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Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach
Li, Xin1; Chung, Lung Wa2; Li, Guohui1
Source PublicationJOURNAL OF CHEMICAL THEORY AND COMPUTATION
2016-11-01
ISSN1549-9618
DOI10.1021/acs.jctc.6b00578
Volume12Issue:11Pages:5453-5464
Indexed BySCI
SubtypeArticle
WOS HeadingsScience & Technology ; Physical Sciences
WOS SubjectChemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS Research AreaChemistry ; Physics
WOS KeywordDENSITY-FUNCTIONAL THEORY ; 2ND-ORDER PERTURBATION-THEORY ; POTENTIAL-ENERGY LANDSCAPE ; SAC CI THEORIES ; PROTEIN CHROMOPHORE ; EXCITED-STATES ; CLUSTER-EXPANSION ; GFP CHROMOPHORE ; WAVE-FUNCTION ; NUCLEIC-ACIDS
AbstractFluorescent RNA aptamer Spinach can bind and activate a green fluorescent protein (GFP)-like chromophore (an anionic DFHBDI chromophore) displaying green fluorescence. Spectroscopic properties, spectral tuning, and the photoisomerization mechanism in the Spinach-DFHBDI complex have been investigated by high-level QM and hybrid ONIOM(QM:AMBER) methods (QM method: (TD)DFT, SF-BHHLYP, SAC-CI, LT-DF-LCC2, CASSCF, or MS-CASPT2), as well as classical Molecular dynamics (MD) simulations. First, our benchmark calculations have shown that TD-DFT and spin-flip (SF) TD-DFT (SF-BHHLYP) failed to give a satisfactory description of absorption and emission of the anionic DFHBDI chromophore. Comparatively, SAC-CI, LT-DF-LCC2, and MSCASPT2 can give more reliable transition energies and are mainly used to further study the spectra of the anionic DFHBDI chromophore in Spinach. The RNA environmental effects on the spectral tuning and the photoisomerization mechanism have been elucidated. Our simulations show that interactions of the anionic cis-DFHBDI chromophore with two G-quadruplexes as well as a UAU base triple suppress photoisomerization of DFHBDI. In addition, strong hydrogen bonds between the anionic cis-DFHBDI chromophore and nearby nucleotides facilitate its binding to Spinach and further inhibit the cis-trans photoisomerization of DFHBDI. Solvent molecules, ions, and loss of key hydrogen bonds with nearby nucleotides could induce dissociation of the anionic trans-DFHBDI chromophore from the binding site. These results provide new insights into fluorescent RNA Spinach and may help rational design of other fluorescent RNAs.
Language英语
WOS IDWOS:000387519400021
PublisherAMER CHEMICAL SOC
Citation statistics
Cited Times:4[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/169709
Collection中国科学院大连化学物理研究所
Corresponding AuthorLi, Xin; Chung, Lung Wa; Li, Guohui
Affiliation1.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Peoples R China
2.South Univ Sci & Technol China, Dept Chem, Shenzhen 518055, Peoples R China
Recommended Citation
GB/T 7714
Li, Xin,Chung, Lung Wa,Li, Guohui. Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2016,12(11):5453-5464.
APA Li, Xin,Chung, Lung Wa,&Li, Guohui.(2016).Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,12(11),5453-5464.
MLA Li, Xin,et al."Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12.11(2016):5453-5464.
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