NMR studies on the base pair dynamics of DNA duplexes and DNA-protein complex

Abstract

Nuclear magnetic resonance (NMR) spectroscopy is very powerful tool to study the dynamic features of bio-molecules in solution state, which is similar with physiological condition. Base pair opening reaction occurring in DNA duplex can be investigated by observing hydrogen exchange of imino protons in guanine and/or thymine residues. Base-catalyzed dynamics experiments provides opening/closing rate of the base pair and thus, equilibrium constant for base pair opening. Subsequently, thermodynamic energies for the base pair opening reaction can be derived from those dynamic parameters. Dynamics of three different DNA duplexes have been studied using the NMR spectroscopy. Methylation of DNA plays a regulatory role in DNA metabolism. Hemimethylated GATC site plays key roles for various cellular processes including negative modulation of replication initiation at oriC by SeqA. Investigation on DNA duplex that contain fully methylated GATC site is need to explain how hemimethylated GATC sites are recognized in vivo in a background of fully methylated ones. NMR was used to characterize the solution structure of the DNA duplex that contained a fully methylated GATC site and the dynamics of the un-, hemi-, and fully methylated GATC duplexes. Unique major groove conformation optimized for entrance into the cleft structure of SeqA was displayed in only hemimethylated GATC site. The apparent equilibrium constants for base pair opening of the three differentially methylated GATC duplexes displayed the effect of N6-methylation of the adenine residue upon the dynamics of its own and adjacent base pairs. Faster base pair opening rate and less energy requirement for the base pair opening of the two G˙C base pairs in the hemimethylated GATC duplex might be an important factor for recognition by SeqA protein. The cis-syn cyclobutane pyrimidine dimer (CPD) is cytotoxic and mutagenic UV-induced DNA photoproducts. In general, the nucleotide excision repair (NER) pathway is re...