Sequence Effect on the Formation of DNA Minidumbbells
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AbstractThe DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base base stacking, and hydrophobic interactions from each of the participating residues. We conclude that in the MDBs formed by tandem repeats, C G loop-closing base pairs are more stabilizing than T A loop-closing base pairs, and thymine residues in both the second and third loop positions are more stabilizing than cytosine residues. The results from this study enrich our knowledge on the sequence criteria for the formation of MDBs, paving a path for better exploring their potential roles in biological systems and DNA nanotechnology.
All Author(s) ListLiu, Lam
Journal nameThe journal of physical chemistry. B
Year2017
Month11
Day16
Volume Number121
Issue Number45
PublisherAmerican Chemical Society
Pages10338 - 10343
ISSN1520-6106
LanguagesEnglish-United Kingdom

Last updated on 2021-17-09 at 23:48