Patent ID: 7313482

Claim:
A method for identifying at least one target site of an RNA molecule for attack with an antisense RNA nucleic acid, the method comprising: (a) for all short pairing regions in an RNA molecule, said short pairing regions having a selected length in the range of 11 to 20 nucleotides (i) calculating the melting energy (ΔGm) required to convert each of said short pairing regions of the RNA molecule to a single-stranded state; (ii) calculating the energy gain (ΔG d ) resulting from hybridization of each of said short pairing regions to an antisense RNA nucleic acid; and (iii) calculating rate factor x wherein x = 1 C ⁢ ⁢ ⅇ Δ ⁢ ⁢ G m / RT + ⅇ Δ ⁢ ⁢ G d / RT , wherein C is a proportionality constant, R is the universal gas constant and T is temperature; (b) identifying at least one region that has a maximal value of rate factor x; and (c) displaying the identified at least one region that has a maximal value of rate factor.