BENDING AND CURVATURE CALCULATIONS IN B-DNA

A simple program, BEND, has been written to calculate the magnitude of local bending and macroscopic curvature at each point along an arbitr ary B-DNA sequence, using any desired bending model that specifies val ues of twist, roll and tilt as a function of sequence. The program has been used to evaluate six different DNA bending models in three categ ories. Two are bent non-A-tract models: (a) A new model based on the n ucleosome positioning data of Satchwell al al 1986 (J. Mol. Biol. 191, 659-675), (b) The model of Calladine et al 1988 (J. Mol. Biol. 201, 1 27-137). Three are bent A-tract models: (c) The wedge model of Bolshoy at al 1991 (Proc. Natl. Acad. Sci. USA 88, 2312-2316), (d) The model of Cacchione at al 1989 (Biochem. 28, 8706-8713), (e) A reversed versi on of model (b). The last is a junction model: (d) The model of Koo an d Crothers 1988 (Proc. Natl. Acad. Sci. USA 85, 1763-1767). Although t hey have widely different assumptions and values for twist, roll and t ilt, all six models correctly predict experimental A-tract curvature a s measured by gel retardation and cyclization kinetics, but only the n ew nucleosome positioning model is successful in predicting curvature in regions containing phased GGGCCC sequences. This model - showing lo cal bending at mixed sequence DNA, strong bends at the sequence GGC, a nd straight, rigid A-tracts - is the only model consistent with both s olution data from gel retardation and cyclization kinetics and structu ral data from x-ray crystallography.