DNA recognition processes and epigenetic features of DNA analysed by molecular dynamics simulations and infrared spectroscopy / presented by Christine Johanna Rauch

• VerfasserIn: Rauch, Christine Johanna
• Place / Publishing House: 2004
• Year of Publication: 2004
• Language: English
• Classification: 35.11 - Quantenchemie. chemische Bindung; 33.07 - Spektroskopie; 35.06 - Computeranwendungen
• Physical Description: II, 151 Bl.; Ill., graph. Darst.

ger: Molecular Dynamics Simulations and Spectroscopic Analysis have proven to be valuable tools for the examination of the structure and dynamics of biologically interesting molecules like DNA and DNA-protein complexes. This work concerns the investigation of DNA, its conformations, different DNA-protein complexes and epigenetic features of DNA. The major outcome are new insights into the mechanistic pathways of type II restriction enzymes, elucidation of the thermodynamic and kinetic influence of methylation on the DNA backbone behaviour, the spectroscopic analysis of Z-DNA and its backbone substates Z1/Z2 and the calculation of the contribution of DNA-methyl groups to protein binding.<br />The first project concerned the analysis of the exact catalysis mode of the PvuII endonuclease. Specific alterations at the catalytically important regions have been discovered. The observed features, especially a decreased intrastrand phosphorus-phosphorus distance and the positioning of a catalytically important amino acid, indicate a substrate assisted catalysis.<br />By means of infrared spectroscopy the backbone dynamics of Z-DNA were investigated. Marker bands for the conformer substates were identified and thus the population ratio and the enthalpy change for the Z1/Z2 equilibrium estimated.<br />A major part of this thesis deals with the methylation of cytosine. The thermodynamic and kinetic consequences of methylation on the BI/BII substate interconversion was analysed. We surmise that the indirect readout mechanism is influenced by the C5-methylation of cytosine. In addition the recognition mode of a methyl cytosine binding protein (MBD1) was investigated and the contributions of the methyl groups to the binding constant were calculated.