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Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy

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Photoinduced Phenomena in Nucleic Acids II

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 356))

Abstract

Ultrafast laser experiments on carefully selected DNA model compounds probe the effects of base stacking, base pairing, and structural disorder on excited electronic states formed by UV absorption in single and double DNA strands. Direct π-orbital overlap between two stacked bases in a dinucleotide or in a longer single strand creates new excited states that decay orders of magnitude more slowly than the generally subpicosecond excited states of monomeric bases. Half or more of all excited states in single strands decay in this manner. Ultrafast mid-IR transient absorption experiments reveal that the long-lived excited states in a number of model compounds are charge transfer states formed by interbase electron transfer, which subsequently decay by charge recombination. The lifetimes of the charge transfer states are surprisingly independent of how the stacked bases are oriented, but disruption of π-stacking, either by elevating temperature or by adding a denaturing co-solvent, completely eliminates this decay channel. Time-resolved emission measurements support the conclusion that these states are populated very rapidly from initial excitons. These experiments also reveal the existence of populations of emissive excited states that decay on the nanosecond time scale. The quantum yield of these states is very small for UVB/UVC excitation, but increases at UVA wavelengths. In double strands, hydrogen bonding between bases perturbs, but does not quench, the long-lived excited states. Kinetic isotope effects on the excited-state dynamics suggest that intrastrand electron transfer may couple to interstrand proton transfer. By revealing how structure and non-covalent interactions affect excited-state dynamics, on-going experimental and theoretical studies of excited states in DNA strands can advance understanding of fundamental photophysics in other nanoscale systems.

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Abbreviations

2AP:

2-Aminopurine

8-oxo-dGuo:

8-Oxo-7,8-dihydro-2′-deoxyguanosine

A:

Adenine

AMP:

Adenosine 5′-monophosphate

ATP:

Adenosine 5′-triphosphate

C:

Cytosine

CASPT2:

Complete active space with second-order perturbation theory

CD:

Circular dichroism

CI:

Conical intersection

CPD:

Cyclobutane pyrimidine dimer

CR:

Charge recombination

CT:

Charge transfer

dAMP:

2′-Deoxyadenosine 5′-monophosphate

DFT:

Density functional theory

ECCD:

Exciton-coupled circular dichroism

ESA:

Excited-state absorption

ESPT:

Excited-state proton transfer

ET:

Electron transfer

FC:

Franck–Condon

FTIR:

Fourier-transformed infrared spectroscopy

FU:

Fluorescence upconversion

G:

Guanine

GSB:

Ground-state bleaching

IC:

Internal conversion

IET:

Intermolecular energy transfer

KIE:

Kinetic isotope effect

MCT:

Mercury-cadmium-telluride

O:

8-Oxo-7,8-dihydro-2′-deoxyguanosine (in a DNA sequence)

PCET:

Proton-coupled electron transfer

PMT:

Photomultiplier tube

PT:

Proton transfer

QM/MM:

Quantum mechanical/molecular mechanical

RI-ADC(2):

Algebraic diagrammatic construction to second-order with resolution of the identity

T:

Thymine

TA:

Transient absorption

TCSPC:

Time-correlated single photon counting

TD-DFT:

Time-dependent density functional theory

TRIR:

Time-resolved infrared spectroscopy

U:

Uracil

UV:

Ultraviolet

VC:

Vibrational cooling

VUV:

Vacuum ultraviolet

WC:

Watson–Crick

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Acknowledgments

This work has been supported by grants from the Chemical Structure, Dynamics and Mechanisms Program of the National Science Foundation and from the NASA Astrobiology Program. Many current and former students, postdoctoral researchers, and collaborators have contributed to this work over the past 15 years. Their efforts, which are documented in the papers cited in this chapter, have been indispensible to the success of this work.

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA

    Jinquan Chen, Yuyuan Zhang & Bern Kohler

  2. Department of Chemistry, Emory University, Atlanta, GA, 30322, USA

    Jinquan Chen

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  1. Jinquan Chen
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  2. Yuyuan Zhang
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  3. Bern Kohler
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Correspondence to Bern Kohler .

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  1. Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany

    Mario Barbatti

  2. Institute of Chemistry, University of São Paulo, São Paulo, Brazil

    Antonio Carlos Borin

  3. Department of Physics and Astronomy, The University of Georgia, Athens, Georgia, USA

    Susanne Ullrich

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Chen, J., Zhang, Y., Kohler, B. (2014). Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy. In: Barbatti, M., Borin, A., Ullrich, S. (eds) Photoinduced Phenomena in Nucleic Acids II. Topics in Current Chemistry, vol 356. Springer, Cham. https://doi.org/10.1007/128_2014_570

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