# Variable Inhibition of DNA Unwinding Rates Catalyzed by the SARS-CoV-2 Helicase Nsp13 by Structurally Distinct Single DNA Lesions

## TL;DR

This study examines how different DNA lesions affect the DNA unwinding activity of the SARS-CoV-2 helicase Nsp13, finding that some lesions strongly inhibit its processivity.

## Contribution

The study reveals that DNA lesions inhibit Nsp13 helicase activity differently, with processivity being a more sensitive measure than unwinding rate constants.

## Key findings

- B[a]P adducts reduced unwinding rate constants by up to ~15x, while photolesions reduced them by ~2–5x.
- A minor-groove-oriented B[a]P adduct reduced processivity by ~11%, while an intercalated adduct reduced it by ~67%.
- The CPD photolesion showed the lowest processivity (~90% reduction) despite having the highest unwinding rate constant.

## Abstract

The SARS-CoV-2 helicase, non-structural protein 13 (Nsp13), plays an essential role in viral replication, translocating in the 5′ → 3′ direction as it unwinds double-stranded RNA/DNA. We investigated the impact of structurally distinct DNA lesions on DNA unwinding catalyzed by Nsp13. The selected lesions include two benzo[a]pyrene (B[a]P)-derived dG adducts, the UV-induced cyclobutane pyrimidine dimer (CPD), and the pyrimidine (6–4) pyrimidone (6–4PP) photolesion. The experimentally observed unwinding rate constants (kobs) and processivities (P) were examined. Relative to undamaged DNA, the kobs values were diminished by factors of up to ~15 for B[a]P adducts but only by factors of ~2–5 for photolesions. A minor-groove-oriented B[a]P adduct showed the smallest impact on P, which decreased by ~11% compared to unmodified DNA, while an intercalated one reduced P by ~67%. However, the photolesions showed a greater impact on the processivities; notably, the CPD, with the highest kobs value, exhibited the lowest P, which was reduced by ~90%. Our findings thus show that DNA unwinding efficiencies are lesion-dependent and most strongly inhibited by the CPD, leading to the conclusion that processivity is a better measure of DNA lesions’ inhibitory effects than unwinding rate constants.