Circular dichroism of flow-oriented nucleic acids: I. Experimental results

Abstract

Specific ultraviolet circular dichroism spectra with light propagating parallel to the helix axis ( ϵ L — ϵ R ) ∥ and perpendicular to the helix axis ( ϵ L — ϵ R ) ⊥ have been measured for DNA in buffer, DNA in high salt, DNA in ethylene glycol, and double-stranded viral RNA in buffer. The data are obtained by measuring both the CD and the absorption spectra of nucleic acid solutions oriented by shear gradient in a multi-capillary flow cell with the incident light beam parallel to the direction of flow. It is shown that the conservative isotropic CD spectrum of DNA in buffer originates almost entirely from ( ϵ L — ϵ R ) ∥; the ( ϵ L — ϵ R ) ⊥ component is nearly zero. The predominance of the conservative ( ϵ L — ϵ R ) ∥ spectrum over the ( ϵ L — ϵ R ) ⊥ spectrum indicates that the base planes of DNA in buffer are essentially perpendicular to the helix axis as in the B-form. The unusual profile of the isotropic CD spectrum of DNA in 6 m-LiCl, as well as in 95% ethylene glycol, is a result of extensive cancellation between the positive conservative ( ϵ L — ϵ R ) ∥ component and the negative non-conservative ( ϵ L — ϵ R ) ⊥ component. For double-stranded RNA, the specific CD pattern observed is very different from that of B-form DNA. The ( ϵ L — ϵ R ) ∥ component is positive non-conservative and ( ϵ L — ϵ R ) ⊥ is positive conservative. The nature of these specific CD spectra implies that the base planes are tilted with respect to the helix axis. The CD measurements on flow-oriented solutions presented here reveal the directional nature of the interaction between light and the nucleic acid molecules; this directional nature is obliterated in conventional CD measurements of isotropic solution.