Nucleic acid linear dichroism

Definition: A linear dichroism (LD) spectrum shows the difference in absorbance of light polarized parallel and perpendicular to an orientation direction (Rodger and Nordén 1997; Nordén et al 2010). The idealized structure of B-DNA has the base pairs oriented perpendicular to the DNA helix axis to a first approximation. This means the π–π* transitions take place in the plane perpendicular to the helix axis, and so these are expected to give a negative LD signal as illustrated in Fig. 1. LD can be used to probe changes in orientation of the DNA bases.

The LD spectrum of B-DNA shown in Fig. 1 is similar to but not exactly the same shape as the negative of its absorbance spectrum, –A. The same information is summarized in the reduced LD spectrum which is fairly constant across the 260 nm band, but not completely so. This tells us that, in solution, the bases are not rigidly perpendicular to the helix axis as implied by the idealized B-DNA structure. Careful analysis of solution LD studies has led to the conclusion that the bases of B-DNA in solution lie at an average angle of ~80° (or even less) from the helix axis (Chou and Johnson 1993) (though we typically assume 86° in a calculation (Matsuoka and Nordén 1982)).

The magnitude of the LD signal of any sample is also affected by the degree of orientation as summarized by the orientation parameter, S.