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Chan RCT, Ma C, Wong AKW, Chan CTL, Chow JCL, Kwok WM. Dual Time-Scale Proton Transfer and High-Energy, Long-Lived Excitons Unveiled by Broadband Ultrafast Time-Resolved Fluorescence in Adenine-Uracil RNA Duplexes. J Phys Chem Lett 2022; 13:302-311. [PMID: 34978832 DOI: 10.1021/acs.jpclett.1c03553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In contrast to the immense amount of research on electronically excited DNA, surprisingly little has been done about the excited states of RNA. Herein, we demonstrate an ultrafast broadband time-resolved fluorescence and fluorescence anisotropy study to probe directly the intrinsic fluorescence and overall dynamics of the fluorescence from a homopolymeric adenine·uracil RNA duplex adopting the A-form structure. The results unveiled complex deactivation through distinctive multichannels mediated by states of varied energy, a character of charge transfer, and a lifetime from sub-picosecond to nanoseconds. In particular, we observed an unprecedented kinetic isotopic effect and participation of unusual proton transfer from states in two discrete energies and time domains. We also identified a high-energy nanosecond emission that we attributed to its fluorescence anisotropy to long-lived weakly emissive excitons not reported in DNA. These distinguishing features originate from the stacking, pairing, and local hydration environment specific to the A-form conformation of the adenine·uracil double helix.
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Affiliation(s)
- Ruth Chau-Ting Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, 518071, Shenzhen, Guangdong, P. R. China
| | - Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, 518071, Shenzhen, Guangdong, P. R. China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Chris Tsz-Leung Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Joshua Chiu-Lok Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
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Zhang Y, de La Harpe K, Hariharan M, Kohler B. Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent. Faraday Discuss 2019; 207:267-282. [PMID: 29383346 DOI: 10.1039/c7fd00205j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA.
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Hernández FJ, Bonafé FP, Aradi B, Frauenheim T, Sánchez CG. Simulation of Impulsive Vibrational Spectroscopy. J Phys Chem A 2019; 123:2065-2072. [DOI: 10.1021/acs.jpca.9b00307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Federico J. Hernández
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
| | - Franco P. Bonafé
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universität Bremen, Bremen 28359, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, Universität Bremen, Bremen 28359, Germany
| | - Cristián G. Sánchez
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
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de La Harpe K, Kohl FR, Zhang Y, Kohler B. Excited-State Dynamics of a DNA Duplex in a Deep Eutectic Solvent Probed by Femtosecond Time-Resolved IR Spectroscopy. J Phys Chem A 2018; 122:2437-2444. [DOI: 10.1021/acs.jpca.7b12677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Kimberly de La Harpe
- Department of Physics, United State Air Force Academy, U.S. Air Force Academy, Colorado 80840, United States
| | - Forrest R. Kohl
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Gobrogge CA, Kong VA, Walker RA. Temperature-Dependent Partitioning of C152 in Binary Phosphatidylcholine Membranes and Mixed Phosphatidylcholine/Phosphatidylethanolamine Membranes. J Phys Chem B 2017; 121:7889-7898. [DOI: 10.1021/acs.jpcb.7b04831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Christine A. Gobrogge
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Victoria A. Kong
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Robert A. Walker
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Remington JM, Philip AM, Hariharan M, Kohler B. On the origin of multiexponential fluorescence decays from 2-aminopurine-labeled dinucleotides. J Chem Phys 2017; 145:155101. [PMID: 27782452 DOI: 10.1063/1.4964718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The fluorescent probe 2-aminopurine (2Ap) has been used for decades to study local conformational fluctuations in DNA. Steady-state and time-resolved measurements of 2Ap fluorescence have been used to predict specific conformational states through suitable modeling of the quenching of the fluorescence of a 2Ap residue incorporated site-specifically into a DNA strand. The success of this approach has been limited by a lack of understanding of the precise factors responsible for the complex, multiexponential decays observed experimentally. In this study, dinucleotides composed of 2Ap and adenine were studied by the time-correlated single-photon counting technique to investigate the causes of heterogeneous emission kinetics. Contrary to previous reports, we argue that emission from 2Ap that is stacked with a neighboring base contributes negligibly to the emission signals recorded more than 50 ps after excitation, which are instead dominated by emission from unstacked 2Ap. We find that the decay kinetics can be modeled using a continuous lifetime distribution, which arises from the inherent distance dependence of electron transfer rates without the need to postulate a small number of discrete states with decay times derived from multiexponential fits. These results offer a new perspective on the quenching of 2Ap fluorescence and expand the information that can be obtained from experiments.
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Affiliation(s)
- Jacob M Remington
- Department of Chemistry, Montana State University, Bozeman, Montana 59715, USA
| | - Abbey M Philip
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Sreekaryam, Thiruvananthapuram, Kerala 695016, India
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Sreekaryam, Thiruvananthapuram, Kerala 695016, India
| | - Bern Kohler
- Department of Chemistry, Montana State University, Bozeman, Montana 59715, USA
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