The circular dichroism of polynucleotides in relation to their conformations

Abstract

AbstractThe circular dichroism of polynucleotide or oligonucleotides reflects their conformations. The CD spectra of oligonucleotides vary depending upon the species of bases involved and their sequence. The amplitude of CD peak is proportional to the degree of stacking and furnishes the way to estimate some thermodynamic parameters of stacking. The CD spectrum of poly (G + C) or poly (A + U) is close to the graphical summation of its constituent homopolymers, except blue shift of the peaks, and decrease in their amplitudes. Double stranded copolymer, poly (A ‐ U) or poly (G ‐ C) has a quite different feature from that of poly (A + U) or poly (G + C), reflecting the difference in mode of base stacking. The CD spectrum of poly dAT is quite different from poly (A ‐ U) and DNA has a different CD pattern from RNA. These differences can be interpreted by the difference in the geometry of the bases. The peak position of CD spectrum of double stranded RNA varied depending on the ratio of (G ‐ C)/(A ‐ U). Thus it is possible to estimate (G ‐ C) or (A ‐ U) content by analyzing the CD spectrum. The CD spectra of tRNA are different depending on the species of it. It is of greatest interest that Met‐tRNAF has quite different CD pattern from Met‐tRNAM. This can be interpreted by the difference in the number of G ‐ C or A ‐ U pairs between them. A remarkable change in CD spectrum was observed when poly dAT is complexed with RNA polymerase or when aminoacyl RNA is complexed with T factor. The conformational change suggested by CD will play an important role for the elucidation of reaction mechanism.