Study of nucleic-acid structure and interactions by resonance Raman scattering

Author: Mgr. Jakub Klener
Supervisor: Prof. RNDr. Josef Štěpánek, CSc.
Type: Doctoral

Annotation: Determination of secondary and tertiary structures of nucleic acids (NA) and their interactions is of a key importance to elucidate mechanisms of genetic-information transfer and expression, which is significant not only for understanding of these fundamental processes in living organisms, but also for design of potential therapeutic strategies that intervene them. Due to the possibility to perform measurements in natural aqueous environment and the relative facileness enabling to study the effects of the interacting species composition as well as of the environmental conditions, Raman spectroscopy is suitable for gaining principal information about the NA structure, structural changes, and complexation with other molecules. The necessity of relatively high NA concentrations and the troubles with a frequent contamination of samples with heterogeneous low-molecular species represent severe disadvantages of standard Raman spectroscopy, which employs visible excitation. These problems are overcome in the case of resonance Raman scattering (RRS), when the excitation radiation from the region of the lowest-wavelength NA absorption band is used. Because of significantly higher demands on the equipment, alignment of the spectrometer, and utilization of approaches that avoid rise of artifacts originating in NA photodamage, RRS is though employed for NA studies only rarely. Basic comparative analyses of resonance Raman scattering of fundamental NA model structures are also missing. The main objective of the thesis will be, besides the contribution to the building-up of a UV resonance Raman spectrometer and development of a suitable technique to handle a UV-sensitive sample, systematic measurements of sets of NA model structures will be performed. Obtained RRS spectra will be compared with standard vibrational and electronic spectra of these compounds in order to find out and interpret conformational and interaction RRS markers. The results will be applied in subsequent studies of distinguished NA structural motifs that play important roles in the transfer and expression of genetic information.