Significant Local Mobility in Double Stranded DNA and RNA
An analysis of X-ray diffraction data from single crystals of double helical DNA and RNA fragments reveals that local mobilities of double stranded DNA and RNA are similar to each other and are intrinsic properties of nucleotides. We have determined the directions and magnitudes of trans-lational and rotational local mobility of phosphate, ribose, and base moieties of double stranded nucleic acids. Our primary findings are: (a) the major base pair motions are propeller twisting, rolling (rocking), buckling, and sliding; (b) the mobility of sugar moieties is coupled to their bases; and (c) the local mobilities are partly dependent on base sequences. These local mobilities help us understand intercalation, protein interaction, large scale motion, and other processes involving DNA and RNA.
It is easy to conceptually understand that double stranded DNA and RNA structures are not static but rather dynamic and flexible, fluctuating among many different conformations and perhaps even different helical forms. However, we have very little knowledge about quantitative magnitudes, directions and types of motion of nucleic acids. At the present time, there is no adequate experimental method by which one can directly measure them. However, such quantities can be derived from crystallographic “thermal” parameters (see Fig. 1) which in turn can be obtained by refinement of a model versus single crystal X-ray diffraction data, based on certain assumptions. The first assumption is that each atom in a base, sugar, or phosphate group is neither independent nor free-moving but, rather, constrained as a member of a group, and that the group can be considered the basic unit of motion. This assumption allows one to reduce the number of independent parameters to be refined using X-ray diffraction data. The second assumption is that in a single crystal, the overall molecular mobility or molecular disorder is relatively small compared to the local motion and local disorder of atomic groups in the molecule (see Fig. 1). This assumption is necessary since disorder and motion are indistinguishable from each other by X-ray diffraction.
KeywordsTranslational Motion Local Mobility Helix Axis Helical Axis Base Subgroup
Unable to display preview. Download preview PDF.
- 2.V. Schomaker and K. N. Trueblood, On the rigid body motion of molecules in crystals, Acta Cryst. B24:63 (1968).Google Scholar
- 6.R. L. Rill, P. R. Hilliard, L. F. Levy, and G. C. Levy, Natural Abundance carbon-13 NMR spectroscopic studies of native and denatured DNA, in: “Biomolecular Stereodynamics”, Vol. 1, R.H. Sarma, ed., Adenine Press, New York (1981).Google Scholar
- 8.R. E. Dickerson, M. L. Kopka, and H. R. Drew, Structural correlations in B-DNA, in: “Structure and Dynamics: Nucleic Acids and Proteins,” E. Clementi and R. H. Sarma, eds., Adenine Press, New York (1983).Google Scholar