Book of Abstracts: Albany 2003
June 17-21 2003
Structural and Energetic Analysis of the DNA A-B Transition Using Spectroscopic and Computational Methods
Right handed nucleotide helices exist in two main conformational families, A and B, which differ structurally at the molecular level. The B helix is the canonical double helix with ten base pairs per helix turn, while the A helix is wider and shorter. This global structural contrast is explained, in large part, by differential puckering of the sugar ring in the A and B forms. More specifically, the A conformational family is characterized by C3?-endo puckering, while the B family is characterized by C2?-endo puckering of the sugar ring. This differential puckering leads to global structural changes, including phosphate spacing, base-pair tilt, rise and rotation per residue, base-pair dislocation, as well as the width and depth of the major and minor grooves. While RNA helices adopt the A conformation under biological conditions, DNA helices typically exist in the B-form. Nonetheless, DNA can and will undergo a conformational transition to the A-form under certain conditions, notably in DNA-RNA hybrid helices or upon binding by certain proteins. Thus, the B-A transition is of biological importance and merits closer inspection. Existing research has demonstrated that this transition is cooperative, environmentally sensitive, and sequence dependent. Specifically, B-form DNA is stabilized by increased hydration levels, whereas A form DNA is stabilized by lower hydration levels; sequences containing a large number of G·C G·C steps favor the B-A transition. Prior work has involved conformational and energetic analysis by either spectroscopic or computational methods. The approach proposed here, however, is a combination of these two methods. Existing MD calculations of the Dickerson-Drew dodecamer (CGCGAATTCGCG) at high and lower water activity levels, performed by Dr. Beveridge?s group, will be compared to results obtained via UV-Resonance Raman and circular diochroism spectroscopy. Comparison of these results will allow for refinement of existing MD calculations as well as a more refined understanding of the B-A transition in structural and thermodynamic terms.
Colin E. Aitken