The proposed work is aimed at developing and refining methods used to obtain nucleic acid conformations in solution from optical measurements. Such information and the corresponding models it produces are prerequisite for understanding the dynamics and biological mechanisms of nucleic acids. The most powerful and widely used optical methods for sensing detailed solution state conformations are circular dichroism and linear dichroism spectroscopies, however both require specific optical information regarding the electric dipole transition moments of the purine and pyrimidine monomeric chromophores. Much of the essential monomer information is just now becoming available, so that the uncertainties that have undermined confidence in the interpretation of the optical properties of oligonucleo- tides and nucleic acids are disappearing. The principal aims of the proposed research is to refine the monomer data, to explore the effects of other groups present in such systems (ribose, phosphate) and to investigate the effects of the various intermolecular interactions in such systems (H-bonding, stacking). It is therefore proposed to obtain absorption curves extending well into the vacuum UV region for radiation polarized along various axes of a multitude of single crystals. The absorption curves will be obtained from experimental polarized reflection spectra through Kramers-Kronig analysis. Exciton coupling will be treated with an iterative procedure in an effort to account for intermolecular interactions and to extract free molecule properties from the crystal spectra. Sequences of crystals including base, nucleoside, nucleotide and ionic forms (as available) will be studied in order to answer long-standing questions about the effects of ribose and phosphate substitution and protonation on the base chromophore. Hydrogen bonded A:T and G:C complexes will be examined to verify and study the striking conclusions drawn from the only previous study of such a complex. We plan to grow and examine dinucleoside phosphate single crystals in order to study the effects of stacking interactions and to refine the protocols for calculating the optical properties of polynucleotides in general. Crystals of longer oligonucleotides and drug bound systems will also be sought for study. As time permits we will begin to examine the amide and peptide groups so as to be prepared when crystal specimens of oligonucleotide/polypeptide complexes become available. Finally, we hope to collect transition moment data on a few simpler molecules. Such data will serve as a guide in the development of MO-theoretical methods as applied to the nucleic acid bases.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Molecular and Cellular Biophysics Study Section (BBCA)
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University of California San Diego
Schools of Arts and Sciences
La Jolla
United States
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Ho, P S; Zhou, G W; Clark, L B (1990) Polarized electronic spectra of Z-DNA single crystals. Biopolymers 30:151-63