CRC TRR C02 - Stability and free energy landscape of C-rich DNA strands and hybrid systems: a computer study

Basic data for this project

Description

In the previous TRR period we have developed and implemented the computational methods to unravel the thermodynamic properties of the i-motif structure and to explore the whole configuration space. In direct collaboration with the Liu group we have verified important predictions of the simulations such as the dominance of the hairpin-structure for neutral conditions. Thus, for the first time a microscopic picture of the properties of the C-rich DNA strand could be gained.The general goal for the next period is, first, to obtain a better mechanistic understanding of a C-rich DNA strand and, second, to introduce additional complexity, thereby approaching the multilevel view of the structure formation. More specifically we will focus on the following four aspects: 1. Effect of defects on the stability; 2. Release of molecules; 3. Effect of external force; 4. Collective unfolding effects; 5. Self-assembly of the DNA/polymer system. Again, several of these proposals are directly related to the experiments performed in the Liu group.