Exploring DNA damage repair through new angles: how the flexibility of DNA affects RAD51 and homologous repair

Exploring DNA damage repair through new angles: how the flexibility of DNA affects RAD51 and homologous repair

An organism’s genome, encoding all the genes and proteins used by an organism for life, is composed of DNA sequences. As it is passed down from generation to generation, the genome needs to be copied and maintained with as little error as possible.

Damage to DNA, such as through double-strand breaks (DSBs), can lead to genome instability and tumorigenesis if left unrepaired. The best error-free repair mechanism, homologous recombination (HR), requires the creation of single-stranded DNA (ssDNA) at the damaged site. ssDNA is rapidly recognized by RAD51, a recombinase protein that catalyses HR-mediated repair. However, exactly how RAD51 preferentially binds to ssDNA over dsDNA is unknown.

The Esashi and Dushek labs worked together to tackle this question. Collaborating with colleagues from the Department of Chemistry and the University of California, Irvine, Federico Paoletti from the Esashi lab explored the problem from a new angle: the difference between the flexibility of ss- and dsDNA. 

Federico and colleagues used surface plasmon resonance and small-angle X-ray scattering to measure the kinetics of RAD51 binding and the flexibility of different DNA substrates, respectively. Combined with mathematical modeling, the interdisciplinary collaborators were able to show that RAD51 is a mechano-sensor, able to polymerize faster on more flexible DNA. While thermodynamically counterintuitive, as stably bound ssDNA has less entropy than unfettered ssDNA, the investigators show that the entropic penalty is offset by the strong RAD51 self-interaction. They also demonstrate that RAD51 binds to DNA through a two-step “Bend-to-Capture” interaction, which is facilitated by more flexible DNA.

In this way, RAD51 is able to rapidly accumulate at sites of DNA damage to start HR repair, and could potentially explain some previously unexplained phenomenon, such as the accumulation of DNA damage at “stiff DNA,” such as poly-A rich regions of the genome.

 

Derek Xu

Federico P, El-Sagheer AH, Allard J, Brown T, Dushek O, Esashi F (2020).

EMBO 39(7):e103002. doi: 10.15252/embj.2019103002.