Thermodynamics and kinetics of antisense oligonucleotide hybridization to a structured mRNA target

Antisense oligonucleotides have the potential to selectively inhibit the expression of any gene with a known sequence. Antisense-based therapies are under development for the treatment of infectious diseases as well as complex genetic disorders. Although there have been some remarkable successes, realizing this potential is proving difficult because of problems with oligonucleotide stability, specificity, affinity, and delivery. Each of these limitations has been addressed experimentally through the use of chemically-modified oligonucleotides and oligonucleotide conjugates, with much success in enhancing oligonucleotide efficacy. These early studies have shown that selection of target site, once considered a trivial problem, is critical to the success of antisense strategies. It has become clear that the efficacy of antisense oligonucleotides is a strong function of the structure of the target mRNA. Though single-stranded, RNA molecules are typically folded into complex three-dimensional structures, formed primarily by intramolecular Watson-Crick base-pairing. If an oligonucleotide is complementary to a sequence embedded in the three dimensional structure, the oligonucleotide may not be able to bind to its target site and exert its therapeutic effect. Because the majority of the structure of RNA molecules is due to Watson-Crick base-pairing, relatively accurate predictions of these folding interactions can be made from algorithms that locate the structure with the most favorable free energy of folding.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Chemical Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2002

Author dc:creator

• Walton, S. Patrick (Stephen Patrick), 1973-

Advisor dc:contributor.advisor

• Martin Y. Yarmush and Gregory N. Stephanopoulos.

• Chemical Engineering.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/43615

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/43615