Recognition of duplex DNA by RNA polynucleotides

Claudia D. Mcdonald, L. James Maher

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


We are interested in creating artificial gene repressors based on duplex DNA recognition by nucleic acids. Homopyrimidine RNA oligonucleotides bind to duplex DNA at homopurine/homopyrimidine sequences under slightly acidic conditions. Recognition is sequence-specific, involving rU·dA·dT and rC+·dG·dC base triplets. Affinities were determined for folded polymeric RNAs (ca. 100-200 nt) containing 0, 1 or 3 copies of a 21 nt RNA sequence that binds duplex DNA by triple helix formation. When this recognition sequence was inserted into the larger folded RNAS, micromolar concentrations of the resulting RNA ligands bound a duplex DNA target at pH 5. However, these binding affinities were at least 20-told lower than the affinity of an RNA oligonucleotide containing only the recognition sequence. Enzymatic probing of folded RNAs suggests that reduced affinity arises from unfavorable electrostatic, structural and topological considerations. The affinity of a polymeric RNA with three copies of the recognition sequence was greater than that of a polymeric RNA wfth a single copy of the sequence. This affinity difference ranged from 2.6- to 13-fold, depending on pH. BindIng of duplex DNA by polymeric RNA might be improved by optimizing the RNA structure to efficiently present the recognition sequence.

Original languageEnglish (US)
Pages (from-to)500-506
Number of pages7
JournalNucleic acids research
Issue number3
StatePublished - Feb 11 1995

ASJC Scopus subject areas

  • Genetics


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