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Sequence-specific recognition of double helical RNA and RNA·DNA by triple helix formation

Han, Hogyu and Dervan, Peter B. (1993) Sequence-specific recognition of double helical RNA and RNA·DNA by triple helix formation. Proceedings of the National Academy of Sciences of the United States of America, 90 (9). pp. 3806-3810. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:HANpnas93

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Abstract

The stabilities of eight triple helical pyrimidine·purine·pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine·pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD, R + RR > > D + RR, D + RD (pH 7.0, 25-degrees-C, 100 mM NaCl/1 mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA·DNA hybrids.


Item Type:Article
Additional Information:Copyright © 1993 by the National Academy of Sciences. Contributed by Peter B. Dervan, January 26, 1993. We are grateful to the National Institutes of Health for grant support. We thank K. Breslauer and D. Crothers for helpful discussions. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.
Subject Keywords:DNA, cleavage
Record Number:CaltechAUTHORS:HANpnas93
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:HANpnas93
Alternative URL:http://www.pnas.org/cgi/content/abstract/90/9/3806
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:948
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:15 Nov 2005
Last Modified:26 Dec 2012 08:42

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