How is the Methylation of Cytosine recognized?

Although the methylation of cytosine on C5 position determines a variety of biological functions of DNA, the structural effects of methylation have not yet been fully understood. Experimental studies indicate that a single methyl group induces only slight structural alterations, mostlc located at the backbone. However, other crystallographic investigations propose that 5-methylcytosine maintains DNA in the A- and Z-form and even a new methylation dependent excentric conformation was controversially discussed. Furthermore, solid state NMR experiments of methylated DNA give evidence that this modification effects DNA backbone dynamics. The backbone phosphate is quenched due to methylation. Additionally analyses of X-ray structures show that methylation surprising enhances the hydration of DNA. Computer simulations by means of molecular dynamics and free energy calculations provide us the optimal tool to attain a detailed structural and energetical understanding of the methylation effect. Our experience in the field of nucleic acids simulation, especially with the focus on the DNA backbone conformations qualifies us optimally for the research. In detail we are interested in the methylation impact on structure flexibility and hydration an din the slective recognition of methylated DNA by naturally occuring proteins.

The biological task of DNA is the storage of genetic information in a sequence of base-pairs. This genetic information is read within the cells and transcribed into RNA. This RNA is translated into a protein sequence, which performs the actual biological task within the body, e.g., in form of an enzyme. However, the read-out of DNA is not only governed by the sequence of base pairs but also by chemical modification of the bases, namely the methylation of cystein. This methylation is of enormous biological significance as it can lead, e.g., to gene silencing and X chromosome inactivation. The project comprised investigations by means of computer simulations into the changes of DNAs structure and flexibility introduced by methylation. We found that the changes predominantly occur in the highly charged backbone of DNA, which governs the approach and binding of proteins, that accomplish and control transcription of DNA into RNA. To evaluate the consequences of these changes we studied on the one hand drugs that bind by intercalation into DNA and on the other hand proteins that bind to methylated or unmethylated DNA. We found also here that changes in the backbone of DNA in all cases play an essential role. Therefore we surmise that the methylation of DNA is read-out substantially over changes in the backbone. Applications of the knowledge gained lie especially in the field of drug-design. Drugs, that bind as specifically as possible to a certain area of DNA and that can change the backbone, offer significant therapeutic potential for many diseases, but especially in cancer treatment. Such drugs could be used to remove certain malfunctions of cells with very little side effects. The know-how generated during the project can be used to search and improve such drugs.