Sequence-dependent recognition of DNA duplexes: Netropsin complexation to the TATA site of the d(G-G-T-A-T-A-C-C) duplex in aqueous solution

✍ Scribed by Dinshaw J. Patel; Lawrence Shapiro

• Publisher: Wiley (John Wiley & Sons)
• Year: 1986
• Tongue: English
• Weight: 1013 KB
• Volume: 25
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360250413

✦ Synopsis

We have recorded one-dimensional exchangeable proton and two-dimensional nonexchangeable proton nmr spectra on the complex of netropsin with the selfcomplementary d(G-G-T-A-T-A-C-C) duplex in aqueous solution between 25" and 35°C. The antibiotic amide, pyrrole, and methylene protons, and the nucleic acid base and sugar Hl', H2, H2", and H 3 protons, have been assigned from an analysis of the two-dimensional nuclear Overhauser effect (NOESY) spectra of the complex. We observe intermolecular NOES between the antibiotic concave face amide, pyrrole, and CH, resonances, and the adenosine H2 and sugar H1' protons of base-pairs T%A6 and A4T5 in the central TATA core of the d(G,-G2-T3-A4-T6-As-C7C,) duplex. We present a molecular model outlining these seven antibiotic-DNA contacts for the complex in solution. The observed linebroadening of several base and sugar protons at the TATA minor groove netropsin binding site in the complex at 35°C are interpreted in terms of intermediate exchange between two orientations of bound netropsin on the duplex.