Modifications of the chromophore of Spinach aptamer based on QM:MM calculations.
J Mol Model
; 23(2): 46, 2017 Feb.
Article
en En
| MEDLINE
| ID: mdl-28154983
ABSTRACT
Spinach aptamer was developed as an RNA analog of the green fluorescent protein. The aptamer interacts with its ligand and modifies its electronic spectrum so that it fluoresces brightly at the wavelength of 501 nm. Song et al. investigated modifications of the ligand in their experimental study and found a molecule emitting at 523 nm upon creating a complex with the Spinach aptamer. The crystal structure of the aptamer in complex with its original ligand has been published, which enabled us to study the system computationally. In this article, we suggest several new modifications of the ligand that shift the emission maximum of the complex to even longer wavelengths. Our results are based on combined quantum mechanical/molecular mechanical calculations with DFT method used for geometry optimization and TD-DFT for calculations of absorption and emission energies.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Teoría Cuántica
/
Spinacia oleracea
/
Aptámeros de Nucleótidos
/
Simulación de Dinámica Molecular
Idioma:
En
Revista:
J Mol Model
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2017
Tipo del documento:
Article
País de afiliación:
Eslovaquia