Biointerphases

Journal for Biophysical Chemistry

Biointerphases Cover Image
Open Access

Sum-frequency-generation spectroscopy of DNA films in air and aqueous environments

  • Caitlin Howell1,
  • Ronny Schmidt1,
  • Volker Kurz1 and
  • Patrick Koelsch1
Biointerphases20093:30300047

https://doi.org/10.1116/1.3064107

Received: 11 November 2008

Accepted: 21 November 2008

Published: 15 January 2009

Abstract

Understanding the organization and orientation of surface-immobilized single stranded DNA (ssDNA) in aqueous environments is essential for optimizing and further developing the technology based on oligonucleotide binding. Here the authors demonstrate how sum-frequency-generation (SFG) spectroscopy can be used to compare the structure and orientation of model monolayers of ssDNA on gold in air, D2O, and phosphate buffered saline (PBS) solution. Films of adenine and thymine homo-oligonucleotides showed significant conformational changes in air versus aqueous environments in the CH stretching region. The thymine films showed changes between D2O and PBS solution, whereas the SFG spectra of adenine films under these conditions were largely similar, suggesting that the thymine films undergo greater conformational changes than the adenine films. Examination of thymine films in the amide I vibrational region revealed that molecules in films of nonthiolated DNA were lying down on the gold surface whereas molecules in films of thiol-linked DNA were arranged in a brushlike structure. Comparison of SFG spectra in the amide I region for thiol-linked DNA films in air and D2O also revealed substantial conformational changes.