CONFORMATIONAL FEASIBILITY OF A DNA HAIRPIN WITH ONE-BASE LOOP

Molecular dynamics calculations and energy minimizations have been use d to provide a conformational rationale for a DNA hairpin (5'-d-C(1)A( 2)G(3)C(4)T(5)G(6)C(7)T(8)G(9)) with one-base (T-5) loop. The loop for ms a ''closed'' structure in which the base, T5 of the loop, is turned towards the center of the loop. The base, T5, is partially stacked up on G6 at the 3'-side of the loop. The bases flanking T5, C4 and C6 are held together by usual Watson-Crick base-pairing with a high buckle a ngle of 25.78 degrees. The Cl'-Cl' distance for the base-pairs in the stem of the hairpin are as expected in the case of a B-DNA conformatio n. (C) 1996 Academic Press, Inc.