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 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 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 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 features a novel isolated Family B DNA polymerase, a Thermococcus polymerase JDF-3, and mutant recombinant forms thereof. Mutant polymerases of the invention are deficient in 3? to 5? exonuclease activity and/or exhibit reduced discrimination against non-conventional nucleotides relative to the wild-type form of the polymerase.

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 features a novel isolated Family B DNA polymerase, a Thermococcus polymerase JDF-3, and mutant recombinant forms thereof. Mutant polymerases of the invention are deficient in 3? to 5? exonuclease activity and/or exhibit reduced discrimination against non-conventional nucleotides relative to the wild-type form of the polymerase.

Abstract: The invention relates to a method of detecting a target nucleic acid by linear amplification. The invention also relates to a method of detecting a target nucleic acid by amplification.

Abstract: The present invention provides a method of preparing a nucleic acid sample comprising template nucleic acid and synthetic nucleic acid for analysis wherein prior to analysis the nucleic acid sample is treated with a substance which selectively cleaves the template nucleic acid without substantially cleaving the synthetic nucleic acid. The invention further provides a method for improving the analysis of capillary-based DNA sequencing reactions, amplification reactions, and/or transcription reactions, wherein after the reaction, the nucleic acid sample comprising template nucleic acid and synthetic nucleic acid is treated with a substance which selectively cleaves the template without substantially cleaving the synthetic nucleic acid.

Abstract: The present invention relates to composition, kits and methods comprising a mutant DNA polymerase exhibiting increased reverse transcriptase activity. The invention also relates to methods of generating modified cDNA.

Abstract: The present invention relates to a method for identifying a nucleotide at a predetermined location on a target polynucleotide. The method involves single nucleotide extension reaction comprising an oligonucleotide primer comprising a first sequence and a second sequence or a tag. The method may further comprises a probe which hybridizes to the second sequence or an anti-tag molecule which interacts with the tag, where the hybridization or interaction causes a detectable signal transfer which is indicative of the identity of the nucleotide base at the predetermined location. The invention further provides compositions and kits for performing the subject method of the invention.

Abstract: The invention relates to a method of detecting a target nucleic acid by linear amplification. The invention also relates to a method of detecting a target nucleic acid by amplification. The method of the invention includes the steps of forming at least a first cleavage structure comprising at least one flap, cleaving the cleavage structure with a cleavage means to release the at least one flap and detecting the at least one flap. In one embodiment of the invention, the method includes the additional steps of forming at least a second cleavage structure comprising the at least one released flap from the first cleavage structure cleaving the second cleavage structure with a cleavage means to release at least one flap from the second cleavage structure and detecting released flaps from the first or second cleavage structure.

Abstract: The present invention provides a polynucleotide encoding a green fluorescent protein from Renilla mulleri comprising a humanized sequence which permits enhanced expression of the encoded polypeptide in mammalian cells.

Abstract: The invention relates to the generation and characterization of Archaeal DNA polymerase mutants with deficient 3?-5? exonuclease activity and reduced base analog detection activity. The invention further provides for Archaeal DNA polymerase mutants with deficient 3?-5? exonuclease activity and reduced base analog detection activity containing additional mutations that modulate other DNA polymerase activities including DNA polymerization or reverse transcriptase activity. The invention also discloses methods and applications of DNA polymerases with deficient 3?-5? exonuclease activity and reduced base analog detection activity.

Abstract: The present invention relates to compositions comprising probes for the detection of a target polynucleotide, and methods for detecting the amount of a target polynucleotide using the subject composition. In particular, the subject method involves the use of both target-hybridizing probes and non-target-hybridizing probes, where the probes generate a detectable signal (e.g., detectable by FRET) for the target polynucleotide detection.

Abstract: The invention relates to recombinant polynucleotides encoding the Green Fluorescent Protein (GFP) from R. reniformis, as well as polynucleotides encoding variants and fusion polypeptides of R. reniformis GFP. The invention further relates to vectors encoding R. Reniformis GFP and variants and fusions thereof, as well as to cells comprising and/or expressing such vectors. The invention also relates to recombinant R. reniformis GFP polypeptides and fusion polypeptides and variants thereof, as well as to methods of making and using such polypeptides both in vivo and in vitro.

Abstract: The present invention relates to a method for identifying a nucleotide at a predetermined location on a target polynucleotide. The method involves single nucleotide extension reaction comprising an oligonucleotide primer comprising a first sequence and a second sequence or a tag. The method may further comprises a probe which hybridizes to the second sequence or an anti-tag molecule which interacts with the tag, where the hybridization or interaction causes a detectable signal transfer which is indicative of the identity of the nucleotide base at the predetermined location. The invention further provides compositions and kits for performing the subject method of the invention.

Abstract: The present invention provides compositions, kits, and methods for detecting polynucleotide sequence differences. The method involves amplifying a polynucleotide in the presence of a labeled nucleotide whose incorporation into the amplified product can indicate the presence of a sequence difference within the polynucleotide template. The invention is particularly useful for differentiating two or more closely related polynucleotide sequences, for example, in determining which allele or alleles of a multiallelic organism are present in a target polynucleotide.