Sequence-dependent conformations of DNA duplexes: the TATA segment of the d(G-G-T-A-T-A-C-C) duplex in aqueous solution.

Abstract

AbstractThe base and sugar protons of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex have been assigned from two‐dimensional correlated (COSY) and nuclear Overhauser effect (NOESY) measurements in D2O solution at 25°C. The nucleic acid protons have been assigned from NOEs between protons on adjacent bases on the same and partner strands, as well as from NOEs between the base protons and their own and 5′‐flanking H1′, H2′, H2″, H3′, and H4′ sugar protons. These assignments are confirmed from coupling constant and NOE connectivities within the sugar protons of a given residue. Several of these NOEs exhibit directionality and demonstrate that the d(G‐G‐T‐A‐T‐A‐C‐C) duplex is a right‐handed helix. The relative magnitude of the NOEs between the base protons and the sugar H2′ protons of its own and 5′‐flanking sugar demonstrate that the TATA segment of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex adopts a B‐DNA type helix geometry in solution, in contrast to the previous observation of a A‐type helix for the same octanucleotide duplex in the crystalline state.