Patent ID: 7715989

Claim:
A method of predicting the melting temperature (T m ) of an oligonucleotide sequence, comprising: inputting into a computer system data representing a sequence of N bases of an identified oligonucleotide having N-1 neighboring base pairs; calculating in the computer system a (T m ) of the identified oligonucleotide sequence using the nearest neighbor thermodynamic parameters for each of the N-1 neighboring base pairs in the identified sequence, wherein said identified sequence includes at least one modified base selected from the group consisting of unsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines, each nearest neighbor thermodynamic parameter defining a thermodynamic contribution of two corresponding neighboring bases; and providing an output to a display or a user using the processing module, wherein said output represents a T m of the identified oligonucleotide sequence.