The Mid-IR Spectra of 9-Ethyl Guanine, Guanosine, and 2-Deoxyguanosine

Abo-Riziq, Ali; Crews, Bridgit; Compagnon, Isabelle; Oomens, Jos; Meijer, Gerard; Helden, Gert von; Kabeláč, Martin; Hobza, Pavel; Vries, Mattanjah S. de

doi:10.1021/jp072183i

Cited by 42 publications

(37 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Abo-Riziq et al [94] have reported the mid-IR spectra of the guanine lesion 9-ethylguanine along with guanosine and 2-deoxyguanosine recorded using IR-UV double resonance spectroscopy. Presence of a single isomer of the molecules was demonstrated through resonant two-photon ionization (R2PI) experiments.…”

Section: -Methyl and 9-ethylguaninementioning

confidence: 99%

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Shanmugasundaram¹,

Puranik²

2009

J Raman Spectroscopy

View full text Add to dashboard Cite

Purines, pyrimidines, and the corresponding ribose monophosphates are ubiquitous biomolecules involved in several cellular processes-in DNA and RNA, signaling, and energy transactions. In the new and exciting field of DNA-inspired nanostructures, they are used as fundamental building blocks. Unique features of the nucleobases are that several tautomeric states are close in energy and the tautomeric equilibria are sensitive to exocyclic substitution and pH. Knowing the exact structure and tautomer(s) at physiological conditions is crucial to understand the substrate specificities and catalytic mechanisms of the many enzymes for which these nucleobases are substrates. Very few spectroscopic methods can distinguish between tautomers and provide solution structures. Vibrational spectroscopy has long been known to be an excellent tool to obtain reliable information on nucleic acids. However, even when good-quality spectra are available, isotope editing is required to make reliable band assignments and identify structures unequivocally. Density functional theoretical (DFT) methods have become indispensible in assisting the assignment of observed spectra to normal modes, identification of tautomers, and modeling of spectra of isotope-edited molecules. We review the performance of DFT methods in the prediction of nucleobases and their analogs. We find that even with modest basis sets, trends in vibrational spectra can be predicted adequately and guide assignments to normal modes of the molecule. Shifts in band positions induced upon isotope labeling are reproduced more reliably than the band positions. Scaling considerably improves the agreement between the computed and experimental spectra, but accurate prediction of vibrations of exocyclic groups like C O requires that solvent effects are taken into account.

show abstract

Section: -Methyl and 9-ethylguaninementioning

confidence: 99%

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Shanmugasundaram¹,

Puranik²

2009

J Raman Spectroscopy

View full text Add to dashboard Cite

show abstract

“…Thus dG •+ and Gs •+ , formed either in the source or from the [Cu II dG 3 ] 2+ and [Cu II Gs 3 ] 2+ precursor complexes, have different structures to those formed from the dimer radical cations. Although this appears to be a novel finding in terms of tautomerisation within gas-phase supramolecular complexes, a search of the literature reveals examples of different gas-phase tautomeric forms of neutral dG and Gs that arise from the way that they are generated in the gas-phase [40][41][42]. Thus IR spectroscopy with resonant two-photon ionisation has been used to show that neutral dG and Gs formed via laser desorption exist in the enol forms D1 and D2 [40], but when hydrated by one or two water molecules, exist in the keto forms C1 and C2 [41,42].…”

Section: Do the Dimeric Radical Cations Have A Unique Structure Contamentioning

confidence: 88%

“…Although this appears to be a novel finding in terms of tautomerisation within gas-phase supramolecular complexes, a search of the literature reveals examples of different gas-phase tautomeric forms of neutral dG and Gs that arise from the way that they are generated in the gas-phase [40][41][42]. Thus IR spectroscopy with resonant two-photon ionisation has been used to show that neutral dG and Gs formed via laser desorption exist in the enol forms D1 and D2 [40], but when hydrated by one or two water molecules, exist in the keto forms C1 and C2 [41,42]. It is also worth mentioning that CID of metal complexes of amino acids and peptides can give rises to isomeric radical cations that depend on the metal complex [43][44][45].…”

Section: Do the Dimeric Radical Cations Have A Unique Structure Contamentioning

confidence: 88%

Gas-phase formation and reactions of radical cations of guanosine, deoxyguanosine and their homodimers and heterodimers

Feketeová

Yuriev

Orbell

et al. 2011

International Journal of Mass Spectrometry

View full text Add to dashboard Cite

“…The absorption peaks at 1445 and 1120 cm À1 are due to strong in-plane OH bending mode and C-C stretching vibrations, 80 respectively. The absorption peaks at 2695 and 775 cm À1 correspond to the CH 2 stretching vibrations.…”

Section: View Article Onlinementioning

confidence: 99%

Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO₂clusters of sol–gel silicate material for understanding DNA photodamage

Chandraboss

Karthikeyan

Senthilvelan

2015

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

We report a first principles density functional theoretical (DFT) investigation of guanine (G) adsorption onto SiO2 clusters, viz., Si2O4, Si3O6, Si4O8 and Si5O10 in terms of geometry, binding energy (EB), binding site, energy gap (Eg), and electronic and spectral properties. Guanine entrapped within a Si9O18 cluster was also studied in terms of geometry, energy gap (Eg), electronic and spectral properties. We observed that the most stable forms of the cluster were Si5O10 and Si9O18. Guanine adsorbed onto SiO2 (G-SiO2) and guanine entrapped within SiO2 (GE-SiO2) were analyzed by the B3LYP/LanL2DZ method. The HOMO-LUMO energies illustrate that charge transfer from ligand to metal (L → M) occurs in G-SiO2 clusters as guanine to SiO2. The composite of guanine with nanostructured silica material was prepared by simple precipitation and chemical sol-gel processes. The prepared G-SiO2 and GE-SiO2 composites were characterized by FT-IR and FE-SEM with EDX analysis. The resulting experimental evidence is included for better understanding the guanine adsorption and entrapment. The adsorption and entrapping of G-SiO2 and GE-SiO2 was also confirmed by UV-vis spectroscopy. Experimental results are compared with the DFT results. Furthermore, the sol-gel silicate material used to protect the DNA base (guanine) from UVA-irradiation has been highlighted.

show abstract

The Mid-IR Spectra of 9-Ethyl Guanine, Guanosine, and 2-Deoxyguanosine

Cited by 42 publications

References 27 publications

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Gas-phase formation and reactions of radical cations of guanosine, deoxyguanosine and their homodimers and heterodimers

Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO₂clusters of sol–gel silicate material for understanding DNA photodamage

Contact Info

Product

Resources

About

The Mid-IR Spectra of 9-Ethyl Guanine, Guanosine, and 2-Deoxyguanosine

Cited by 42 publications

References 27 publications

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Gas-phase formation and reactions of radical cations of guanosine, deoxyguanosine and their homodimers and heterodimers

Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO2clusters of sol–gel silicate material for understanding DNA photodamage

Contact Info

Product

Resources

About

Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO₂clusters of sol–gel silicate material for understanding DNA photodamage