The flexible DNA double helix. I. Average dimensions and distribution functions

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Abstract
A scheme has been developed to treat the spatial arrangements and properties of double‐helical DNA in terms of the constituent atoms and bonds of the system. Heretofore the behavior of DNA in solution has been interpreted in terms of various artificial theoretical models. In this work the flexibility of the DNA double helix is taken to arise from minor perturbations of the rotation angles along the polynucleotide backbone. The rotational motions of the chain are limited to conformations within the B‐DNA family of helices that permit base stacking. The disruptions of hydrogen bonding associated with these angular fluctuations are offered as a plausible description of the well‐known breathing of double‐stranded DNA. Radii of gyration 〈s2〉0 computed on the basis of this model are found to agree with experimental measurements on B‐DNA helices spanning a wide range of molecular weights. Moreover, the three‐dimensional spatial distribution functions Wa(ρ) generated by these limited internal rotations are compatible with various macroscopic descriptions (i.e., rigid rod, wormlike coil, ideal Gaussian) previously ascribed to DNA of different chain lengths. It is further evident from the Wa(ρ) that the “rigid” B‐DNA backbone modeled here, if long enough, can bend into compact conformations. Thus it does not appear necessary to invoke the occurrence of sharp bends or links to account for the condensed forms of DNA in naturally occurring systems.