Structure of a B-DNA dodecamer: II. Influence of base sequence on helix structure☆

摘要: Abstract Detailed examination of the structure B-DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G, obtained by single-crystal X-ray analysis (Drew et al., 1981), reveals that local helix parameters, twist, tilt and roll, are much more strongly influenced base sequence than crystal packing or any other external forces. The central EcoRI restriction endonuclease recognition site, G-A-A-T-T-C, is a B with an average 9.8 base-pairs per turn. It flanked on either side single-base-pair steps having aspects A-like character. suggests several general principles, whose validity must be tested analyses. (1) When bending moment applied to double helix, it bends smoothly, without kinks breaks, relatively little effect parameters. (2) Purine-3′,5′-pyrimidine open their planes towards major groove, pyrimidine-purine toward minor homopolymer (Pur-Pur, Pyr-Pyr) resist rolling in direction. This behavior related preference pyrimidines for negative glycosyl torsion angles. (3) CpG have smaller helical twist angles do GpC, as though compensation intrinsic overlap. Data A-T insufficient generalization. (4) G.C propellor A · T, this arises mainly from interstrand overlap rather presence third hydrogen bond. (5) DNAase I cuts preferentially at positions high perhaps because increased exposure backbone attack. correlation digestion patterns solution argues essential identity two environments. (6) In places where TpCpG occurs, C slips under T order stack efficiently over G. At paired bases step, G tilted so angle between splayed out outside helix. TpC most favored cutting site factor 4.5 (Lomonossoff 1981). (7) methylase both appear prefer type purine-purine-A-T-T-pyrimidine, involving adjacent triplets, may consequence relative stiffness base-stacking observed dodecamer.