Characterization of molecular and cellular events limiting the effectiveness of antisense oligonucleotides

S. P. Walton, A. Jayaraman, M. L. Yarmush, C. M. Roth

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

Abstract

Antisense oligonucleotides (AS ONs) are a powerful means to inhibit the expression of specific genes, but their effectiveness is limited by factors including cellular delivery, biochemical attack, and poor binding to target. We are developing rational approaches to improve effectiveness through high affinity binding. We developed a molecular thermodynamic model based on ON and mRNA folding that predicts accurately the affinity of ON-mRNA binding, and we have found that it successfully selects those ONs that are most successful in cell culture. We have experimentally measured both thermodynamic and kinetic binding events in solution and found strong correlation between association kinetics and binding affinity. Binding association rates as a function of temperature have provided evidence for our hypothesis that RNA restructuring is the limiting step in ON binding. We are currently integrating these results with additional measurements on delivery and ribonuclease H cleavage of RNA in DNA-RNA duplexes to form a whole cell model that can serve as the basis for optimization of ON chemistry, dosing and timing. Taken together, these tools may help accelerate the development of this promising technology.

Original languageEnglish (US)
Title of host publicationAnnual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
Pages610-611
Number of pages2
Volume1
StatePublished - 2002
Externally publishedYes
EventProceedings of the 2002 IEEE Engineering in Medicine and Biology 24th Annual Conference and the 2002 Fall Meeting of the Biomedical Engineering Society (BMES / EMBS) - Houston, TX, United States

Other

OtherProceedings of the 2002 IEEE Engineering in Medicine and Biology 24th Annual Conference and the 2002 Fall Meeting of the Biomedical Engineering Society (BMES / EMBS)
CountryUnited States
CityHouston, TX
Period10/23/0210/26/02

Profile

RNA
Hexosaminidase A
Anthralin
Alkynes
Kinetics
Oligonucleotides
Association reactions
Thermodynamics
Acyclic Acids
Acetanilides
Buccal Administration
Bile Pigments
Cyclic AMP Receptor Protein
Cell culture
Basement Membrane
DNA
Genes
Temperature

Keywords

  • Hybridization
  • Real-time PCR
  • RNA folding

ASJC Scopus subject areas

  • Bioengineering

Cite this

Walton, S. P., Jayaraman, A., Yarmush, M. L., & Roth, C. M. (2002). Characterization of molecular and cellular events limiting the effectiveness of antisense oligonucleotides. In Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings (Vol. 1, pp. 610-611)

Characterization of molecular and cellular events limiting the effectiveness of antisense oligonucleotides. / Walton, S. P.; Jayaraman, A.; Yarmush, M. L.; Roth, C. M.

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. Vol. 1 2002. p. 610-611.

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

Walton, SP, Jayaraman, A, Yarmush, ML & Roth, CM 2002, Characterization of molecular and cellular events limiting the effectiveness of antisense oligonucleotides. in Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. vol. 1, pp. 610-611, Proceedings of the 2002 IEEE Engineering in Medicine and Biology 24th Annual Conference and the 2002 Fall Meeting of the Biomedical Engineering Society (BMES / EMBS), Houston, TX, United States, 23-26 October.
Walton SP, Jayaraman A, Yarmush ML, Roth CM. Characterization of molecular and cellular events limiting the effectiveness of antisense oligonucleotides. In Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. Vol. 1. 2002. p. 610-611.

Walton, S. P.; Jayaraman, A.; Yarmush, M. L.; Roth, C. M. / Characterization of molecular and cellular events limiting the effectiveness of antisense oligonucleotides.

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. Vol. 1 2002. p. 610-611.

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

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