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. 1992 Aug 15;89(16):7586–7590. doi: 10.1073/pnas.89.16.7586

Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin.

M Mrksich 1, W S Wade 1, T J Dwyer 1, B H Geierstanger 1, D E Wemmer 1, P B Dervan 1
PMCID: PMC49755  PMID: 1323845

Abstract

The designed peptide 1-methylimidazole-2-carboxamide netropsin (2-ImN) binds specifically to the sequence 5'-TGACT-3'. Direct evidence from NMR spectroscopy is presented that this synthetic ligand binds DNA as a 2:1 complex, which reveals that the structure is an antiparallel dimer in the minor groove of DNA. This is in contrast to the 1:1 complexes usually seen with most crescent-shaped minor groove binding molecules targeted toward A+T-rich tracts but reminiscent of a dimeric motif found for distamycin at high concentrations. These results suggest that sequence-dependent groove width may play an important role in allowing an expanded set of DNA binding motifs for synthetic peptides.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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