Analysis of CW-EPR spectra and the internal dynamics of DNA

Abstract

A new lineshape analysis program is developed to accurately extract the relaxation rate R$\sb2$ from CW-EPR spectra in the fast motion limit, taking into account instrumental broadening, saturation from R$\sb{\rm 1e}$, and $\sp$C isotope effects. The broadening effects of spin label concentration and oxygen concentration on R$\sb2$ are quantitated and a deoxygenation protocol developed.The internal dynamics of short (100 base pairs or less) DNA molecules spin labeled with two different spin-labeled base pairs are examined. The acetylene-linked C derivative is shown useful for studies of internal dynamics, thus permitting examination of both CG and AT base pairs. The quinolone T derivative, Q, is used to quantitate the length and position dependence of internal DNA dynamics, consistent with the weakly bending rod model's prediction with only a simplistic modification. The dynamic flexural persistence length and rms amplitude of oscillation are estimated. Q is further used to systematically examine the dependence of internal DNA dynamics on base sequence, and the dinucleotide and trinucleotide repeats are ranked for flexibility.