Modifications of the chromophore of Spinach aptamer based on QM:MM calculations

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• 作者：Katarína Skúpa ; Ján Urban
• 关键词：Fluorescence ; ONIOM ; Redshift ; RNA aptamer ; TD ; DFT
• 刊名：Journal of Molecular Modeling
• 出版年：2017
• 出版时间：February 2017
• 年：2017
• 卷：23
• 期：2
• 全文大小：
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Computer Applications in Chemistry; Molecular Medicine; Computer Appl. in Life Sciences; Characterization and Evaluation of Materials; Theoretical and Computational Chemistry;
• 出版者：Springer Berlin Heidelberg
• ISSN：0948-5023
• 卷排序：23

文摘

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.