The subject of my research at USP is the chemistry of DNA rearrangements and DNA-protein interactions. Currently, we are investigating Integration Host Factor (IHF), a protein that bends DNA. IHF bends DNA in order to allow other proteins to interact with DNA sequences that are well separated on a linear DNA molecule. For example, with the integrase protein of bacteriophage lambda, IHF works to create a structure that looks like this:



We have developed a fluorescence based assay that allows us to measure DNA bending in real time. Fluorescent dyes were placed at the ends of a piece of DNA containing an IHF recognition sequence. The bending of the DNA brings the dyes in close proximity, causing a change in the relative intensity of the fluorescence from the two dyes caused by fluorescence resonance energy transfer:

We will use this system to determine many properties of the IHF-DNA interaction, including measurements of the rigidity of the bent DNA, influences of DNA sequence changes and protein mutations on the magnitude of the bend, and speed with which this complex can form.

‡ Undergraduate Student
* Graduate Student

R. Sha, F. Liu, M. F. Bruist, and N. C. Seeman, 1999, "Parallel Helical Domains in DNA Branched Junctions Containing 5',5' and 3',3' Linkages," Biochemistry, 38, 2832.

M.F. Bruist, 1998, "A Simple Demonstration of How Intermolecular Forces Make DNA Helical," J. Chem. Ed., 75, 53.

M.F. Bruist, 1998, "Use of a Spreadsheet to Simulate Enzyme Kinetics," J. Chem. Ed., 75, 372-375.

A.W. Kirby‡, M.N. Gaskin‡, M.A. Antezana‡, S.J. Goodman‡, E. Myers, and M.F. Bruist, 1997 "Triple-Helical DNA as a Reversible Block of the Branch Point in a Partially Symmetric DNA Four-Arm Junctions," J. Mol. Bio. 271, 349-361.

E. Myers and M.F. Bruist, 1997, "Why a Particle Physicist is Interested in DNA Branch Migration," Nuclear Physics B (Proc. Suppl.) 53, 856-858.

R.L. Patsey and M.F. Bruist, 1995, "Characterization of the Interaction between the Lambda Intasome and att B," J. Mol. Biol., 252, 47-58.