biostudies-literatureUnknown127(7)Howe CPScience and Technology Facilities CouncilUniversity of YorkTime-resolved temperature-jump/drop infrared (IR) spectroscopy has been used to measure the impact of stem base sequence on the melting and refolding dynamics of ribonucleic acid (RNA) tetraloops. A series of three 12-nucleotide RNA hairpin sequences were studied, each featuring a UACG tetraloop motif and a double-stranded stem containing four base pairs. In each case, the stem comprised three GC pairs plus a single AU base pair inserted at the closing point of the loop (RNA_loop), in the middle of the stem (RNA_mid), or at the stem terminus (RNA_end). Results from analogous DNA tetraloop (TACG) sequences were also obtained. Inclusion of AU or AT base pairs in the stem leads to faster melting of the stem-loop structure compared to a stem sequence featuring fouThe journal of physical chemistry. B1586-1597https://www.ebi.ac.uk/biostudies/studies/S-EPMC9969394biostudies-literatureSequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy.PMC9969394Greetham GMHunt NTParker AWHowe CPProcacci BfalseSequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy.Time-resolved temperature-jump/drop infrared (IR) spectroscopy has been used to measure the impact of stem base sequence on the melting and refolding dynamics of ribonucleic acid (RNA) tetraloops. A series of three 12-nucleotide RNA hairpin sequences were studied, each featuring a UACG tetraloop motif and a double-stranded stem containing four base pairs. In each case, the stem comprised three GC pairs plus a single AU base pair inserted at the closing point of the loop (RNA_loop), in the middle of the stem (RNA_mid), or at the stem terminus (RNA_end). Results from analogous DNA tetraloop (TACG) sequences were also obtained. Inclusion of AU or AT base pairs in the stem leads to faster melting of the stem-loop structure compared to a stem sequence featuring fou2023-01-01T00:00:00Z2023 Feb2025-05-29T19:43:14.013Z2025-05-29T19:43:14.013ZS-EPMC99693943678717710.1021/acs.jpcb.2c08709