The regulatory mechanisms of SARS-CoV-2 N protein helicase and its annealing activity.

The nucleocapsid (N) protein of SARS-CoV-2 performs multiple functions essential for viral replication and host adaptation. Here, we identify ionic strength as a critical determinant of its dual nucleic acid-manipulating activities. Under low-salt conditions (≤100 mM NaCl), SARS-CoV-2 N primarily promotes strand annealing, whereas at high ionic strength (≥300 mM NaCl), its helicase activity is additively enhanced. SARS-CoV-2 N also preferentially acts on DNA rather than RNA substrates and modulates the helicase activity of Nsp13 in an ion-dependent manner-inhibiting it under low-salt conditions but enhancing it under high-salt conditions. These findings reveal an ion concentration-dependent regulatory mechanism that enables SARS-CoV-2 N to dynamically switch between distinct biochemical states, thereby supporting viral adaptability and providing new insights into antiviral development.