Conformational analysis of DNA shows that the origin of the B-form double helix can be substantially attributed to the atomic charge pattern in the base pairs. The pattern favors specific helical stacking of the various base pairs. The base pairs alone, without the sugar-phosphate backbone have a strong tendency to be helical. The backbone appears to play a relatively passive role in determining the helix form of DNA. Both electrostatic and van der Waals interactions play a role, but electrostatic interactions are particularly important in A-form DNA. The asymmetries of conformational fluctuations were calculated. These directional preferences were used to a construct specific sequence models for bending DNA around a protein of known structure, based on DNA footprinting. The TATA box is especially flexible because of alternating large fluctuations in roll and twist; this suggests the role of TATA as a """"""""swivel"""""""" joint. Models of a specific sequence DNA bending around a protein were built, based on footprinting data and flexibility calculations. Other models have been built for tight hairpin loops and for various triple helices.
