Abstract: The identity of a nucleotide of interest in a target nucleic acid molecule is determined by combining the target with two primers, where the first primer hybridizes to and extends from a location 3′ of the nucleotide of interest in the target, so as to incorporate the complement of the nucleotide of interest in a first extension product. The second primer then hybridizes to and extends based on the first extension product, at a location 3′ of the complement of the nucleotide of interest, so as to incorporate the nucleotide of interest in a second extension product. The first primer then hybridizes to and extends from a location 3′ of the nucleotide of interest in the second extension product, so as to form, in combination with the second extension product, a nucleic acid fragment. The first and second primers are designed to incorporate a portion of the recognition sequence of a restriction endonuclease that recognizes a partially variable interrupted base sequence. i.e.

Abstract: The invention provides a method for identifying a nucleotide at a defined position in a target nucleic acid using restriction endonucleases and fluorescence polarization. The invention further provides compounds, compositions, and kits related to the method.

Abstract: The identity of a nucleotide of interest in a target nucleic acid molecule is determined by combining the target with two primers. The first primer is immobilized to a substrate and hybridizes to and extends from a location 3′ of the nucleotide of interest in the target, so as to incorporate the complement of the nucleotide of interest in a first extension product. The second primer then hybridizes to and extends based on the first extension product, which is immobilized to the substrate via the first primer, at a location 3′ of the complement of the nucleotide of interest, so as to incorporate the nucleotide of interest in a second extension product. The second extension product then dissociates from the first extension product and thus from the substrate and re-hybridizes to another first primer molecule that has not extended.

Abstract: Compositions and methods are provided for increasing the specificity of a probe nucleic acid for a target nucleic acid in a hybridization solution. An abasic residue, deoxyNebularine residue, or a hybotrope is used to increase specificity. A method is provided for identifying useful hybotropes, including salts, water miscible organic solvents, aprotic solvents and organic solvents, on the basis of enthalpy considerations. Hybotropic hybridization and modified oligonucleotides may be used in amplification reactions, such as PCR, sequence analysis methods, and genomic screening methods.