Design and characterization of symmetric nucleic acids via molecular dynamics simulations.
Biopolymers
; 107(4)2017 Apr.
Article
em En
| MEDLINE
| ID: mdl-27861723
ABSTRACT
Asymmetry (5'â3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C3' to C2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C5' to C2' ) can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Ácidos Nucleicos
/
Simulação de Dinâmica Molecular
Idioma:
En
Revista:
Biopolymers
Ano de publicação:
2017
Tipo de documento:
Article
País de afiliação:
Índia