Patent ID: 7751982

Claim:
A method for designing a preferred oligonucleotide sequence having a selected duplex stability comprising: a) providing an oligonucleotide sequence having N bases and N−1 neighboring base pairs, b) modifying the oligonucleotide sequence to provide modified oligonucleotide sequences wherein said modified oligonucleotide sequences comprise at least one modified base selected from the group consisting of unsubstituted pyrazolo[3,4-d]pyrimidines, 3-substituted pyrazolo[3,4-d]pyrimidines, and 5-substituted pyrimidines; c) calculating the duplex stabilities of said modified oligonucleotide sequences using an algorithm applying a nearest-neighbor model for duplex formation thermodynamics for each of the N−1 neighboring base pairs, each nearest neighbor thermodynamic parameter defining a thermodynamic contribution of two corresponding neighboring bases; d) selecting a preferred oligonucleotide sequence from the modified oligonucleotide sequences having a selected duplex stability; and e) creating an oligonucleotide comprising the preferred oligonucleotide sequence.