DNA bending due to sequence-induced torsional stress

Abstract

Three sequences with 60 base pairs each are studied, using an all-atom force field. One is a 60 base pair A-tract, the second has 30 A–T steps and the third is equal to the first, except in base pairs 11–16, where a TATA box is inserted. The first two sequences form straight helices but the second helix has an alternating pattern of compression of the minor and major groove from one base pair to the next, an anomolously rigid backbone and is undertwisted compared with the first. The main finding is that the sequence with the TATA box leads to a structure with a bend of 180°. The bend is smooth and its apex is found 20 base pairs away from the TATA box. The bend is towards the minor groove and is effected with only a small distortion of the double helical geometry. It is possibly due to a long-range effect of the mismatch between the structures of the A-tract and the TATA box, coupled with the fact that the TATA box is more rigid. Some biological implications of these findings are discussed.