Computational identification of antisense oligonucleotides that rapidly hybridize to RNA

Jian Ying Wang, Karl Drlica

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


The ability of a computational model to determine the relative rate of hybridization between antisense oligonucleotides and RNA was tested using HIV-1 tat mRNA. The model, which was based on the assumptions that hybridization is a second-order reaction and that early in the hybridization reaction the concentrations of intermediates are approximately constant (steady-state), allows calculation of a rate factor that is proportional to the reaction constant. Formation of oligodeoxynucleotide (ODN)-RNA hybrid, detected by RNase H-dependent cleavage, increased nearly linearly during an initial incubation period, consistent with the steady-state approximation. The initial hybridization rate increased linearly with substrate RNA concentration and with ODN concentration, indicating a second-order reaction. The logarithm of the second-order reaction constant, determined from the initial rate for hybridization between tat mRNA and 16 ODNs targeted to various sites, was linearly related to the logarithm of the calculated rate factor (r = 0.83, p < 0.001). Thus, the rate factor can be used to identify rapidly hybridizing antisense sequences using target nucleotide sequence information.

Original languageEnglish (US)
Pages (from-to)167-175
Number of pages9
Issue number3
StatePublished - 2004

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Molecular Biology
  • Genetics

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