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Photochemistry of Nucleic Acid Bases and Their Thio- and Aza-Analogues in Solution

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Photoinduced Phenomena in Nucleic Acids I

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 355))

Abstract

The steady-state and time-resolved photochemistry of the natural nucleic acid bases and their sulfur- and nitrogen-substituted analogues in solution is reviewed. Emphasis is given to the experimental studies performed over the last 3–5 years that showcase topical areas of scientific inquiry and those that require further scrutiny. Significant progress has been made toward mapping the radiative and nonradiative decay pathways of nucleic acid bases. There is a consensus that ultrafast internal conversion to the ground state is the primary relaxation pathway in the nucleic acid bases, whereas the mechanism of this relaxation and the level of participation of the 1πσ*, 1 nπ*, and 3ππ* states are still matters of debate. Although impressive research has been performed in recent years, the microscopic mechanism(s) by which the nucleic acid bases dissipate excess vibrational energy to their environment, and the role of the N-glycosidic group in this and in other nonradiative decay pathways, are still poorly understood. The simple replacement of a single atom in a nucleobase with a sulfur or nitrogen atom severely restricts access to the conical intersections responsible for the intrinsic internal conversion pathways to the ground state in the nucleic acid bases. It also enhances access to ultrafast and efficient intersystem crossing pathways that populate the triplet manifold in yields close to unity. Determining the coupled nuclear and electronic pathways responsible for the significantly different photochemistry in these nucleic acid base analogues serves as a convenient platform to examine the current state of knowledge regarding the photodynamic properties of the DNA and RNA bases from both experimental and computational perspectives. Further investigations should also aid in forecasting the prospective use of sulfur- and nitrogen-substituted base analogues in photochemotherapeutic applications.

Lara Martínez-Fernández participated as a visiting graduate research assistant.

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Notes

  1. 1.

    This is contrary to the accepted use of the term. See, for instance, International Union of Pure Applied Chemistry. Division of Organic Chemistry. Commission on Nomenclature of Organic Chemistry. A Guide to IUPAC Nomenclature of Organic Compounds, Recommendations 1993; R. Panico, W. H. Powell, J.-C. Richer, eds.; Blackwell Scientific Publications, Oxford, UK (1993).

  2. 2.

    Usually fractional amplitudes are reported. The fluorescence amplitudes stated here are taken as given in [212].

Abbreviations

2tCyd:

2-Thiocytidine

2tCyt:

2-Thiocytosine

2t-dThd:

2-Thiodeoxythymidine

2tThd:

2-Thiothymidine (ribose)

2tThy:

2-Thiothymine

2tUra:

2-Thiouracil

2tUrd:

2-Thiouridine

4t-dThd:

4-Thiodeoxythymidine

4tThy:

4-Thiothymine

4tUra:

4-Thiouracil

4tUrd:

4-Thiouridine

5azaCyt:

5-Azacytosine

6aza-2tThy:

6-Aza-2-thiothymine

6azaUra:

6-Azauracil

6azaUrd:

6-Azauridine

6Me-tGua:

6-Methylthioguanine

6Me-tPur:

6-Methylthiopurine

6tGua:

6-Thioguanine

6tGuo:

6-Thioguanosine

6tIno:

6-Thioinosine

6tPur:

6-Thiopurine

7Me-8azaGua:

7-Methyl-8-azaguanine

8azaAde:

8-Azaadenine

8azaAdo:

8-Azaadenosine

8azaGua:

8-Azaguanine

8azaGuo:

8-Azaguanosine

8azaIno:

8-Azainosine

8Me-8azaGua:

8-Methyl-8-azaguanine

Ac:

2′-3′-5′-Tri-O-acetylated ribose

ACN:

Acetonitrile

Ade:

Adenine

Ado:

Adenosine

AMP:

Adenosine 5′-monophosphate

Br-4tUrd:

5-Bromo-4-thiouridine (2′-3′-5′-tri-O-acetylated ribose)

CASPT2:

Complete Active Space Perturbation Theory

CASSCF:

Complete Active Space Self-Consistent Field

CD3-4tUra:

1-Methyl-3-trideuteriomethyl-4-thiouracil

CIS:

Configuration Interaction Singles

Cl-4tUrd:

5-Chloro-4-thiouridine (2′-3′-5′-tri-O-acetylated ribose)

CMP:

Cytidine 5′-monophosphate

COSMO:

COnductor-like Screening MOdel

CPCM:

Conductor-like Polarizable Continuum Model

Cyd:

Cytidine

Cyt:

Cytosine

dAdo:

2′-Deoxyadenosine

dAMP:

2′-Deoxyadenosine 5′-monophosphate

DCM:

Dichloromethane

dCMP:

2′-Deoxycytidine 5′-monophosphate

dCyd:

2′-Deoxycytidine

dGMP:

2′-Deoxyguanosine 5′-monophosphate

dGuo:

2′-Deoxyguanosine

DMTU:

1,3-Dimethyl-4-thiouracil

dThd:

2′-Deoxythymidine

dTMP:

2′-Deoxythymidine 5′-monophosphate

dtUra:

2,4-Dithiouracil

dtUrd:

2,4-Dithiouridine

dUrd:

2′-Deoxyuridine

Em:

Emission

EOM-CC2:

Equation Of Motion Coupled Cluster

F-4tUrd:

5-Fluoro-4-thiouridine (2′-3′-5′-tri-O-acetylated ribose)

Fl:

Fluorescence

FU:

Fluorescence Up-conversion

GMP:

Guanosine 5′-monophosphate

Gua:

Guanine

Guo:

Guanosine

I-4tUrd:

5-Iodo-4-thiouridine (2′-3′-5′-tri-O-acetylated ribose)

Ino:

Inosine

LIOAS:

Laser-Induced OptoAcoustic Spectroscopy

MRCI:

MultiReference Configuration Interaction

NE:

Non-Emissive

NR:

Non-Radiative

PBS:

Phosphate Buffer Solution

Pch:

Photochemical

PFDMCH:

Perfluoro-1,3-dimethylcyclohexane

Ph:

Phosphorescence

Pr-4tThy:

1-Propyl-4-thiothymine

Pr-4tUra:

1-Propyl-4-thiouracil

Pr-6tPur:

9-Propyl-6-thiopurine

Pur:

Purine

Sh:

Shoulder

TAS:

Transient Absorption Spectroscopy

TCSPC:

Time-Correlated Single Photon Counting

TD-DFT:

Time-Dependent Density Functional Theory

Thd:

Thymidine (ribonucleoside)

THF:

Tetrahydrofuran

Thy:

Thymine

TMP:

Thymidine 5′-monophosphate (ribonucleotide)

TQP:

Two-Quanta Photolysis

TRF:

Time-Resolved Fluorescence

TRIS:

Tris(hydroxymethyl)aminomethane buffer

TRL:

Time-Resolved Luminescence

TRPES:

Time-Resolved PhotoElectron Spectroscopy

TRTL:

Time-Resolved Thermal Lensing

Ura:

Uracil

Urd:

Uridine

UVA:

UltraViolet, electromagnetic radiation subtype A (400 to 315 nm)

UVC:

UltraViolet, electromagnetic radiation subtype C (280 to 100 nm)

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Acknowledgements

The authors acknowledge the CAREER program of the National Science Foundation (Grant.No.CHE-1255084) for financial support. LMF acknowledges the financial support of MICINN for a FPU grant and the Project No.CTQ2012-35513-C02-01.

Authors' noteSpace limitations preclude a comprehensive review, and it is unfitting to include all references to relevant work from many research groups working in this area (particularly in Sect. 2). We apologize for any unintentional omissions.

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Authors and Affiliations

  1. Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclic Avenue, Cleveland, OH, 44106, USA

    Marvin Pollum & Carlos E. Crespo-Hernández

  2. Departamento de Química, Universidad Autónoma de Madrid, 28049, Cantoblanco, Madrid, Spain

    Lara Martínez-Fernández

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  1. Marvin Pollum
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  2. Lara Martínez-Fernández
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  3. Carlos E. Crespo-Hernández
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Correspondence to Carlos E. Crespo-Hernández .

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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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Pollum, M., Martínez-Fernández, L., Crespo-Hernández, C.E. (2014). Photochemistry of Nucleic Acid Bases and Their Thio- and Aza-Analogues in Solution. In: Barbatti, M., Borin, A., Ullrich, S. (eds) Photoinduced Phenomena in Nucleic Acids I. Topics in Current Chemistry, vol 355. Springer, Cham. https://doi.org/10.1007/128_2014_554

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