Prediction of antisense oligonucleotide binding affinity and activity in cell culture

S. Patrick Walton, Arul Jayaraman, Gregory N. Stephanopoulos, Martin L. Yarmush, Charles M. Roth

Research output: ResearchConference contribution

Abstract

We have developed a method that uses RNA secondary structure prediction and an appropriate thermodynamic cycle to predict the free energy of hybridization between an antisense oligonucleotide and its target mRNA. We applied this method to determine, theoretically, the oligonucleotides which bind most strongly to the rabbit β-globin (RBG) mRNA, for which a large experimental data set is available. The model accurately predicts the trend in binding affinity and, more importantly, identifies the highest binding affinity sequences quite accurately (six out of the highest ten). Recent data indicate that the method also yields sequences that inhibit the production of the gp130 cytokine signaling protein in the H35 rat hepatoma cell line.

LanguageEnglish (US)
Title of host publicationAnnual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
PublisherIEEE
Pages96
Number of pages1
Volume1
ISBN (Print)0780356756
StatePublished - 1999
Externally publishedYes
EventProceedings of the 1999 IEEE Engineering in Medicine and Biology 21st Annual Conference and the 1999 Fall Meeting of the Biomedical Engineering Society (1st Joint BMES / EMBS) - Atlanta, GA, USA
Duration: Oct 13 1999Oct 16 1999

Other

OtherProceedings of the 1999 IEEE Engineering in Medicine and Biology 21st Annual Conference and the 1999 Fall Meeting of the Biomedical Engineering Society (1st Joint BMES / EMBS)
CityAtlanta, GA, USA
Period10/13/9910/16/99

Profile

Antisense Oligonucleotides
Cell culture
Messenger RNA
Oligonucleotides
beta-Globins
Free energy
Rats
Cells
Thermodynamics
RNA
Cytokines
Proteins

ASJC Scopus subject areas

  • Bioengineering

Cite this

Walton, S. P., Jayaraman, A., Stephanopoulos, G. N., Yarmush, M. L., & Roth, C. M. (1999). Prediction of antisense oligonucleotide binding affinity and activity in cell culture. In Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings (Vol. 1, pp. 96). IEEE.

Prediction of antisense oligonucleotide binding affinity and activity in cell culture. / Walton, S. Patrick; Jayaraman, Arul; Stephanopoulos, Gregory N.; Yarmush, Martin L.; Roth, Charles M.

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. Vol. 1 IEEE, 1999. p. 96.

Research output: ResearchConference contribution

Walton, SP, Jayaraman, A, Stephanopoulos, GN, Yarmush, ML & Roth, CM 1999, Prediction of antisense oligonucleotide binding affinity and activity in cell culture. in Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. vol. 1, IEEE, pp. 96, Proceedings of the 1999 IEEE Engineering in Medicine and Biology 21st Annual Conference and the 1999 Fall Meeting of the Biomedical Engineering Society (1st Joint BMES / EMBS), Atlanta, GA, USA, 10/13/99.
Walton SP, Jayaraman A, Stephanopoulos GN, Yarmush ML, Roth CM. Prediction of antisense oligonucleotide binding affinity and activity in cell culture. In Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. Vol. 1. IEEE. 1999. p. 96.
Walton, S. Patrick ; Jayaraman, Arul ; Stephanopoulos, Gregory N. ; Yarmush, Martin L. ; Roth, Charles M./ Prediction of antisense oligonucleotide binding affinity and activity in cell culture. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. Vol. 1 IEEE, 1999. pp. 96
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