Determination of aliphatic side-chain conformation using cross-correlated relaxation: Application to an extraordinarily stable 2 '-aminoethoxy-modified oligonucleotide triplex

The structural basis for the extraordinary stability of a triple-stranded o ligonucleotide in which the third strand contains 2'-aminoethoxy-substitute d riboses is investigated by NMR spectroscopy. The enhanced stability of th e modified triplex in comparison to the unmodified DNA triplex of the same sequence can be attributed to strong interactions of the aminoethoxy groups of the third strand with the phosphate groups of the purine strand. In mol ecular dynamics calculations the aminoethoxy side chain was found to be rat her flexible, allowing for the presence of hydrogen bonds between the amino ethoxy group of the third strand and two different phosphates of the backbo ne of the second strand. To investigate the conformational. preference of t he aminoethoxy side chain a new NMR method has been developed which relies on CH-CH dipolar-dipolar cross-correlated relaxation rates. The results ind icate that the aminoethoxy side chains adopt mainly a gauche(+) conformatio n, for which only one of the two hydrogen bonds inferred by NMR and molecul ar dynamics simulations is possible. This demonstrates a highly specific in teraction between the amino group of the third strand and one of the phosph ate groups of the purine, strand.