Circular dichroism calculations for double‐stranded polynucleotides of repeating sequence

Abstract

Optical property calculations are presented for poly(A·U), poly[(A‐U)·(A‐U)], poly(G·C), and poly[(G‐C)·(G‐C)] in RNA, B‐DNA, and C‐DNA conformations. An all‐order classical coupled oscillator polarizability theory was used, and an effective dielectric constant of 2 was assumed. The calculated CD spectra were found to be sensitive to both geometry and sequence. Agreement with the measured CD spectra of poly(A·U), poly(G·C), and poly(dG·dC) is very good. Calculations for other sequences and geometries are less satisfactory and are particularly poor for poly[(G‐C)·(G‐C)] in RNA geometry and poly(A·T) in B‐DNA geometry. Attempts to improve agreement with measured spectra by varying monomer properties have been only partially successful for these calculations, but they illustrate the types of changes that may prove to be necessary. Calculations using other published X‐ray coordinates for certain deoxypolynucleotides of simple sequence, some of which are quite different from B‐DNA coordinates, did not result in better agreement with measured spectra. Finally, the dependence of the calculated CD on chain length is examined. Results show that non‐nearest neighbor interactions can be important when runs of 3 or more identical base pairs appear in a given sequence.

The analysis of circular dichroism spectra of natural DNAs using spectral components from synthetic DNAs

“…Therefore, we chose T-matrix 14 as the standard, against which Fraction No. 14) Fraction No. 14) Fraction No.…”

“…14) Fraction No. 14) Fraction No. 14) d the results of other T-matrices may be compared for individual DNAs.…”

“…14) Fraction No. 14) d the results of other T-matrices may be compared for individual DNAs. The spectral components of T-matrix 14 are listed in Appendix Table AII.…”

Circular dichroism of nucleic acid monomers. I. Calculated adenosine and 2′‐deoxyadenosine CD spectra

“…For adenosine, the calculated CD Table I and Ref. 9). The monomer conformation is that found in double-helical A-form RNA ( Table 11).…”

“…Hug et al 7 have applied the theory to calculate the CD due to aromatic side chains in stereoregular copolymers. Tinoco and coworkers1, [8][9][10] have applied the theory to calculate the CD and absorption spectra of ApA and oligo(A), the CD spectrum of poly(I), and the CD spectra of double-stranded nucleic acids of repeating s e q~e n c e .~ However, in these calculations, the optical contributions of nonchromophoric (i.e., between 200 and 300 nm of the spectrum) groups (e.g., polymer backbones) were not explicitly considered.…”