University of Illinois at Chicago physics professor Anjum Ansari hopes to find some answers, supported by a new five-year, $1.14 million National Science Foundation grant.
Ansari and her UIC laboratory team are studying two classes of DNA-bending proteins. One is a "damage recognition" protein that recognizes a mismatched base-pair, binds to that site, and then signals for helper proteins to gather and aid in the repair. The other protein is an enzyme that targets invader DNA, cutting it apart.
Ansari is collaborating with other researchers at UIC, University of Pittsburgh, Wesleyan University and Arizona State University to study different aspects of these proteins.
Ansari's lab is one of only a few equipped to monitor the dynamics of DNA bending in complex with these proteins on timescales ranging from several milliseconds down to as fast hundreds of nanoseconds -- or less than one-millionth of a second.
The instruments in her lab are designed to look at macromolecules as they change their shapes within this time window -- "which is precisely the time window in which proteins recognize their specific binding sites," she said.
Researchers have made measurements at the longer timescales on which proteins diffuse along DNA in search of target sites Ansari said, "but not much is known about the timescale of the recognition process, for virtually any protein."
Her lab's experiments "are designed to make time-resolved measurements of how a protein, when it reaches its target site, transforms the DNA from a conformation in which it is straight to one which is kinked and bent," Ansari said, and to "learn about the recognition mechanism by watching the dynamics -- or time scales -- on which this happens."
Many other biophysical questions about this protein-DNA interaction will be investigated by the team, including the presence of subtle kinks in DNA structure at the damage sites in the absence of a bound protein.
"Clearly, the kinked conformation of the DNA facilitates the [protein's] recognition that something is wrong at the site," Ansari said. "The question we're addressing is, 'Is it the protein that bends and kinks the DNA when it reaches that site?' Or does the DNA, on its own, have a propensity to adopt these locally bent conformations because there's a mismatch -- and the protein, when it is moving along on the DNA, recognizes that something is not right at certain spots?"
DNA gets damaged in various ways -- sometimes during replication, sometimes by ultraviolet radiation, and sometimes through more subtle cellular processes. Damaged DNA can lead to serious diseases, so a better understanding of how proteins make repairs can help when designing new and better therapies.
Ansari will incorporate some aspects of her research in undergraduate physics labs that she plans to develop as part of a new biophysics curriculum at UIC.
Paul Francuch | Newswise Science News
Newly designed molecule binds nitrogen
23.02.2018 | Julius-Maximilians-Universität Würzburg
Atomic Design by Water
23.02.2018 | Max-Planck-Institut für Eisenforschung GmbH
A newly developed laser technology has enabled physicists in the Laboratory for Attosecond Physics (jointly run by LMU Munich and the Max Planck Institute of Quantum Optics) to generate attosecond bursts of high-energy photons of unprecedented intensity. This has made it possible to observe the interaction of multiple photons in a single such pulse with electrons in the inner orbital shell of an atom.
In order to observe the ultrafast electron motion in the inner shells of atoms with short light pulses, the pulses must not only be ultrashort, but very...
A group of researchers led by Andrea Cavalleri at the Max Planck Institute for Structure and Dynamics of Matter (MPSD) in Hamburg has demonstrated a new method enabling precise measurements of the interatomic forces that hold crystalline solids together. The paper Probing the Interatomic Potential of Solids by Strong-Field Nonlinear Phononics, published online in Nature, explains how a terahertz-frequency laser pulse can drive very large deformations of the crystal.
By measuring the highly unusual atomic trajectories under extreme electromagnetic transients, the MPSD group could reconstruct how rigid the atomic bonds are...
Quantum computers may one day solve algorithmic problems which even the biggest supercomputers today can’t manage. But how do you test a quantum computer to...
For the first time, a team of researchers at the Max-Planck Institute (MPI) for Polymer Research in Mainz, Germany, has succeeded in making an integrated circuit (IC) from just a monolayer of a semiconducting polymer via a bottom-up, self-assembly approach.
In the self-assembly process, the semiconducting polymer arranges itself into an ordered monolayer in a transistor. The transistors are binary switches used...
Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale
Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...
15.02.2018 | Event News
13.02.2018 | Event News
12.02.2018 | Event News
23.02.2018 | Physics and Astronomy
23.02.2018 | Health and Medicine
23.02.2018 | Physics and Astronomy