Abstract: This invention discloses multi-part primers for primer-dependent nucleic acid amplification methods. Also disclosed are multiplex assay methods, related reagent kits, and oligonucleotides for such methods.

Abstract: This invention discloses multi-part primers for primer-dependent nucleic acid amplification methods. Also disclosed are multiplex assay methods, related reagent kits, and oligonucleotides for such methods.

Abstract: A method of sorting mixtures of nucleic acid strands comprising hybridizing the strands to an array of immobilized oligonucleotides, each of which includes a constant segment adjacent to a variable segment. The constant segment of the immobilized oligonucleotides can be made complementary to the ends of strands obtained by digesting a double-stranded nucleic acid with a restriction enzyme and restoring the restriction sites, thereby permitting the sorting of strands according to their variable sequences adjacent to their constant terminal restored restriction sites.

Abstract: A method of sorting mixtures of nucleic acid strands comprising hybridizing the strands to an array of immobilized oligonucleotides, each of which includes a constant segment adjacent to a variable segment. The constant segment of the immobilized oligonucleotides can be made complementary to the ends of strands obtained by digesting a double-stranded nucleic acid with a restriction enzyme and restoring the restriction sites, thereby permitting the sorting of strands according to their variable sequences adjacent to their constant terminal restored restriction sites.

Abstract: A method of sorting mixtures of nucleic acid strands comprising hybridizing the strands to an array of immobilized oligonucleotides, each of which includes a constant segment adjacent to a variable segment. The constant segment of the immobilized oligonucleotides can be made complementary to the ends of strands obtained by digesting a double-stranded nucleic acid with a restriction enzyme and restoring the restriction sites, thereby permitting the sorting of strands according to their variable sequences adjacent to their constant terminal restored restriction sites.

Abstract: The present invention provides a replicatable and hybridizable recombinant single-stranded RNA probe molecule comprising: a recognition sequence for the binding of an RNA-directed RNA polymerase; a sequence required for the initiation of product strand synthesis by the polymerase; and a heteroloqus RNA sequence inserted at a specific site in the internal region of the recombinant molecule and complementary to an oligo or polynucleotide of interest. This invention also provides methods for determining the presence of concentration of an oligo- or polynucleotide of interest in a sample and for simultaneously determining the presence or concentration of several different oligo- or polynucleotides of interest in a sample.

Abstract: Ligation methods for manipulating nucleic acid stands and oligonucleotides utilizing hybridization arrays of immobilized oligonucleotides. The oligonucleotide arrays may be plain or sectioned, comprehensive or non-comprehensive. The immobilized oligonucleotides may in some cases be binary oligonucleotides having constant as well as variable segments. Some embodiments include amplification of ligated products.

Abstract: Nucleic acid hybridization probes having a first conformation when not interacting with a target and a second conformation when interacting with a target, and having the ability to bring a label pair into touching contact in one conformation but not the other, are labeled with a non-FRET pair of chromophores and generate a fluorescent or absorbance signal. Kits may include such probes, and assays, including multiplex assays, may utilize such probes.

Abstract: A method of sorting mixtures of nucleic acid strands comprising hybridizing the strands to an array of immobilized oligonucleotides, each of which includes a constant segment adjacent to a variable segment. The constant segment of the immobilized oligonucleotides can be made complementary to the ends of strands obtained by digesting a double-stranded nucleic acid with a restriction enzyme and restoring the restriction sites, thereby permitting the sorting of strands according to their variable sequences adjacent to their constant terminal restored restriction sites.

Abstract: This invention provides a method for producing a mutant virus or viroid, or a mutant recombinant RNA molecule comprising a single stranded virus genome or a single stranded viroid genome, a circular virus genome or a circular viroid genome, or a segment of a virus genome or a segment of a viroid genome which comprises incubating a recombinant single-stranded RNA molecule comprising a recognition sequence for the binding of an RNA directed RNA polymerase, a sequence for the initiation of product strand synthesis by the polymerase and a heterologous sequence of interest derived from a different RNA molecule inserted at a specific site in the internal region of the recombinant molecule under appropriate selective conditions and for a sufficient period of time permitting the selection of a mutant population, the heterologous sequence of interest comprising the RNA of the single stranded virus genome or the single stranded viroid genome, the circular virus genome or the circular viroid genome or a segment of the v