Energy Landscapes of Mini-Dumbbell DNA Octanucleotides

Single-stranded DNA structures play a significant role in biological systems, in particular during replication, translation, and DNA repair. Tracts of simple repetitive DNA are associated with slipped-strand mispairing, which can lead to genetic diseases. Recent NMR studies of TTTA and CCTG repeats...

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Bibliographic Details
Published in:Journal of chemical theory and computation 2018-07, Vol.14 (7), p.3870-3876
Main Authors: Klimavicz, James S, Röder, Konstantin, Wales, David J
Format: Article
Language:English
Subjects:
Base Sequence
Bonding strength
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
Frameshift Mutation
Models, Molecular
Mutation
NMR
Nuclear magnetic resonance
Nucleic Acid Conformation
Oligonucleotides - chemistry
Oligonucleotides - genetics
Thermodynamics
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Summary:Single-stranded DNA structures play a significant role in biological systems, in particular during replication, translation, and DNA repair. Tracts of simple repetitive DNA are associated with slipped-strand mispairing, which can lead to genetic diseases. Recent NMR studies of TTTA and CCTG repeats have shown that these sequences form mini-dumbbells (MDBs), leading to frameshift mutations. Here we explore the energy landscapes of (CCTG)2 and (TTTA)2, which are currently the smallest known molecules to form MDBs. While (CCTG)2 MDBs are stable, (TTTA)2 exhibits numerous other structures with lower energies. A key factor identified in the stabilization of MDB structures is the bonding strength between residues 1 and 4, and 5 and 8.
ISSN:1549-9618
1549-9626
DOI:10.1021/acs.jctc.8b00262