Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase

Sean P. Carney, Wen Ma, Kevin D. Whitley, Haifeng Jia, Timothy M. Lohman, Zaida Luthey-Schulten and Yann R. Chemla ()
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Sean P. Carney: University of Illinois at Urbana-Champaign
Wen Ma: University of Illinois at Urbana-Champaign
Kevin D. Whitley: University of Illinois at Urbana-Champaign
Haifeng Jia: Washington University in St. Louis School of Medicine
Timothy M. Lohman: Washington University in St. Louis School of Medicine
Zaida Luthey-Schulten: University of Illinois at Urbana-Champaign
Yann R. Chemla: University of Illinois at Urbana-Champaign

Nature Communications, 2021, vol. 12, issue 1, 1-14

Abstract: Abstract UvrD, a model for non-hexameric Superfamily 1 helicases, utilizes ATP hydrolysis to translocate stepwise along single-stranded DNA and unwind the duplex. Previous estimates of its step size have been indirect, and a consensus on its stepping mechanism is lacking. To dissect the mechanism underlying DNA unwinding, we use optical tweezers to measure directly the stepping behavior of UvrD as it processes a DNA hairpin and show that UvrD exhibits a variable step size averaging ~3 base pairs. Analyzing stepping kinetics across ATP reveals the type and number of catalytic events that occur with different step sizes. These single-molecule data reveal a mechanism in which UvrD moves one base pair at a time but sequesters the nascent single strands, releasing them non-uniformly after a variable number of catalytic cycles. Molecular dynamics simulations point to a structural basis for this behavior, identifying the protein-DNA interactions responsible for strand sequestration. Based on structural and sequence alignment data, we propose that this stepping mechanism may be conserved among other non-hexameric helicases.

Date: 2021
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DOI: 10.1038/s41467-021-27304-6

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