STRUCTURAL FEATURES OF THE DNA HAIRPIN D(ATCCTA-GTTA-TAGGAT) - FORMATION OF A G-A BASE-PAIR IN THE LOOP

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA -TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and t he last residues of the tetraloop of this hairpin form a sheared G-A b ase pair on top of the six Watson-Crick base pairs in the stem. The gl ycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high-anti domain (similar to-60 degr ees) respectively. Several dihedral angles in the loop adopt non-stand ard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residu e is directed away from the loop region. The loop structure can be cla ssified as a so-called type-I loop, in which the bases at the 5'-end o f the loop stack in a continuous fashion. In this situation, loop stab ility is unlikely to depend heavily on the nature of the unpaired base s in the loop, Moreover, the present study indicates that the influenc e of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair.