Skip to main content
SpringerLink
Log in

Improving real-time measurement of H/D exchange using a FTIR biospectroscopic probe

  • Original Paper
  • Published:
Analytical and Bioanalytical Chemistry Aims and scope Submit manuscript

Abstract

We describe the improvement of a novel approach to investigating hydrogen/deuterium (H/D) exchange kinetics in biomolecules using transmission infrared spectroscopy. The method makes use of a Fourier transform infrared spectrometer coupled with a microdialysis flow cell to determine exchange rates of labile hydrogens. With this cell system, the monitoring of exchange reactions has been studied here as a function of some cell characteristics such as: (a) dialysis membrane surface contacting both the H2O and D2O compartments; (b) molecular cutoff of dialysis membrane; and (c) distance between the cell-filling holes. The best improvement has been obtained by increasing the dialysis membrane surface followed by increase of molecular cutoff. However, not significant differences were found using various distances between filling holes. The fastest exchange rate which can be measured with the cell system used here is found to be k = 0.41 ± 0.02 min−1, that is, about threefold greater than the one got in a previous work. This microdialysis flow cell has been used here for the study of H/D exchange in nucleic acids with subsequent structural analysis by 2D correlation spectroscopy.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Dostal L, Chen CY, Wang AHJ, Welfle H (2004) Biochemistry 43:9600–9609

    Article  CAS  Google Scholar 

  2. Jung C (2008) Anal Bioanal Chem 392:1031–1058

    Article  CAS  Google Scholar 

  3. Benevides JM, Overman SA, Thomas GJ Jr (2005) J Raman Spectrosc 36:279–299

    Article  CAS  Google Scholar 

  4. Noda I, Ozaki Y (2004) Two-dimensional correlation spectroscopy. Applications in vibrational and optical spectroscopy. Wiley, Chichester, UK

    Google Scholar 

  5. Wu Y, Murayama K, Ozaki Y (2001) J Phys Chem B 105:6251–6259

    Article  CAS  Google Scholar 

  6. Rodríguez-Casado A, Molina M, Carmona P (2006) Anal Bioanal Chem 385:134–138

    Article  CAS  Google Scholar 

  7. Raussens V, Ruysschaert JM, Goormaghtigh E (2004) Appl Spectrosc 58:68–82

    Article  CAS  Google Scholar 

  8. Tuma R, Thomas GJ Jr (1996) Biophys J 71:3454–3466

    Article  CAS  Google Scholar 

  9. Nakanishi M, Tsuboi MJ (1978) Mol Biol 124:61–71

    Article  CAS  Google Scholar 

  10. Mandal C, Kallenbach NR, Englander SW (1979) J Mol Biol 135:391–411

    Article  CAS  Google Scholar 

  11. Li T, Johnson JE, Thomas GJ Jr (1993) Biophys J 65:1963–1972

    Article  CAS  Google Scholar 

  12. Teitelbaum H, Englader SW (1975) J Mol Biol 92:55–78

    Article  CAS  Google Scholar 

  13. Markovits J, Ramstein J, Roques BP, Le Pecq JB (1985) Nucleic Acids Res 13:3773–3788

    Article  CAS  Google Scholar 

  14. Basu HS, Shafer RH, Marton LJ (1987) Nucleic Acids Res 15:5873–5886

    Article  CAS  Google Scholar 

  15. Shimanouchi T, Tsuboi M, Kyogoku Y (1964) Infrared spectra of nucleic acids and related compounds. In: Duchesne J (ed) The structure and properties of biomolecules and biological systems. Advances in Chemical Physics. Interscience, London, pp 435–498

    Google Scholar 

  16. Miles HT, Frazier J (1978) Biochemistry 17:2920–2927

    Article  CAS  Google Scholar 

  17. Liquier J, Taillandier E, Klinck R, Guittet E, Gouyette C, Huynh-Dinh T (1995) Nucleic Acids Res 23:1722–1728

    Article  CAS  Google Scholar 

  18. Rodríguez-Casado A, Bartolomé J, Carreño V, Molina M, Carmona P (2006) Biophys Chem 124:73–79

    Article  CAS  Google Scholar 

  19. Sarkar M, Dornberger U, Rozners E, Fritzsche H, Strömberg R, Gräslund A (1997) Biochemistry 36:15463–15471

    Article  CAS  Google Scholar 

  20. Lindqvist M, Gräslund A (2001) J Mol Biol 314:423–432

    Article  CAS  Google Scholar 

  21. Taillandier E, Liquier J (1992) Methods Enzymol 211:307–335

    Article  CAS  Google Scholar 

  22. Ouali M, Letellier R, Sim JS, Akhebat A, Adnet F, Liquier J, Taillandier E (1993) J Am Chem Soc 115:4264–4270

    Article  CAS  Google Scholar 

  23. Taillandier E, Liquier J, Taboury JA (1985) In: Clark RH, Hester RE (eds) Advances in infrared and Raman spectroscopy, vol. 12. Wiley-Heyden, New York, pp 65–114

    Google Scholar 

  24. Herbeck R, Zundel G (1976) Biochim Biophys Acta 418:52–62

    CAS  Google Scholar 

  25. Liquier J, Akhebat A, Taillandier E, Ceolin F, Huynh-Dinh T, Igolen J (1991) Spectrochim Acta A 47:177–186

    Article  Google Scholar 

  26. Letelier R, Ghomi M, Taillandier E (1989) J Biomol Struct Dyn 6:755–768

    Google Scholar 

  27. Dohy D, Ghomi M, Taillandier E (1989) J Biomol Struct Dyn 6:741–754

    CAS  Google Scholar 

  28. Banyay M, Sarkar M, Gräslund A (2003) Biophys Chem 104:477–488

    Article  CAS  Google Scholar 

  29. Saenger W (1984) Principles of nucleic acid structure, chap. 10. Springer, New York

    Google Scholar 

  30. Burrows CJ, Rokita SE (1994) Acc Chem Res 27:295–301

    Article  CAS  Google Scholar 

  31. Chastain M, Tinoco I (1991) Prog Nucleic Acids Res Mol Biol 41:131–177

    Article  CAS  Google Scholar 

  32. Westhof E, Masquida B, Jaenger L (1996) Folding Design 1:R78–R89

    Article  CAS  Google Scholar 

  33. Raussens V, Ruysschaert JM, Goormaghtigh E (2004) Appl Spectrosc 58:68–82

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors gratefully acknowledge financial support from the Spanish Ministerio de Ciencia e Innovación (project CTQ2006-04161/BQU).

Author information

Authors and Affiliations

  1. Instituto de Estructura de la Materia (CSIC), Serrano 121, 28006, Madrid, Spain

    Pedro Carmona

  2. IMDEA Alimentación, 28049, Madrid, Spain

    Arantxa Rodríguez-Casado

  3. Departamento de Química Orgánica I, Escuela Universitaria de Optica, 28037, Madrid, Spain

    Marina Molina

Authors
  1. Pedro Carmona
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Arantxa Rodríguez-Casado
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marina Molina
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pedro Carmona.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Carmona, P., Rodríguez-Casado, A. & Molina, M. Improving real-time measurement of H/D exchange using a FTIR biospectroscopic probe. Anal Bioanal Chem 393, 1289–1295 (2009). https://doi.org/10.1007/s00216-008-2535-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00216-008-2535-5

Keywords

Search

Navigation