The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application.
Biophys Chem
; 267: 106492, 2020 12.
Article
en En
| MEDLINE
| ID: mdl-33035750
ABSTRACT
Aptamers are oligonucleotides and peptides around 15-100 bases in length and are suitable as detection probes or as therapeutics molecules. There are growing interests in the aptamer screening approach through computational simulation methods. DNA and RNA modelling lacks of validation on their predicted 3D structures due to less number of validation tools, unlike protein structures. We suggest an approach to design the stem-loop/hairpin for the three dimensional structure of DNA aptamers through serial applications of computational prediction methods by comparing the simulated structures with the experimental data deposited in PDB Data bank, followed by MD simulations. The result shows minimal structural differences were observed between the designed and the original NMR aptamers, and the stem-loop conformational structures were also retained during the MD thus suggesting the proposed aptamers designing methods are able to synthesize a high quality molecular structure of hairpin aptamers, comparable to the NMR structures.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
ADN
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Aptámeros de Nucleótidos
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Simulación de Dinámica Molecular
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Química Computacional
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Biophys Chem
Año:
2020
Tipo del documento:
Article