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