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

Abstract

SynopsisA comhination of the DeVoe and Kirkwood polarizahility concepts is developed to calculate CD spectra of nucleic acid monbmers. The method is perfectly general and applies t o any system where the constituents have absorption properties which are widely separated in terms o f frequency. T h e theory is applied to calculate the C I j spectra of adenosine and 2'-deoxyadenosine conformers. Bond polarizahilities are evaluated for the rihosyl moiety of adenosine, as a function of glycosidic rotational angles and polarizahility anisotropies. It is found that a wide range of C-C and C -0 bond polarizahilities give similar CD results. Isotropic atom polarizabilities are also evaluated. It is found that the CD results using these polarizahilities d o not differ significantly from those obtained with bond polarizabilities. T h e ('I) spectra of adenosine and Tdeoxyadenosine are calculated for three x-ray diffraction determined geometries: A-form RNA, B-form DNA, and C-form DNA. T h e results indicate that the monomer CD spectra are strongly dependent on the precise geometry and appear t o he o f importance in understanding the spectra of oligomcrs and polymers. T h e deoxyadenosine conformers are found to have calculated CD spectra which are less intense than those o f t he rihosyl conformers. These results indicate that the measured differences hetween the ('1) magnitudes of riho-and deoxyrihoadenositie are due to the presence o r ahsence of the 2'-hydroxyl. Weighted averaged adenosine CL) spectra are calculated with the aid of prohahility distributions from conformational energy calculations. The results suggest a new method tor obtaining empirical monomer parameters for use in optical calculations. The calculations in this paper indicate for the first time that DeVoe theory, in comhination with the Kirkwood theory, provides a useful method for the calculation of the CD spectra of nonpolvnieric tnolecules.

Polarizability tensor theory by Green’s function matrix: Circular dichroism and ultraviolet absorption band shape calculations of cyclo(Gly-Pro-Gly-D-Ala-Pro) having β- and γ-turns

“…14,16,18,19 Recently, we have rewritten this partial polymer ͑N-mer͒ scalar polarizability theory in terms of ␣ mm f f () and U mn f g in a new tractable tensor matrix form ͑m,nϭ1,2,.., N and f ,gϭ1,2,...͒: 31…”

“…͑5d͒ has never been considered except in the computations of the first term of Eq. ͑5d͒, 14,16,18,19 although Moore and Williams 19 have shown such a chiral polarizability term in their equation, but have not included it in the CD calculations of nucleic acids. Both the DeVoe scalar theory of Eq.…”

“…͑18a͒ describing Kirkwood-Moffitt mechanism has often been assumed to be origin-independent, 7,16,18,19,24 since R mn f g ϵR n g ϪR m f removes origin-dependence. However, as had already been recognized by Stiles, 39 this is not generally true, since the shifts of the local origins of R m f and R n g by vectors r m f and r n g lead to…”

“…[10][11][12][13][14][15][16][17][18][19] Representative polarizability theories include the Fano-DeVoe model, 2,9,17,[20][21][22][23][24][25] decorrelation approximation, [3][4][5][6] Green's operator method, 11,12,[26][27][28] and so on. 1 It may safely be said that these various polarizability theories have arrived at one theoretical working formula.…”

Differential Absorption and Differential Scattering of Circularly Polarized Light: Applications to Biological Macromolecules

“…Recently, Williams & Moore (120) developed a semiempirical procedure to derive nucleic acid transition monopoles. The nucleic acid transition parameters are derived by adjusting them to optimize the fit between calculated and measured CD spectra of cyclic mononucleotides (120,127,129,130).…”