Patent ID: 6994998

Claim:
A method for detecting a polymorphism in a polynucleotide, comprising: providing a target polynucleotide; replacing a natural nucleotide at greater than 90% of its points of occurrence in the target polynucleotide, provided the points of occurrence are not in a primer sequence, by amplification or primer extension using a base-modified nucleotide and three natural nucleotides to give a modified target polynucleotide; contacting the modified target polynucleotide with a reagent or combination of reagents that cleaves it at greater than 90% of the base-modified nucleotides to give a set of fragments; and, analyzing the fragments to detect a polymorphism, wherein the base-modified nucleotide comprises the following structure: wherein: R is a ribose or a deoxyribose moiety of a polynucleotide; R 1 and R 2 are independently selected from the group consisting of hydrogen, alkyl, cycloalkyl, alkenyl, alkynyl, aryl, aralkyl and alkaryl, wherein, if R 1 or R 2 contains two or more contiguous methylene (—CH 2 —) groups, any two such methylene groups may have interjected between them a group selected from the group consisting of —O—, —C(O)NH—, —C(O)NHC(O)—, —NH—, —C(S)NH—, —CO—, —CS—, —S— and (—CF 2 —) m , wherein m is 1–10; R 3 is hydrogen or —N H 2 ; and, n is 0, 1 or 2.