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

  • Marvin Pollum
  • Lara Martínez-Fernández
  • Carlos E. Crespo-HernándezEmail author
Chapter
Part of the Topics in Current Chemistry book series (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.

Keywords

Azabases DNA and RNA analogues DNA and RNA monomers Excited singlet and triplet states Excited-state dynamics Femtochemistry Fluorescence up-conversion Photochemistry Pump-probe transient absorption Quantum-chemical calculations Thiobases 

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)

Notes

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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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Marvin Pollum
    • 1
  • Lara Martínez-Fernández
    • 2
  • Carlos E. Crespo-Hernández
    • 1
    Email author
  1. 1.Department of Chemistry and Center for Chemical DynamicsCase Western Reserve UniversityClevelandUSA
  2. 2.Departamento de QuímicaUniversidad Autónoma de MadridMadridSpain

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