Structure and Function of Holliday Junctions Complexed with Ions and HU Protein

摘要: DNA four-way junctions (4WJ) are central intermediates in processes such as replication and recombination. This project studies how different conformations of the junction relate to function, proteins interact with enhance or repress function. Previously, we have examined 4WJ structure presence ions, used Forster Resonance Energy Transfer (FRET) map binding site protein HU onto junction. It was found that high salt concentrations is stabilized into a stacked form rather than open form. These FRET measurements were build four models for Holliday Junction, an interaction stoichiometry 2 1. followed by molecular dynamics simulation ensure energetically stable. The three stable included bound major groove, minor face face. fourth model, which contained junction, though stable, did not agree data acquired system, therefore considered plausible. To distinguish between these further needed narrow possible orientations address function new, migrating way being created characterized. will be analyzed ions possibly well compare characteristics stationary previous experiments. We also examining free energy both mobile immobile analyze stability each construct on their own when complexed HU.