SOLUTION STRUCTURE OF A HOMOPYRIMIDINE-HOMOPURINE DODECAMER ENCODED BY THE HIV-1 ENVELOPE GENE - NMR AND MOLECULAR SIMULATION STUDIES

The solution structure of the nonpalindromic dodecanucleotide homopyri midine:homopurine, d(5'-TTTCTCCTTTCT):d(5'-AGAAAGGAGAAA), was determin ed by two-dimensional nuclear magnetic resonance spectroscopy combined with molecular simulation, The dodecamer sequence studied was found w ithin the HIV-1 enveloppe sequence and had all four Gs substituted by A in two hypermutants. A set of low-energy B-DNA conformations satisfy ing the quantitative NOE data were obtained. These highly related stru ctures had neither peculiar helical parameters for the base pairs nor axis curvature, Analysis of the dihedral angles (epsilon-zeta) suggest s that the A stretches flanking the GpA dinucleotides were more flexib le.