Thermodynamic analysis of SL1 1x2 internal loop in SARS‐CoV‐2

Abstract

SARS‐CoV‐2 utilizes a positive‐sense single stranded RNA as its genomic material. This single stranded mRNA hijacks the host cell’s ribosome to translate its own proteins. Upon infection of a host cell, SARS‐CoV‐2 produces polyprotein 1ab which is then cleaved into 16 non‐structural proteins. Non‐structural protein 1 (Nsp1) inhibits host cell translation by binding to the 40S ribosomal subunit. Stem loop 1(SL1) in the 5’‐UTR of the mRNA mediates the binding of Nsp1 to the ribosome. SARS‐CoV‐2 specifically contains a 1x2 internal loop within the SL1 that is not seen in other coronaviruses. In this study, we are examining the thermodynamic properties of the 1x2 internal loop of SL1. UV‐visible thermal melts and isothermal titration calorimetry (ITC) were performed on various DNA and RNA constructs containing the 1x2 internal loop in SL1 in the presence of 1 M KCl or 10 mM magnesium chloride at two different pHs. Initial results show additional base pairing at lower pH in 1 M KCl buffer, indicating the formation of an A+•C base pair.