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 these essential data have never been available, and this lack of monomer data has undermined the interpretation of the optical properties of polynucleotides. The overall aim of the proposed research is to provide all necessary missing information. It is therefore proposed to obtain absorption curves extending well into the vacuum UV region for radiation polarized along various axes of purine and pyrimidine 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 crystal intermolecular interaction effects and to extract free molecule properties for the crystal spectra. The adenine and thymine chromophores are the least well studied, so that crystals containing these systems will form the bulk of the initial effort. In addition to determining the principal polarization direction of each transition we hope whenever possible to obtain the other components of the absorptivity tensor. Sequences of crystals involving base, nucleoside, nucleotide and ionic forms (if available) will be studied in order to answer long-standing questions about the effect 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 complexes. 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 the polynucleotide in general. Longer oligonucleotide systems will also be sought for study.
| Daniels, Malcolm; Hart, Lucas P; Ho, P Shing et al. (2007) Intrinsic fluorescence of B and Z forms of poly d(G-m5C).poly d(G-m5C), a synthetic double-stranded DNA: spectra and lifetimes by the maximum entropy method. Photochem Photobiol Sci 6:883-93 |
| Xu, S; Gantzel, P K; Clark, L B (1994) Glycoluril. Acta Crystallogr C 50 ( Pt 12):1988-9 |
| Ho, P S; Zhou, G W; Clark, L B (1990) Polarized electronic spectra of Z-DNA single crystals. Biopolymers 30:151-63 |
