Nucleic acid circular dichroism

Deoxyribonucleic acid, DNA, is composed of planar aromatic nucleic acid bases linked to a sugar and a phosphate as illustrated in Fig. 1. Ribonucleic acid, RNA, differs from DNA by an extra oxygen on the sugar and also thymine is replaced by uracil which does not have the methyl substituent. Most of the DNA and RNA transitions we measure with UV spectroscopy is due to the π–π* transitions of the bases. These transitions have no intrinsic CD signal since the bases are planar and hence achiral. However, the isolated bases acquire asymmetry in their electronic transitions by coupling with the chiral ribose sugar units of the backbone. The magnitude of Δε max (the molar difference in absorbance of left and right circularly polarized light) for each base is of the order of 2 mol−1 dm3 cm−1 at 270 nm; the purine bases have a negative signal whereas the pyrimidine ones have a positive CD in that region. When the bases are linked by phosphodiester bonds to form DNA or RNA, an additional (and usually larger) source of chirality results from the coupling between bases that are stacked in a helix (Berova et al in press; Nordén et al 2010).