Abstract: Contemplated systems and methods allow analysis of multiple and distinct patient samples using a labeling scheme that entirely avoids carry-over of a label or reagent to the analytic platform, typically an addressable solid phase. In preferred aspects, a hybridization portion, a fluorophore, and/or a quencher are removed by a 5?-3?-exonuclease activity of a polymerase from a reporter oligonucleotide to so remove the oligonucleotide from the pool of molecules that bind to the solid phase and/or or to provide signal differentiation by removal of a fluorophore or quencher.

Abstract: Individual patient- and disease-specific test results are obtained from a mixture of one or more distinct tests from multiple combined and distinct patient samples or reactions. In an especially preferred aspect, multiple reaction products from oligonucleotides having unique identifier portions are prepared or received from a clinician and combined for hybridization on a chip. Test results are deconvoluted using a deconvolution table in which associative data are employed to provide access to the individual patient- and disease-specific test results.

Abstract: Contemplated systems and methods allow analysis of multiple and distinct patient samples using a labeling scheme that entirely avoids carry-over of a label or reagent to the analytic platform, typically an addressable solid phase. In preferred aspects, a hybridization portion, a fluorophore, and/or a quencher are removed by a 5?-3?-exonuclease activity of a polymerase from a reporter oligonucleotide to so remove the oligonucleotide from the pool of molecules that bind to the solid phase and/or or to provide signal differentiation by removal of a fluorophore or quencher.

Abstract: This invention relates generally to compositions and methods for detection of pathogenic bacteria that express extracellular chaperonin proteins. In one embodiment, it relates to Mycobacterium tuberculosis (Mtb) detection and provides for novel probes for a specific and sensitive diagnostic test for Mycobacterium tuberculosis complex (TBC) that hybridize with the groEL-1 gene. Arrays comprising the novel probes immobilized on a support for hybridization analysis and methods for TBC detection using the probes are also provided.

Abstract: A method, composition and kit for synthesizing multiple copies of a target nucleic acid sequence autocatalytically under conditions of substantially constant temperature, ionic strength, and pH are provided in which multiple RNA copies of the target sequence autocatalytically generate additional copies using a mixture of blocked and unblocked primers and/or promoter-primers to initiate DNA and RNA synthesis, preferably with reduced non-specific product formation. The invention is useful for generating copies of a nucleic acid target sequence for purposes that include assays to quantitate specific nucleic acid sequences in clinical, environmental, forensic and similar samples, cloning and generating probes.

Abstract: This invention relates generally to nucleic acid hybridization analysis. More specifically, oligonucleotide probes containing hairpin structures, or arrays of such oligonucleotide probes immobilized on a solid support, that are suitable for hybridization analysis are provided. Methods for nucleic acid hybridization analysis using the probes or array of immobilized probes are also provided.

Abstract: This invention relates generally to Group B streptococci (GBS) Streptococcus agalactiae detection. More specifically, the present invention provides for novel probes for a specific and sensitive diagnostic test of GBS. These GBS-specific probes hybridize with the the surface immunogenic protein (sip) gene. Arrays comprising the probes immobilized on a support for hybridization analysis and methods for GBS detection using the probes are also provided.

Abstract: This invention relates generally to Group B streptococci (GBS) Streptococcus agalactiae detection. More specifically, the present invention provides for novel probes for a specific and sensitive diagnostic test of GBS. These GBS-specific probes hybridize with the capsular polysaccharide synthesis (cps) gene. Arrays comprising the probes immobilized on a support for hybridization analysis and methods for GBS detection using the probes are also provided.

Abstract: This invention relates generally to Mycobacterium tuberculosis complex (TBC) detection. More specifically, the present invention provides for novel IS6110 probes for a direct, specific and sensitive diagnostic test of tuberculosis (TB). These probes hybridize with the IS6110 DNA sequence that is believed to be present only in the Mycobacterium tuberculosis complex (TBC). Arrays comprising the novel IS6110 probes immobilized on a support for hybridization analysis and methods for TBC detection using the probes or arrays of immobilized probes are also provided.

Abstract: This invention relates to methods of signal amplification in nucleic acid hybridization reactions without the use of direct amplification of the target sequence. More particularly, it relates to methods of detecting target nucleic acids in samples such that detection is accomplished via probe-target and target-target hybridization. In one aspect, the present invention relates to methods of detecting genomic target nucleic acids such that the signal is amplified via formation of target-probe complexes.

Abstract: The present invention relates to methods and compositions for analyzing nucleic acids. In particular, the invention provides for methods and combinations for analyzing nucleic acids in a plurality of samples using a plurality of detectably different signature labels and a probe that is hybridizable to each of the target nucleic acids. The invention also provides for a method for quantifying a nucleic acid by analyzing the amount of a label, e.g., a photoactivatable label, attached to the target nucleic acid.

Abstract: The present invention relates to methods and compositions for analyzing nucleic acids. In particular, the invention provides for methods and combinations for analyzing nucleic acids in a plurality of samples using a plurality of detectably different signature labels and a probe that is hybridizable to each of the target nucleic acids. The invention also provides for a method for quantifying a nucleic acid by analyzing the amount of a label, e.g., a photoactivatable label, attached to the target nucleic acid.

Abstract: This invention relates generally to nucleic acid hybridization analysis. More specifically, an oligonucleotide probe for hybridization analysis is provided, which probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with. Arrays comprising the hairpin probes immobilized on a solid support and methods for nucleic acid hybridization analysis using the probes or array of immobilized probes are also provided. Methods for transcribing and/or amplifying a probe DNA sequence using a hairpin probe are further provided.

Abstract: This invention relates generally to nucleic acid hybridization analysis. More specifically, a method for detecting a point mutation in a DNA strand is provided, which method uses, inter alia, a test nucleic acid strand complementary to a target DNA strand, said nucleic acid strand comprises a sufficient number of ribonucleotide residues that span the position of said point mutation to be detected to form a target DNA strand/test nucleic acid strand duplex and RNase H cleavage of said target DNA strand/test nucleic acid strand duplex. Kits and arrays for detecting a point mutation in a DNA strand comprising test nucleic acid strand comprising a sufficient number of ribonucleotide residues that span the position of said point mutation to be detected are also provided.

Abstract: This invention relates generally to nucleic acid hybridization analysis. More specifically, an oligonucleotide probe for hybridization analysis is provided, which probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with. Arrays comprising the hairpin probes immobilized on a solid support and methods for nucleic acid hybridization analysis using the probes or array of immobilized probes are also provided. Methods for transcribing and/or amplifying a probe DNA sequence using a hairpin probe are further provided.

Abstract: This invention relates generally to nucleic acid hybridization analysis. More specifically, oligonucleotide probes containing hairpin structures, or arrays of such oligonucleotide probes immobilized on a solid support, that are suitable for hybridization analysis are provided. Methods for nucleic acid hybridization analysis using the probes or array of immobilized probes are also provided.

Abstract: This invention relates generally to nucleic acid hybridization analysis. More specifically, an oligonucleotide probe for hybridization analysis is provided, which probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with. Arrays comprising the hairpin probes immobilized on a solid support and methods for nucleic acid hybridization analysis using the probes or array of immobilized probes are also provided. Methods for transcribing and/or amplifying a probe DNA sequence using a hairpin probe are further provided.

Abstract: This invention relates generally to nucleic acid hybridization analysis. More specifically, a method for detecting a point mutation in a DNA strand is provided, which method uses, inter alia, a test nucleic acid strand complementary to a target DNA strand, said nucleic acid strand comprises a sufficient number of ribonucleotide residues that span the position of said point mutation to be detected to form a target DNA strand/test nucleic acid strand duplex and RNase H cleavage of said target DNA strand/test nucleic acid strand duplex. Kits and arrays for detecting a point mutation in a DNA strand comprising test nucleic acid strand comprising a sufficient number of ribonucleotide residues that span the position of said point mutation to be detected are also provided.

Abstract: Methods for amplifying target nucleic acid sequences using a nucleic acid polymerase lacking 5? exonuclease activity and a set of oligonucleotide primers. Preferably, a primer array is used. The primer array contains two sets of primers. One set contains at least two complementary primers. The other set contains at least two sense primers. Using the described methods amplification can be carried out under essentially constant environmental conditions without the requirement for exonuclease activity or restriction endonuclease activity.

Abstract: Methods for amplifying target nucleic acid sequences using a nucleic acid polymerase lacking 5? exonuclease activity and a set of oligonucleotide primers. Preferably, a primer array is used. The primer array contains two sets of primers. One set contains at least two complementary primers. The other set contains at least two sense primers. Using the described methods amplification can be carried out under essentially constant environmental conditions without the requirement for exonuclease activity or restriction endonu- clease activity.