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: Chapter in Book/Report/Conference proceedingConference 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.

Original 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

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

Oligonucleotides
Hemerythrin
Anthralin
Staphylococcal Pneumonia
Alkynes
Castration
Cell culture
RNA
Free energy
Rats
Cells
Thermodynamics
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: Chapter in Book/Report/Conference proceedingConference 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, 13-16 October.
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. p. 96.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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