Linear Response Polarizability Theory of the UV, ORD, and CD Bandshapes of Helical Biopolymers. Single- and Double-Stranded Polyadenylic Acids

Abstract

Abstract The UV, ORD, and CD spectral bandshapes of polyadenylic acid (poly A) have been investigated theoretically in order to challenge the problems of whether discrimination of the single- and double-stranded poly A’s is computationally possible and of what structure poly A holds in a neutral solution. A linear response polarizability theory is applied to the derivation of UV, ORD, and CD bandshape functions of a polymer composed of N identical monomers. Using the observed and/or assumed values for the spectral bandshape of the adenine monomer, the UV, ORD, and CD spectra of both single- and double-stranded poly A’s are calculated by changing geometrical parameters. The single-stranded poly A at neutral pH is assumed to have a regular helical structure which is regarded as a counterpart of the double helix form of the double-stranded poly A. This model leads to the chainlength (N) effect which in turn suggests that the structure of poly A in a neutral solution is very flexible and is such that it can be approximated as a random assembly of adenine dirners and/or trimers, when the theoretical spectra of both the single- and double-stranded poly A’s are compared.