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Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared
C P Howe1, G M Greetham2, B Procacci1
1Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
The placement of adenine-uracil (AU) base pairs in RNA and DNA tetraloop stems affects their stability and dynamics. AU base pairs accelerate melting but slow refolding, with distinct melting mechanisms observed between RNA and DNA hairpin structures.
Area of Science:
- Biophysics
- Molecular Biology
- Spectroscopy
Background:
- Ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) form complex secondary structures like hairpins.
- Tetraloops are common structural motifs in RNA, influencing stability and function.
- The sequence and composition of the stem region significantly impact hairpin dynamics.
Purpose of the Study:
- To investigate the influence of stem base sequence on the melting and refolding dynamics of RNA and DNA tetraloops.
- To compare the dynamics of RNA and DNA tetraloops with varying base pair compositions in the stem.
- To elucidate position-specific effects of adenine-uracil (AU) or adenine-thymine (AT) base pairs on hairpin stability.
Main Methods:
- Time-resolved temperature-jump/drop infrared (IR) spectroscopy was employed to monitor dynamic changes.
- Ring vibrational modes of guanine (G_R) and adenine (A_R) were used to track melting and refolding timescales.
- Three 12-nucleotide RNA hairpin sequences with a UACG tetraloop and varying stem compositions (GC-rich vs. AU-containing) were synthesized.
- Analogous DNA tetraloop (TACG) sequences were also studied for comparative analysis.
Main Results:
- Inclusion of AU/AT base pairs in the stem accelerated melting but slowed refolding compared to GC-rich stems, indicating reduced stability.
- DNA sequences exhibited faster melting (0.5–0.7 μs at 70 °C) than RNA sequences (4.3–4.4 μs at 70 °C).
- Melting initiated from the stem terminus in DNA, whereas RNA melting initiated from the loop.
- Refolding was generally similar, but specific placements of AU/AT pairs (RNA_end, DNA_loop) significantly slowed the process.
Conclusions:
- The position of AU/AT base pairs critically influences the melting and refolding pathways of RNA and DNA tetraloops.
- RNA and DNA tetraloops exhibit distinct mechanisms for conformational changes and melting initiation.
- Stem base composition plays a crucial role in determining the stability and dynamic behavior of nucleic acid hairpins.
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