Patent ID: 7200531

Claim:
A computer-based method of predicting biological activity of an oligonucleotide sequence comprising: drawing the oligonucleotide sequence using chemical drawing software; creating a three dimensional model of the drawn sequence; displaying a solvent accessible surface of the three dimensional model on a display means; identifying globular and linear domains in the three dimensional model; identifying phosphates in a globular domain which form a phosphate necklace; evaluating spatial orientation of bases in the three dimensional model for electropositive framing with respect to the phosphates in the globular domain; measuring a first interatomic distance X between a first phosphate and a last phosphate of the globular domain; measuring a second interatomic distance alpha between the first phosphate of the globular domain and an amido/amino group in the base attached to the first phosphate of the globular domain; measuring a third interatomic distance beta as the furthest interatomic distance between amido or amino groups in the globular domain; measuring a fourth interatomic distance Z as a distance between one side of the oligonucleotide sequence and an opposite side of the oligonucleotide sequence; and, measuring a fifth interatomic distance Y as a longest distance between the first phosphate of the globular domain and the farthest atom in the base attached to the first phosphate of the globular domain; and, predicting that the oligonucleotide sequence has biological activity if the oligonucleotide sequence contains at least one centrum.