In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form.
Nucleic Acids Res
; 37(16): 5568-77, 2009 Sep.
Article
em En
| MEDLINE
| ID: mdl-19586933
ABSTRACT
To understand how underwinding and overwinding the DNA helix affects its structure, we simulated 19 independent DNA systems with fixed degrees of twist using molecular dynamics in a system that does not allow writhe. Underwinding DNA induced spontaneous, sequence-dependent base flipping and local denaturation, while overwinding DNA induced the formation of Pauling-like DNA (P-DNA). The winding resulted in a bimodal state simultaneously including local structural failure and B-form DNA for both underwinding and extreme overwinding. Our simulations suggest that base flipping and local denaturation may provide a landscape influencing protein recognition of DNA sequence to affect, for examples, replication, transcription and recombination. Additionally, our findings help explain results from single-molecule experiments and demonstrate that elastic rod models are strictly valid on average only for unstressed or overwound DNA up to P-DNA formation. Finally, our data support a model in which base flipping can result from torsional stress.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
DNA
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2009
Tipo de documento:
Article
País de afiliação:
Estados Unidos