Detection of DNA structural changes upon drug-binging by a combination of site-selective deutaretation and difference Raman intensity changes

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The goal of my research is to understand the mechanism of drug-DNA interaction by using of"isotope-edited UV resonance Raman spectroscopy -a combination of site-selective isotope labeling and ultraviolet resonance Raman (UVRR) spectroscopy The aim of this project is to find the correlation between the structure and UVRR intensity of DNA bases.UV Raman spectra of adenine and guanine derivatives were recorded in several solvents and the intensities of UV Raman bands were analyzed by using three solvent parameters proposed by Kamlet and Taft : the hydrogen-bond donor acidy, hydrogen-bond acceptor basicity, and polarity-polarizability. As a result, we have found that the Raman intensity of the purine rings depends mostly on hydrogen bonding but little on environmental polarity-polarizability.However, it is also known that base stacking interactions suppress the Raman intensity of DNA bases (Raman hypochromism). In order to determine either hydrogen-bonding or stacking is dominant in Raman … More intensity, isotope-edited UVRR spectra were measured of a 22-mer oligonucleotide (LacDNA) bound by cyclic AMP (cAMP) receptor protein (CRP). CRP-(cAMP)2 complex forms strong hydrogen bonds with guanine residues of LacDNA, but base stacking of the guanine rings are not significantly altered by the complex. For isotope-edited UVRR spectra of the guanine residues of LacDNA, some Raman bands showed appreciable frequency changes but did not show meaningful intensity changes upon CRP-(cAMP)2 binding. It is indicated that the UVRR intensities of aqueous DNA must predominantly be determined by the strength of the base stacking. Isotope edited UVRR spectra of a 19-mer oligonucleotide containing a AC-mismatched base pair were also measured to evaluate the sensitivity of the UVRR intensity to the base stacking. A significant intensity change was detected at the pre-melting state of the DNA. This observation demonstrates the utility of isotope-edited UVRR spectroscopy as a probe of the base staking of DNA bases. Less