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Energy Landscapes of Mini-Dumbbell DNA Octanucleotides.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Klimavicz, James S 

Abstract

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.

Description

Keywords

Base Sequence, DNA, Frameshift Mutation, Models, Molecular, Nucleic Acid Conformation, Oligonucleotides, Thermodynamics

Journal Title

J Chem Theory Comput

Conference Name

Journal ISSN

1549-9618
1549-9626

Volume Title

14

Publisher

American Chemical Society (ACS)
Sponsorship
EPSRC (1652488)
Engineering and Physical Sciences Research Council (EP/N035003/1)
PhD studentship EPSRC