(Excerpted from abstract) Complex protein-nucleic acid interactions are essential to many biological processes. Often proteins that are far apart in the sequence of the nucleic acid must be brought close together in space. Specific proteins achieve this by bending the nucleic acid between the bound proteins. The flexibility of bent DNA will be investigated using FRET. In a rigidly bent DNA-protein complex, energy transfer reveals a narrow distribution of distances between dyes attached to the ends of the DNA. In a flexible structure, a wide range of distances is detected. First a model system consisting of a family of DNAs with varying bends and flexibility will be developed to establish the sensitivity of the energy transfer techniques. Then the dynamics of the DNA in a complex containing integration host factor (IHF) will be studied. On the basis of preliminary results and reports in the literature, it is hypothesized that IHF makes a flexible bend that depends on DNA sequence. The effects of sequence changes on bending will be assessed. Molecular dynamics calculations will be employed to determine whether the bend ranges of the IHF-DNA complex can be predicted. If initial tries are successful, molecular dynamics calculations will be used to decode atomic details and dynamics of DNA bending by IHF.
