Kinks, Bends & Repairs: DNA-Bending Protein Studied

DNA, deoxyribonucleic acid, forms a blueprint of life represented by billions of chemical “base-pairs.” But mismatch just one of these complementary pairs, and the genetic code gets altered. While certain proteins can diffuse along DNA strands to search for damaged sites, how they find them — and how quickly — remain unanswered questions.

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.

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