Advertisement

Gas-Phase Spectroscopy of Nucleic Acids

  • Valérie Gabelica
  • Frédéric Rosu
Chapter
Part of the Physical Chemistry in Action book series (PCIA)

Abstract

We describe here frequency-resolved gas-phase spectroscopy of nucleic acids. Frequency resolved means that the effect of photons on the nucleic acid molecules is measured as a function of the photon frequency. The present chapter is primarily focused on experimental aspects, and intended as a compass to navigate a rather interdisciplinary field. Indeed, gas-phase spectroscopy usually combines photonics, mass spectrometry (when ions are detected), and theoretical chemistry. Although theory is of prime importance for the interpretation of the results, as it is the comparison between experimental and theoretical energies of the resonance transitions that allow the structural interpretation of the experimental spectra, extended discussion of theory levels will not be provided here, but relevant literature will be indicated along the text. We will cover rotational, vibrational, and electronic spectroscopy from isolated nucleobases to oligonucleotides and nucleic acid higher-order structures.

Keywords

Spectroscopy Infrared Ultraviolet Microwave Base stacking Hydrogen bonding Photoionization Excited states Oligonucleotides Isolated bases Duplex Quadruplex Base pairs Tautomers 

Abbreviations

CD

Circular dichroism

CID

Collision-induced dissociation

CLIO

Centre Laser Infrarouge d’Orsay

FELIX

Free-Electron Lasers for Infrared eXperiments

FTICRMS

Fourier transform ion cyclotron resonance mass spectrometry

IC

Internal conversion

IP

Ionization potential

IR

Infrared

IRMPD

Infrared multiple photon dissociation

IR-UV

Infrared-ultraviolet double resonance spectroscopy

IVR

Intramolecular vibrational energy redistribution

LA-MB-FTMW

Laser ablation molecular beam Fourier transform microwave spectroscopy

LIF

Laser-induced fluorescence

NMR

Nuclear magnetic resonance

PD

Photodissociation

R1PI

Resonance-enhanced single-photon ionization

R2PI

Resonance-enhanced two-photon ionization

REMPI

Resonance-enhanced multiphoton ionization

S0

Electronic ground state

S1

First electronically excited state

UV

Ultraviolet

UVMPD

Ultraviolet multiple photon dissociation

UV-UV

Ultraviolet–ultraviolet double resonance spectroscopy

Vis

Visible

VUV

Vacuum ultraviolet

References

  1. 1.
    Taillandier E, Liquier J (1992) Infrared spectroscopy of DNA. Methods Enzymol 211:307–335CrossRefGoogle Scholar
  2. 2.
    Tataurov AV, You Y, Owczarzy R (2008) Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids. Biophys Chem 133:66–70CrossRefGoogle Scholar
  3. 3.
    Clark LB, Peschel GG, Tinoco I Jr (1965) Vapor spectra and heats of vaporization of some purine and pyrimidine bases. J Phys Chem 69:3615–3618CrossRefGoogle Scholar
  4. 4.
    Kleinermanns K, Nachtigallová D, de Vries MS (2013) Excited state dynamics of DNA bases. Int Rev Phys Chem 32:308–342CrossRefGoogle Scholar
  5. 5.
    Vaya I, Gustavsson T, Miannay FA, Douki T, Markovitsi D (2010) Fluorescence of natural DNA: from the femtosecond to the nanosecond time scales. J Am Chem Soc 132:11834–11835CrossRefGoogle Scholar
  6. 6.
    de Vries MS, Hobza P (2007) Gas-phase spectroscopy of biomolecular building blocks. Annu Rev Phys Chem 58:585–612CrossRefGoogle Scholar
  7. 7.
    Belau L, Wilson KR, Leone SR, Ahmed M (2007) Vacuum-ultraviolet photoionization studies of the microhydration of DNA bases (guanine, cytosine, adenine, and thymine). J Phys Chem A 111:7562–7568CrossRefGoogle Scholar
  8. 8.
    Yang X, Wang XB, Vorpagel ER, Wang LS (2004) Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy. Proc Natl Acad Sci USA 101:17588–17592CrossRefGoogle Scholar
  9. 9.
    Danell AS, Parks JH (2003) Fraying and electron autodetachment dynamics of trapped gas phase oligonucleotides. J Am Soc Mass Spectrom 14:1330–1339CrossRefGoogle Scholar
  10. 10.
    Weber JM, Ioffe IN, Berndt KM, Loffler D, Friedrich J, Ehrler OT, Danell AS, Parks JH, Kappes MM (2004) Photoelectron spectroscopy of isolated multiply negatively charged oligonucleotides. J Am Chem Soc 126:8585–8589CrossRefGoogle Scholar
  11. 11.
    Nagornova NS, Guglielmi M, Doemer M, Tavernelli I, Rothlisberger U, Rizzo TR, Boyarkin OV (2011) Cold-ion spectroscopy reveals the intrinsic structure of a decapeptide. Angew Chem Int Ed Engl 50:5383–5386CrossRefGoogle Scholar
  12. 12.
    Nagornova NS, Rizzo TR, Boyarkin OV (2010) Highly resolved spectra of gas-phase Gramicidin S: a benchmark for peptide structure calculations. J Am Chem Soc 132:4040CrossRefGoogle Scholar
  13. 13.
    Stearns JA, Seaiby C, Boyarkin OV, Rizzo TR (2009) Spectroscopy and conformational preferences of gas-phase helices. Phys Chem Chem Phys 11:125–132CrossRefGoogle Scholar
  14. 14.
    Rodriguez JD, Lisy JM (2009) Infrared spectroscopy of multiply charged metal ions: methanol-solvated divalent manganese 18-crown-6 ether systems. J Phys Chem A 113:6462–6467CrossRefGoogle Scholar
  15. 15.
    Garand E, Kamrath MZ, Jordan PA, Wolk AB, Leavitt CM, McCoy AB, Miller SJ, Johnson MA (2012) Determination of noncovalent docking by infrared spectroscopy of cold gas-phase complexes. Science 335:694–698CrossRefGoogle Scholar
  16. 16.
    Bierau F, Kupser P, Meijer G, von Helden G (2010) Catching proteins in liquid helium droplets. Phys Rev Lett 105:133402CrossRefGoogle Scholar
  17. 17.
    Choi MY, Miller RE (2006) Four tautomers of isolated guanine from infrared laser spectroscopy in helium nanodroplets. J Am Chem Soc 128:7320–7328CrossRefGoogle Scholar
  18. 18.
    Shukla MK, Leszczynski J (2013) Tautomerism in nucleic acid bases and base pairs: a brief overview. Comput Mol Sci 3:637–649CrossRefGoogle Scholar
  19. 19.
    Nir E, Janzen C, Imhof P, Kleinermanns K, de Vries MS (2001) Guanine tautomerism revealed by UV–UV and IR–UV hole burning spectroscopy. J Chem Phys 115:4604CrossRefGoogle Scholar
  20. 20.
    Mons M, Piuzzi F, Dimicoli I, Gorb L, Leszczynski J (2006) Near-UV resonant two-photon ionization spectroscopy of gas phase guanine: evidence for the observation of three rare tautomers. J Phys Chem A 110:10921–10924CrossRefGoogle Scholar
  21. 21.
    Abo-riziq A, Crews BO, Compagnon I, Oomens J, Meijer G, Von Helden G, Kabelac M, Hobza P, de Vries MS (2007) The mid-IR spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine. J Phys Chem A 111:7529–7536CrossRefGoogle Scholar
  22. 22.
    Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B (2004) Ultrafast excited-state dynamics in nucleic acids. Chem Rev 104:1977–2019CrossRefGoogle Scholar
  23. 23.
    Middleton CT, de La Harpe K, Su C, Law YK, Crespo-Hernandez CE, Kohler B (2009) DNA excited-state dynamics: from single bases to the double helix. Annu Rev Phys Chem 60:217–239CrossRefGoogle Scholar
  24. 24.
    Alonso JL, Pena I, Lopez JC, Vaquero V (2009) Rotational spectral signatures of four tautomers of guanine. Angew Chem Int Ed Engl 48:6141–6143CrossRefGoogle Scholar
  25. 25.
    Alonso JL, Vaquero V, Pena I, Lopez JC, Mata S, Caminati W (2013) All five forms of cytosine revealed in the gas phase. Angew Chem Int Ed Engl 52:2331–2334CrossRefGoogle Scholar
  26. 26.
    Lopez JC, Pena MI, Sanz ME, Alonso JL (2007) Probing thymine with laser ablation molecular beam Fourier transform microwave spectroscopy. J Chem Phys 126:191103CrossRefGoogle Scholar
  27. 27.
    Vaquero V, Sanz ME, Lopez JC, Alonso JL (2007) The structure of uracil: a laser ablation rotational study. J Phys Chem A 111:3443–3445CrossRefGoogle Scholar
  28. 28.
    Nir E, Plützer C, Kleinermanns K, de Vries M (2002) Properties of isolated DNA bases, base pairs and nucleosides examined by laser spectroscopy. Eur Phys J D 20:317–329CrossRefGoogle Scholar
  29. 29.
    Jurecka P, Sponer J, Cerny J, Hobza P (2006) Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Phys Chem Chem Phys 8:1985–1993CrossRefGoogle Scholar
  30. 30.
    Kabelac M, Hobza P (2007) Hydration and stability of nucleic acid bases and base pairs. Phys Chem Chem Phys 9:903–917CrossRefGoogle Scholar
  31. 31.
    Kabelac M, Plutzer C, Kleinermanns K, Hobza P (2004) Isomer selective IR experiments and correlated ab initio quantum chemical calculations support planar H-bonded structure of the 7-methyl adenine?adenine and stacked structure of the 9-methyl adenine?adenine base pairs. Phys Chem Chem Phys 6:2781CrossRefGoogle Scholar
  32. 32.
    Nir E, Kleinermanns K, de Vries MS (2000) Pairing of isolated nucleic-acid bases in the absence of the DNA backbone. Nature 408:949–951CrossRefGoogle Scholar
  33. 33.
    Sobolewski AL, Domcke W, Hattig C (2005) Tautomeric selectivity of the excited-state lifetime of guanine/cytosine base pairs: the role of electron-driven proton-transfer processes. Proc Natl Acad Sci USA 102:17903–17906Google Scholar
  34. 34.
    Plutzer C, Hunig I, Kleinermanns K, Nir E, de Vries MS (2003) Pairing of isolated nucleobases: double resonance laser spectroscopy of adenine-thymine. Chemphyschem 4:838–842CrossRefGoogle Scholar
  35. 35.
    Salpin JY, Guillaumont S, Tortajada J, MacAleese L, Lemaire J, Maitre P (2007) Infrared spectra of protonated uracil, thymine and cytosine. Chemphyschem 8:2235–2244CrossRefGoogle Scholar
  36. 36.
    Bakker JM, Sinha RK, Besson T, Brugnara M, Tosi P, Salpin JY, Maitre P (2008) Tautomerism of uracil probed via infrared spectroscopy of singly hydrated protonated uracil. J Phys Chem A 112(48):12393–12400CrossRefGoogle Scholar
  37. 37.
    Bakker JM, Salpin J-Y, Maître P (2009) Tautomerism of cytosine probed by gas phase IR spectroscopy. Int J Mass Spectrom 283:214–221CrossRefGoogle Scholar
  38. 38.
    Yang B, Wu RR, Berden G, Oomens J, Rodgers MT (2013) Infrared multiple photon dissociation action spectroscopy of proton-bound dimers of cytosine and modified cytosines: effects of modifications on gas-phase conformations. J Phys Chem B 117(46):14191–201CrossRefGoogle Scholar
  39. 39.
    Nei YW, Hallowita N, Steill JD, Oomens J, Rodgers MT (2013) Infrared multiple photon dissociation action spectroscopy of deprotonated DNA mononucleotides: gas-phase conformations and energetics. J Phys Chem A 117:1319–1335CrossRefGoogle Scholar
  40. 40.
    Nei YW, Crampton KT, Berden G, Oomens J, Rodgers MT (2013) Infrared multiple photon dissociation action spectroscopy of deprotonated RNA mononucleotides: gas-phase conformations and energetics. J Phys Chem A 117:10634–10649CrossRefGoogle Scholar
  41. 41.
    Rosu F, Gabelica V, Joly L, Gregoire G, De Pauw E (2010) Zwitterionic i-motif structures are preserved in DNA negatively charged ions produced by electrospray mass spectrometry. Phys Chem Chem Phys 12:13448–13454CrossRefGoogle Scholar
  42. 42.
    Gabelica V, Rosu F, De Pauw E, Lemaire J, Gillet JC, Poully JC, Lecomte F, Gregoire G, Schermann JP, Desfrancois C (2008) Infrared signature of DNA G-quadruplexes in the gas phase. J Am Chem Soc 130:1810–1811CrossRefGoogle Scholar
  43. 43.
    Marian C, Nolting D, Weinkauf R (2005) The electronic spectrum of protonated adenine: theory and experiment. Phys Chem Chem Phys 7:3306–3316CrossRefGoogle Scholar
  44. 44.
    Pedersen SO, Stochkel K, Byskov CS, Baggesen LM, Nielsen SB (2013) Gas-phase spectroscopy of protonated adenine, adenosine 5'-monophosphate and monohydrated ions. Phys Chem Chem Phys 15:19748–19752CrossRefGoogle Scholar
  45. 45.
    Cheong NR, Nam SH, Park HS, Ryu S, Song JK, Park SM, Perot M, Lucas B, Barat M, Fayeton JA et al (2011) Photofragmentation in selected tautomers of protonated adenine. Phys Chem Chem Phys 13:291–295CrossRefGoogle Scholar
  46. 46.
    Marcum JC, Halevi A, Weber JM (2009) Photodamage to isolated mononucleotides–photodissociation spectra and fragment channels. Phys Chem Chem Phys 11:1740–1751CrossRefGoogle Scholar
  47. 47.
    Marcum JC, Kaufman SH, Weber JM (2011) UV-photodissociation of non-cyclic and cyclic mononucleotides. Int J Mass Spectrom 303:129–136CrossRefGoogle Scholar
  48. 48.
    Nielsen LM, Pedersen SO, Kirketerp MB, Nielsen SB (2012) Absorption by DNA single strands of adenine isolated in vacuo: the role of multiple chromophores. J Chem Phys 136:064302CrossRefGoogle Scholar
  49. 49.
    Gabelica V, Rosu F, De Pauw E, Antoine R, Tabarin T, Broyer M, Dugourd P (2007) Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores. J Am Soc Mass Spectrom 18:1990–2000CrossRefGoogle Scholar
  50. 50.
    Gabelica V, Tabarin T, Antoine R, Rosu F, Compagnon I, Broyer M, De Pauw E, Dugourd P (2006) Electron photodetachment dissociation of DNA polyanions in a quadrupole ion trap mass spectrometer. Anal Chem 78:6564–6572CrossRefGoogle Scholar
  51. 51.
    Rosu F, Gabelica V, De Pauw E, Antoine R, Broyer M, Dugourd P (2012) UV spectroscopy of DNA duplex and quadruplex structures in the gas phase. J Phys Chem A 116:5383–5391CrossRefGoogle Scholar
  52. 52.
    Dao NT, Haselsberger R, Michel-Beyerle ME, Phan AT (2013) Excimer formation by stacking g-quadruplex blocks. Chemphyschem 14:2667–2671CrossRefGoogle Scholar
  53. 53.
    Chingin K, Chen H, Gamez G, Zenobi R (2009) Exploring fluorescence and fragmentation of ions produced by electrospray ionization in ultrahigh vacuum. J Am Soc Mass Spectrom 20:1731–1738CrossRefGoogle Scholar
  54. 54.
    Bian QZ, Forbes MW, Talbot FO, Jockusch RA (2010) Gas-phase fluorescence excitation and emission spectroscopy of mass-selected trapped molecular ions. Phys Chem Chem Phys 12:2590–2598CrossRefGoogle Scholar
  55. 55.
    Talbot FO, Rullo A, Yao H, Jockusch RA (2010) Fluorescence resonance energy transfer in gaseous, mass-selected polyproline peptides. J Am Chem Soc 132:16156–16164CrossRefGoogle Scholar
  56. 56.
    Danell AS, Parks JH (2003) FRET measurements of trapped oligonucleotide duplexes. Int J Mass Spectrom 229:35–45CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.IECB, ARNA LaboratoryUniv. BordeauxPessacFrance
  2. 2.U869, ARNA Laboratory, InsermBordeauxFrance
  3. 3.UMS 3033 and Inserm US001, IECB, CNRSPessacFrance

Personalised recommendations