Normal Mode Calculation for Methylated Z-DNA Poly(dG-m5dC).(dG-m5dC)

摘要

Normal modes of methylated deoxyribonucleic acid Z-DNA poly(dG-m5-dC) (dG-m5dC) are computed by helix lattice dynamics. Good agreement with Raman spectral data is obtained. We discuss improvements in the formulation of the problem which allow us to greatly reduce the size of the matrix used. This leads to greatly reduced calculation times. The improvements come from using knowledge of the C2 and time reversal symmetries. Theoretical Formalism: Let us consider an infinite double-helical molecule. The helical symmetry axis is taken as Z axis in cartesian coordinates. Helical symmetry implies that each unit cell is transformed geometrically into the next by the operation H(p, psi) where p is the pitch along Z-axis and psi is the pitch angle about Z-axis.