Abstract: The invention relates to a method of generating a signal indicative of the presence of a target nucleic acid sequence in a sample, where the method includes forming a cleavage structure by incubating a sample containing a target nucleic acid sequence with a nucleic acid polymerase and cleaving the cleavage structure with a nuclease to generate a cleaved nucleic acid fragment. The invention also relates to methods of detecting or measuring a target nucleic acid sequence, where the method includes forming a cleavage structure by incubating a target nucleic acid sequence with a nucleic acid polymerase, cleaving the cleavage structure with a nuclease and detecting or measuring the release of a fragment.

Abstract: The invention relates to generating a signal indicative of a target nucleic acid sequence, comprising forming a complex by incubating a sample comprising a target nucleic acid sequence with a probe comprising a first and second subunit, and a binding moiety, and dissociating the first and second subunit to release the first subunit and generate a signal. The invention also relates to a method of generating a signal indicative of the presence of a target nucleic acid sequence in a sample, comprising forming a complex by incubating a target nucleic acid sequence, an upstream primer and a probe comprising a first and second subunit, and a binding moiety. The primer is extended with a nucleic acid polymerase to displace a portion of the first subunit from the target nucleic acid strand thereby dissociating the first subunit from the second subunit to release the first subunit and generate a signal.

Abstract: The present invention relates to probes useful for the detection and measurement of target nucleic acids, as well as compositions and kits containing such probes. The probes of the present invention include an interactive pair of labels, as well as a hairpin sequence that does not hybridize to a target nucleic acid. According to the present invention, the probe generates a detectable signal indicative of a presence of a target nucleic acid. The detectable signal emitted by one of the pair of labels is substantially constant upon binding of the probe to target nucleic acid, and the detectable signal increases by at least 2 fold upon cleavage of the probe between the pair of labels.

Abstract: The invention relates to a method of generating a signal indicative of the presence of a target nucleic acid in a sample, where the method includes forming a cleavage structure by incubating a sample comprising a target nucleic acid with a probe having a secondary structure that changes upon binding of the probe to the target nucleic acid and further comprising a binding moiety. The invention also includes the steps of cleaving the cleavage structure with a nuclease to release a nucleic acid fragment to generate a signal, wherein generation of the signal is indicative of the presence of a target nucleic acid in a sample, and detecting and/or measuring the amount of the fragment captured by binding of a binding moiety to a capture element on a solid support.

Abstract: The invention is related to a labeled oligonucleotide pair for detecting a target nucleic acid and methods, kits and compositions containing the labeled oligonucleotide pair. The labeled oligonucleotide pair forms a complex comprising a nucleic acid primer and a nucleic acid probe.

Abstract: The present invention is directed to methods of generating a signal indicative of the presence of said target nucleic acid sequence in a sample, comprising, incubating a sample comprising a an amplified target nucleic acid and a nucleic acid polymerase which substantially lacks 5? to 3? exonuclease activity, adding a thermostable fen nuclease consisting of 5? to 3? exonuclease and/or endonuclease activity so as to cleave a cleavage structure and generate a signal.

Abstract: The present invention provides methods, kits and compositions for the detection of an analyte. The invention is particularly suited for the detection and quantification of analytes in solution. In the methods of the invention a complex is formed between two or more analyte specific probes (ASP) and an analyte. The reactive moieties of the probes interact upon the binding of the analyte specific probes to the analyte. The reactive moieties generate a nucleic acid cleavage product which is detected and indicative of the presence of the analyte.

Abstract: The invention relates to compositions and methods for generating a signal indicative of the presence of a target nucleic acid in a sample utilizing a primer-probe duplex.

Abstract: The present invention provides methods, products, and kits for detection of target nucleic acids. Detection is based, at least in part, on detection of chromophores that have different chromogenic properties depending on their association with double-stranded nucleic acids. In general, labeled reagents are exposed to denatured nucleic acids, and the nucleic acids are permitted to renature. Incorporation of the chromogenic labels into the renaturing nucleic acids produces a detectable signal, which can be correlated to the presence and amount of target nucleic acid in the sample. The method is particularly suitable for detection of in vitro amplification products.

Abstract: The invention provides compositions, kits and methods of generating a signal indicative of the presence of a target nucleic acid sequence in a sample by forming a cleavage structure. The cleavage structure is formed by incubating a sample containing a target nucleic acid with a downstream probe that forms a 3? flap when hybridized to the target. The cleavage structure is cleaved with a 3? nuclease and a detectable signal is produced.

Abstract: The invention relates to compositions and methods of generating a signal indicative of the presence of a target nucleic acid in a sample, where the method includes forming a cleavage structure by incubating a sample comprising a target nucleic acid with a probe. The invention also includes the steps of cleaving the cleavage structure with a nuclease to release a nucleic acid fragment to generate a signal, wherein generation of the signal is indicative of the presence of a target nucleic acid in a sample.

Abstract: The subject invention provides for a method of selectively cloning homoduplex nucleic acid molecules, in particular, by using a strain of host cells that contains a conditionally expressed and/or conditionally active mismatch-recognizing enzyme, e.g., a temperature sensitive variant of the gene encoding the endonuclease VII from phage T4. Using this host strain, the invention features a novel cloning method that selects for PCR products that are devoid of PCR-generated mutations.

Abstract: The invention relates to a method of generating a signal indicative of the presence of a target nucleic acid sequence in a sample, where the method includes forming a cleavage structure by incubating a sample containing a target nucleic acid sequence with a nucleic acid polymerase and cleaving the cleavage structure with a nuclease to generate a cleaved nucleic acid fragment. The invention also relates to methods of detecting or measuring a target nucleic acid sequence, where the method includes forming a cleavage structure by incubating a target nucleic acid sequence with a nucleic acid polymerase, cleaving the cleavage structure with a nuclease and detecting or measuring the release of a fragment.

Abstract: The present invention relates to a method for isolating from the immunological gene repertoire a gene coding for a receptor having the ability to bind a preselected ligand. Receptors produced by the gene isolated by the method, particularly catalytic receptors, are also contemplated.

Abstract: The subject invention provides novel compositions containing a mixture of (a) an enzyme that possesses substantial 3?–5? exonuclease activity (b) a DNA polymerase with less 3?–5? exonuclease activity than the enzyme with substantial 3?–5? exonuclease activity. Preferably, the DNA polymerase for inclusion in the compositions are DNA polymerases that substantially lack 3?–5? exonuclease activity. A preferred embodiment of the invention is a composition comprising the Taq DNA polymerase (isolated from Thermus aquaticus) and the Pfu DNA polymerase (isolated from Pyrococcus furiosus). Another aspect of the invention is to provide methods for synthesizing polynucleotides, typically DNA, using compositions comprising an enzyme that possesses substantial 3?–5? exonuclease activity and a DNA polymerase with less 3?–5? exonuclease activity than the enzymes possessing substantial 3?–5? exonuclease activity, preferably a DNA polymerase that substantially lacks 3?–5? exonuclease activity.

Abstract: The present invention is directed compositions having a Fen nuclease consisting of a 5? to 3? exonuclease and/or endonuclease activity and pyrophosphate.

Abstract: The present invention is directed to methods of generating a signal indicative of the presence of a target nucleic acid in a sample by forming a cleavage structure comprising duplex and single-stranded nucleic acid by incubating a sample comprising a target nucleic acid with a thermostable nucleic acid polymerase substantially lacking 5? to 3? exonuclease activity and cleaving said cleavage structure with a thermostable Fen nuclease lacking 5? to 3? synthetic activity to generate a signal.

Abstract: The present invention is directed compositions having a Fen nuclease consisting of a 5? to 3? exonuclease and/or endonuclease activity and one or more dNTPs.

Abstract: The invention relates to compositions and methods for generating a signal indicative of the presence of a target nucleic acid in a sample utilizing a cleavage resistant probe.

Abstract: The invention relates to methods and compositions for detecting a target nucleic acid. The methods include subjecting a target, template, cleavage agent, polymerase and first, second and third oligonucleotide to reaction conditions that permit: (1) formation of a duplex between the target and first oligonucleotide; (2) extension of the first oligonucleotide; (3) cleavage of a first cleavage structure; (4) formation of a second duplex with a released flap; (5) extension of the released flap and (6) cleavage of a second cleavage structure within the third oligonucleotide. A signal generated by the release of the third oligonucleotide produces a signal that is detected and indicative of the presence of the target in the sample.