The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to...

Area of Science:

• Molecular Biology
• Structural Biology
• Virology

Background:

• The SARS-CoV-2 genome contains structured RNA elements crucial for viral function.
• Understanding the structure of these elements, like the 5'-terminal stem loop SL1, is vital for therapeutic development.

Purpose of the Study:

• To elucidate the solution structure of the SARS-CoV-2 5'-terminal stem loop SL1.
• To identify functional regions within SL1, particularly binding sites for small molecules.
• To investigate pH-dependent structural features and their implications.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy for solution structure determination.
• Residual dipolar coupling (RDC) and small-angle X-ray scattering (SAXS) for conformational validation.
• pH-differential mutational profiling (PD-MaP) for assessing pH sensitivity.

Main Results:

• The solution structure of SL1 reveals two helical elements and non-canonical apical and internal loops.
• The internal loop of SL1 is identified as the primary binding site for low molecular weight fragments.
• An A12-C28 interaction stabilizes the internal loop via a transient A+•C base pair, shifting adenosine's pKa.
• PD-MaP analysis confirmed SL1 findings and identified other pH-sensitive sites in the 5'-UTR.

Conclusions:

• The structure of SL1 and its internal loop provide a target for antiviral drug design.
• The pH-dependent stabilization of the internal loop suggests a regulatory mechanism for viral RNA.
• The study highlights the utility of integrated structural and biochemical methods for probing viral RNA structures.