Soft Modes and the Structure of the DNA Double Helix

Abstract

We have applied the method of vibrational mode softening to investigate conformation changes (i.e., changes in three-dimensional structure) in double-helical DNA. Conformation changes of these macromolecules are analogous to displacive phase changes in crystalline solids. We have calculated a mode softening which would drive the double helix from its B conformation to its A conformation. The mode is not softened by temperature change, but rather by changes in the macromolecular environment which mimics the conditions which cause the conformation change experimentally,The DNA double helix can take on several conformations. 1 When dissolved in water or in gels at high humidity (much water of hydration) it is found in the B conformation. Upon drying the gel in an atmosphere of less than 92% relative humidity, it converts to the A conformation. RNA on the other hand is found only in A-type conformations. It has been suggested that DNA switches to A conformation locally when transcribing RNA in vivo and that this conformation change is an important switching mechanism in the biological function of nucleic acid. 2 We have carried on extensive theoretical investigations of the lattice dynamics of DNA and RNA helices. 3 These calculations were made using valence and Urey-Bradley force fields which were 7 I. S. Sokoknikoff andR. M. Redheffer, Mathematics of Physics and Modern Engineering man, Phhs. Rev. B 12, 4434 (1975), 12 P. C. Arnett and 3. H. Yun, Appl. Phys. Lett. 26, 94 (1975). 13 H. Scher and E. W. Montroll, Phys. Rev. B 12, 2455 (1975).obtained, by various authors, by refinement from the observed spectra of the constituent parts of nucleic acid. The calculations were done for artificial homopolymer DNA in which all the base units in a single helix were the same. Two such double-helical DNA compounds exist-poly(dA)* poly(dT) and poly (dG) • poly (dC)-where the bases are adenine, thymine, guanine, and cytosine, respectively. These homopolymer duplexes are available and a considerable amount of experimental ir and Raman analysis has been done for all the occurring conformations. A comparison of our theoretical lines with those observed shows quite good agreement for those regions of the spectrum where data exist. 3 In our calculations for both poly (dG)-poly (dC) and poly(dA)-poly(dT) the lowest-lying optical mode is one in which the two single helices move up and down relative to each other along the double-helix axis. It is this mode which softens in our calculations.The eigenvector of the mode that softens agrees very well with the description of the B to A conformation change. The B conformation has the bases of the helix perpendicular to the helix axes. In the A conformation, the bases are tilted from the perpendicular. The soft mode in which the two helices displace relative to each other along the axis does lead to such a tilting of the bases.In doing our calculations for the soft mode, weWe show that a soft mode arises when the vibrational modes of double-helical DNA are perturbed by increasing the electrost...

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