SOLUTION STRUCTURE OF AN INTRAMOLECULAR DNA TRIPLEX LINKED BY HEXAKIS(ETHYLENE GLYCOL) UNITS - D(AGAGAGAA-(EG)(6)-TTCTCTCT-(EG)(6)-TCTCTCTT)

A DNA molecule was designed and synthesized with three octanucleotide stretches linked by two hexakis(ethylene glycol) chains to form an int ramolecular tripler in solution. The structural data obtained from a s eries of NMR NOESY spectra yielded interproton distances, and COSY exp eriments provided dihedral angle information for analysis of deoxyribo se ring pucker. Using distance geometry followed by simulated annealin g with restrained molecular dynamics and relaxation matrix refinement, a well-refined ensemble of conformations was calculated. Although som e NOE cross-peaks involving protons of the hexakis(ethylene glycol) li nker could be identified, most could not be assigned and the conformat ions of the linkers were not determined. The deoxyribose conformations are predominantly of the S type, except for the protonated cytosine r esidues in the third strand which show hybrid N and S character. Overa ll, the duplex part of the molecule resembles a B-DNA double helix wit h the third strand bound in its major groove by Hoogsteen hydrogen bon ds. This structure provides a basis for comparison with triplexes cont aining noncanonical or nonnatural nucleotides.