DNA Backbone Conformations and their influence on sequenc recognition.

Research project P 13845 DNA-Backbone Conformations Klaus R LIEDL 11.10.1999 The DNA-backbone consists of repeated desoxyribonucleoside and negatively charged phosphate diester units. These exposed centers of strong electrostatic interaction are playing a decisive role in DNA-protein binding processes. The phosphate diester is known to occupy two distinct spatial arrangements (i.e., B, and BI, for B-DNA, Z, and Z11 for Z-DNA). Whereas formerly these rearrangements were attributed to crystal packing effects, recently a significant population of both B-DNA conformers was observed in solution. Hence, we surmize that these conformers substantially influence the DNA-recognition and binding processes. Based on our current studies we plan to investigate the mechanism of these phophate rearrangements both for B- and Z-DNA. We are specially interested in the dependence on sequence and ionic strength. We further intend to analyse the free energy changes as well as other thermodynamic contributions along the interconversion pathway. To provide a step towards the understanding of biological implications we finally plan to focus on complexes of small ligands with DNA. In close and successful cooperation with spectroscopists we are prepared to apply a variety of suitable computational simulation methods to the elucidation of the abovementioned questions.

The genetic information is passed in the form of desoxyribo nucleic acids (DNA) from generation to generation. Starting from the DNA-strands all further biomolecules are built within each cell. The DNA-double helix does not only consist of base-pairs, that ultimately carry the genetic information, but also contains a backbone, that consists of sugar units (the so-called desoxyribose units), which are connected by phosphodiester bridges. A molecule approaching DNA is primarily guided by the strong electrostatic interaction emerging from these phosphodiester units. The actual sequence information can only be read, once a direct contact to the minor or major groove of the DNA-double strand is established. Therefore alternative conformations of the DNA-backbone are of considerable importance. Nearly all DNA-binding proteins exhibit intensive contacts to the DNA-backbone emphasising this importance. There are even proteins that form contacts exclusively to the backbone. In the beginning of the project the mechanism of DNA backbone rearrangements was investigated. It turned out, that water molecules play a crucial role during the rearrangement processes. In the following we analysed, how linear molecules, that bind to the minor groove of DNA, sequence specifically influence the structure of the DNA- backbone. We primarily observed freezing of the otherwise rather flexible backbone to specific configurations. In combination with our finding, that changes in the minor groove mediated by backbone rearrangements progress into the major groove, we could demonstrate that binding processes of proteins to the major groove could be influenced by complexation to the minor groove by induced backbone rearrangements. We therefore probed the possibility to modify bases and/or ligands in the minor groove to specifically influence the backbone rearrangements. Finally we analysed the dynamics of various protein-DNA binding processes, to recognise the restraints imposed to the DNA-backbone conformations in protein-DNA complexes. The overall view of the different results shows that it should be indeed possible to control binding processes to DNA and therefore the transcription and translation of genetic information by sequence specific ligands within the minor groove.