Abstract: The present invention relates, in part, to control nucleic acid molecules having no significant sequence homology to any known nucleic acid, and predefined G/C-content. The present invention further relates to method of using control nucleic acid molecules to validate microarray analyses, compositions comprising control nucleic acid molecules, and kits comprising control nucleic acid molecules.

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 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 sequence in a sample, comprising forming a complex by incubating a sample comprising a target nucleic acid sequence with a probe comprising a first and second subunit, and/or an upstream primer, and binding the probe to the target nucleic acid such that the first and second subunits dissociate to release the first subunit and generate a signal. In certain embodiments, the upstream primer is extended with a nucleic acid polymerase to displace at least a portion of the first subunit of the probe from the target nucleic acid strand and dissociate the first and second subunits to release the first subunit of the probe and generate a signal.

Abstract: The invention relates to compositions and methods for detection of specific nucleic acid sequences during an amplification reaction. The invention further relates to a kit format of said compositions for detection of nucleic acid sequences. The Snapback oligonucleotide probes of the invention comprise a target binding sequence, a hairpin forming sequence, and a reporter binding sequence. The action of a nucleic acid polymerase or a flap endonuclease cleaves off a “snapback segment” of the probe containing the hairpin forming sequence and reporter binding sequence, causing the probe to “snap back” and form a hairpin structure. The further action of a nucleic acid polymerase or a flap endonuclease cleaves off a label moiety from a reporter oligonucleotide hybridized to the reporter binding sequence, resulting in a detectable signal.

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 provides oligonucleotide primers, compositions, methods, and kits for determining the amount of gDNA or the number of cells from which a cell lysate originated. The invention relies on detection and amplification of unique genomic sequences within the genome of an organism of interest to determine the amount of genomic nucleic acid in a sample. The invention can be used to normalize samples from particular cells, cell types, or organism, and provide an accurate basis for comparison of expression of genes across the samples.

Abstract: The invention relates to compositions and methods for detection of nucleic acid sequences. The invention further relates to kit format of said compositions for detection of nucleic acid sequences. Oligonucleotide probes of the invention comprise a target binding sequence and a sequence at least partially complementary thereto, joined by an optional linker to form a hairpin structure in the absence of the target nucleic acid sequence. The probes of the invention comprise a pair of moieties that produce a detectable signal when the probe hybridizes to the target sequence.

Abstract: The present invention provides oligonucleotide primers, compositions, methods, and kits for determining the number of cells from which a cell lysate originated. The invention relies on detection and amplification of unique genomic sequences within the genome of an organism of interest to determine the amount of genomic nucleic acid in a sample. The invention can be used to normalize samples from particular cells, cell types, or organism, and provide an accurate basis for comparison of expression of genes across the samples.

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 invention relates to a method of generating a signal indicative of the presence of a target nucleic acid in a sample, as well as a method of detecting or measuring a target nucleic acid in a sample. The invention comprises 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 provides methods, nucleic acids, compositions, and kits for detecting microRNA (miRNA) in samples. The methods comprise ligating two oligonucleotides together in an miRNA mediated fashion, and detection of the ligation product. The methods can further comprise amplification of the ligation product, such as by PCR. The nucleic acids, compositions, and kits typically comprise some or all of the components necessary to practice the method of the invention.

Abstract: The invention provides methods of covalently joining nucleic acid molecules and methods of molecular cloning. The methods provide either sequential or simultaneous ligation of flanking or vector nucleic acid molecules to nucleic acid insert molecules by topoisomerase and DNA ligase. The methods provide for directional and non-directional covalent joining and cloning of nucleic acid molecules.

Abstract: The present invention provides composition and methods for the detection and measurement of target nucleic acids. The probes of the present invention, or triplex probes, comprise a complex of three oligonucleotide probes including: (1) a first oligonucleotide probe, (2) a second oligonucleotide probe, and (3) a bridging oligonucleotide probe. In most aspects of the invention, the first and second oligonucleotide probes preferentially hybridize to the bridging oligonucleotide in the absence of a target nucleic acid. The first oligonucleotide probe contains one member of an interactive pair of labels and the second oligonucleotide probe contains the other member of the interactive pair of labels. Separation of the first and second oligonucleotide probes (e.g., binding to target, cleavage of first, second, or bridging oligonucleotide) generates a detectable signal indicating the presence of a target nucleic acid.

Abstract: The invention provides cells and methods of circularizing linear DNA molecules. The cell is an isolated Escherichia coli cell which transiently expresses the Cre recombinase protein from an integrated Cre recombinase gene, and which is at least transiently repressed for RecBCD activity. The cells are used in a method of circularizing a linear DNA molecule comprising at least two loxP sites. The DNA molecule is introduced into the cells, and the linear DNA molecule is joined at said loxp sites.

Abstract: The invention relates to nucleic acid, flap-mediated, sequential amplification methods which permit detection of a nucleic acid target in a nucleic acid sample. The invention provides for nucleic acid synthesis dependent, flap-mediated amplification methods for sequentially producing detectable, released flaps to detect a target nucleic acid. The invention provides for both linear, and exponential nucleic acid synthesis dependent, flap-mediated, sequential amplification methods.

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 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 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.