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Science 20 September 1991:
Vol. 253. no. 5026, pp. 1408 - 1411
DOI: 10.1126/science.1716784
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Articles

Science, Vol 253, Issue 5026, 1408-1411
Copyright © 1991 by American Association for the Advancement of Science

articles

A combinatorial approach toward DNA recognition

DH Pei, HD Ulrich, and PG Schultz

Department of Chemistry, University of California, Berkeley 94720.

A combinatorial approach has been used to identify individual RNA molecules from a large population of sequences that bind a 16-base pair homopurine-homopyrimidine DNA sequence through triple-helix formation. Fourteen of the seventeen clones selected contained stretches of pyrimidines highly homologous to the target DNA sequence (T.AT and C+.GC). In addition, these RNA molecules contained hairpin loops, interior loops, and nonstandard base triplets [C+(or C).AT, U.GC, G.GC, and A.AT] at various positions. Affinity cleavage experiments confirmed the ability of selected sequences to bind specifically to the target DNA. Systematic variation in both the target DNA sequence and buffer components should provide increased insight into the molecular interactions required for triple-helix-mediated recognition of natural DNA.


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