Helical Periodicity of DNA, Poly(dA)·Poly(dT) and Poly(dA‐dT)·Poly(dA‐dT) in Solution

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Abstract
Helical periodicity of DNA, poly(dA)·poly(dT) and poly(dA-dT)·poly(dA-dT) has been measured in solution by using the band shift method of Wang [Wang, J. (1979) Proc. Natl Acad. Sci. USA, 76, 200–203]. The method makes use of the effect, on the superhelicity of closed circular DNA molecules, of the insertion of specific nucleotide sequences of known length. The method was applied to a variety of recombinant plasmid DNAs which were constructed by inserting DNA, poly(dA)·poly(dT) or poly(dA-dT)·poly(dA-dT) into pBR322 DNA. When compared to DNA, poly(dA)·poly(dT) was found to have a smaller pitch (by about 0.5 base pair/turn), whereas poly(dA-dT)·poly(dA-dT) has a slightly larger pitch (by 0.1 base pair/turn). These features correlate well with the known ability of the alternating copolymer to reconstitute nucleosomes upon incubation with histones, in contrast to the non-alternating one which fails to do so. Finally, a detailed analysis of the principles underlying the methods developed by Wang [reference quoted above and Wang, J. (1978) Cold Spring Harb. Symp. Quant. Biol. 42, 29–33] leads to an increase in the estimate of the helical periodicity of DNA of 0.15 base pair/turn, over the reported value of 10.4 base pairs/turn (references quoted above). This essentially accounts for the discrepancy observed with the value of 10.6 base pairs/turn obtained by nuciease digestion of DNA immobilized on a surface [Rhodes, D. & Klug, A. (1980) Nature (Lond.) 286, 573–578].