Structural basis of DNA aptamer A58 targeting the N-terminal domain of sarbecoviruses nucleocapsid protein

TL;DR

This paper reveals how a DNA aptamer called A58 binds to a key part of the coronavirus nucleocapsid protein, potentially offering a broad-spectrum antiviral treatment.

Contribution

The study provides the first crystal structure of DNA aptamer A58 bound to the N-terminal domain of the SARS-CoV-2 nucleocapsid protein, revealing its unique binding mechanism.

Findings

A58 binds to the N-NTD via a three-tiered stem-loop structure with specific octanucleotide motifs.

A58 inhibits the N-NTD's binding to viral RNA, disrupting interactions important for immune responses.

A58 shows broad-spectrum activity against N proteins from SARS-CoV-2 variants and related sarbecoviruses.

Abstract

In the post-pandemic era, the persistent threat of coronaviruses demands broad-spectrum antiviral therapeutic strategies. The SARS-CoV-2 nucleocapsid protein (N protein), an essential factor for genome packaging and immune modulation, poses a promising antiviral target. Here, we determined the crystal structure of the DNA aptamer A58-T10 in complex with the N-terminal domain of the N protein (N-NTD). A58-T10 binds to the N-NTD via a unique three-tiered stem-loop that interacts with the nucleic acid-binding site of N-NTD through extensive hydrogen bonding and stacking. Structural analysis reveals that A58 contains two stem-loops with octanucleotide motifs (5′-11ACCGGATT19-3′ and 5′-26ATCGGATT33-3′) that specifically recognize N-NTD. Functionally, A58 inhibits N-NTD’s binding to viral RNA, disrupting N protein-host cell interactions involved in immune responses. Notably, A58 exhibits broad-spectrum binding activity against N proteins from SARS-CoV-2 variants and related sarbecoviruses. These findings elucidate the specific interaction mechanism between A58 and N-NTD, highlighting its potential as an anti-sarbecovirus agent.

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