety and a polymerase. The method further includes detecting the produced ATP. Also provided are adenosine-2?-deoxynucleoside tetraphosphate moieties that find use in the subject methods. Also provided are kits containing the adenosine-2?-deoxynucleoside tetraphosphate moieties for use in the subject methods.

Abstract: Systems and methods for analysis of polymers, e.g., polynucleotides, are provided. The systems are capable of analyzing a polymer at a specified rate. One such analysis system includes a structure having a nanopore aperture and a molecular motor, e.g., a polymerase, adjacent the nanopore aperture.

Abstract: A method for sequencing a nucleic acid is provided. In certain embodiments, the method includes contacting a nucleic acid duplex comprising a nucleic acid template and a primer annealed to the template with a reagent mix under primer extension conditions to produce an extended primer and ATP. The reagent mix may contain an adenosine-2?-deoxynucleoside tetraphosphate moiety and a polymerase. The method further includes detecting the produced ATP. Also provided are adenosine-2?-deoxynucleoside tetraphosphate moieties that find use in the subject methods. Also provided are kits containing the adenosine-2?-deoxynucleoside tetraphosphate moieties for use in the subject methods.

Abstract: In particular embodiments in accordance with the present invention, a wax-embedded tissue specimen is digested and the resulting digested tissue specimen is purified to provide a purified RNA fraction. The purified RNA fraction is treated with one or more enzymes to provide a sample containing dephosphorylated RNA; the sample is contacted with an enzyme having an RNA ligation activity in the presence of a labeled substrate to provide labeled RNA. Kits for performing the described methods are described. Methods of performing an array analysis of a labeled RNA sample are also described.

Abstract: Embodiments of labeled nucleotide compositions are described. Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled nucleotide composition to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.

Abstract: Methods and reagents are disclosed which provide for more sensitive, more accurate and higher through-put analyses of target nucleic acid sequences. The methods and reagents of the present invention may be generically applied to generally any target nucleic acid sequence and do not require a priori information about the presence, location or identity of mutations in the target nucleic acid sequence. The reagents of the invention are mixtures of oligonucleotide precursors having a high level of coverage and mass number complexity, and also having tags analyzable by mass spectrometry which are covalently linked to the precursors through cleavable bonds. A method is also disclosed for analyzing a target nucleic acid sequence employing the mixtures of oligonucleotide precursors having tags analyzable by mass spectrometry covalently linked to the oligonucleotide precursors through cleavable bonds, and chemical or enzymatic assays to alter the mass of the oligonucleotide precursors prior to mass spectral analysis.

Abstract: Embodiments of labeled nucleotide compositions are described. Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled nucleotide composition to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.

Abstract: The present invention provides a system and methods for assaying nucleic acid molecules with reduced levels of background signal and enhanced specificity and sensitivity. In particular, the present invention provides a system and methods for detecting, sorting, tracking and characterizing nucleic acid molecules using hybridization assays with reduced levels of undesirable cross hybridization and reduced levels of intramolecular secondary structure.

Abstract: A polymerase chain reaction (PCR) mixture containing at least one unstructured nucleic acid primer pair is provided. In certain embodiments, the mixture may also contain: nucleotides, a DNA polymerase, and PCR reaction reagents, as well as a nucleic acid sample. The reaction mixture may be employed in, for example, a PCR reaction.

Abstract: Oligonucleotide arrays having features that include cleavable oligonucleotides are disclosed, as well as methods of making such arrays. Methods of synthesizing an oligonucleotide on a surface of a substrate are described.

Abstract: Systems and methods for analysis of polymers, e.g., polynucleotides, are provided. The systems are capable of analyzing a polymer at a specified rate. One such analysis system includes a structure having a nanopore aperture and a molecular motor, e.g., a polymerase, adjacent the nanopore aperture.

Abstract: A method of tracking machine breakdown (10) comprising, listing each breakdown relative to a first machine (20) and listing the corrective action taken on the first machine relative to each of the breakdowns (30).

Abstract: Methods and reagents are disclosed for quantitatively analyzing a set of target nucleic acid sequences. In the method a unique set of oligonucleotide probe precursors is hybridized to the target nucleic acid sequences to produce hybrids. The hybrids are processed to alter the mass of each of the oligonucleotide probe precursors in the hybrids in a target sequence-mediated reaction to produce oligonucleotide products, each of which has a unique mass that is not a result of the presence of a mass tag in the oligonucleotide product. The processing of the hybrids may involve polymerase extension or ligation. The products are analyzed by means of mass spectrometry and the results are related to the amount of the target nucleic acid sequences in the set. Kits for carrying out the above methods are also disclosed.

Abstract: The present invention provides an improved method of detecting differential expression of a gene of interest using modified nucleotides that reduce the levels of secondary structure in a nucleic acid molecule. In certain embodiments of the invention, multiple genes of interest are provided on the surface of a solid support, such as in the form of a microarray. The presence of carefully chosen unstructured nucleic acid bases (UNAs) in the samples being assayed and in the probes on the surface of the solid support provides an internal referenced measurement that is suitable for detecting the differential expression of a gene of interest in the samples. Also provided are arrays of pairs UNA probes that are capable of detecting differential expression of a particular gene of interest in two samples of nucleic acid.

Abstract: The present invention provides general affinity based methods for separating parental genetic material. Without limitation, the inventive methods may be used to separate maternal genetic material from paternal genetic material for haplotyping purposes. According to such embodiments, once the maternal genetic material has been separated from the paternal genetic material any method of SNP genotyping can be used, and the SNP genotypes will be, by definition the genetic haplotypes.

Abstract: The present invention provides a system for generating nucleic acid molecules having a reduced ability to hybridize to form intermolecular and intramolecular base pairs between regions of substantial complementarity as compared with nucleic acid molecules having the same nucleotide sequence containing naturally-occurring nucleotides. Furthermore, nucleic acid molecules of the present invention are characterized by the ability to form intermolecular base pairs with other nucleic acid molecules of choice.