Pyrimidine oligonucleotides exhibit sequence-specific binding to purine sequences in double-helical DNA. Molecular recognition occurs through triple-helix formation, mediated by Hoogsteen hydrogen bonding of the pyrimidine strand parallel to the double-helical DNA purine strand. Oligonucleotide-directed DNA triple-helix formation has been shown to inhibit the recognition of double-helical DNA by sequence-specific binding proteins. This observation provides the potential for new approaches to both the analysis of nucleic acids, and the study of nucleic acid–protein interactions. We wish to understand molecular mechanisms whereby such complexes affect protein–DNA interactions involved in eukaryotic transcription.
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