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Vibrational stark effect probes for nucleic acids.

Lisa N Silverman1, Michael E Pitzer, Peter O Ankomah

  • 1Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.

The Journal of Physical Chemistry. B
|September 20, 2007
PubMed
Summary
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Researchers explored electric fields in nucleic acids using vibrational Stark effect (VSE) spectroscopy. Nitrile probes on nucleosides showed promise for studying DNA electric fields, with specific probes demonstrating high sensitivity and ease of use.

Area of Science:

  • Molecular Biophysics
  • Spectroscopy
  • Biochemistry

Background:

  • The vibrational Stark effect (VSE) is a powerful technique for measuring electric fields within biological molecules, primarily proteins.
  • Its application to nucleic acids, however, remains less explored, limiting our understanding of electric field dynamics in DNA and RNA.

Purpose of the Study:

  • To investigate the feasibility and effectiveness of using VSE spectroscopy to study electric fields in nucleic acids.
  • To identify suitable infrared probes for probing electric fields within DNA structures.

Main Methods:

  • Synthesized nine structurally diverse nucleosides incorporating nitrile or azide probes at key positions.
  • Performed Stark spectroscopy on these modified nucleosides to analyze their response to electric fields.

Related Experiment Videos

  • Characterized probe absorption frequencies and Stark tuning rates.

    • Main Results:

    • Nitrile probes exhibited favorable characteristics, with absorption frequencies spanning 2102 cm⁻¹ to 2253 cm⁻¹.
    • The largest Stark tuning rate observed was 1.1 cm⁻¹/(MV/cm) for 5-cyano-2'-deoxyuridine and N2-nitrile-2'-deoxyguanosine.
    • N2-nitrile-2'-deoxyguanosine showed a high extinction coefficient and facile incorporation into oligomers.

    Conclusions:

    • Vibrational Stark spectroscopy is a viable method for studying electric fields in nucleic acids.
    • Nitrile-based probes are effective for this purpose, with N2-nitrile-2'-deoxyguanosine being a particularly promising candidate for future research.