Accession Number:

ADA482470

Title:

Nucleobase Orientation and Ordering in Films of Single-Stranded DNA on Gold

Descriptive Note:

Journal article

Corporate Author:

MARYLAND UNIV COLLEGE PARK DEPT OF PHYSICS

Report Date:

2005-04-01

Pagination or Media Count:

3.0

Abstract:

Understanding the structure of single-stranded DNA ssDNA immobilized on surfaces is critical for applications exploiting the molecular recognition function of nucleic acids. Here we show how the structure of ssDNA monolayers can be characterized using complementary spectroscopies that probe electronic and vibrational states of nucleobasessX-ray photoelectron XPS, Fourier transform infrared FTIR, and near-edge X-ray absorption fine structure NEXAFS spectroscopies. XPS reveals core-level shifts sensitive to DNA surface chemistry NEXAFS probes electron transitions between core levels and empty valence orbitals that are sensitive to nucleobase orientation and FTIR provides vibrational fingerprints sensitive to orientation and molecular interactions., Existing approaches for using these surface analysis methods to characterize self-assembled monolayers SAMs are not directly applicable to studies of ssDNA monolayers, which share very few properties with prototypical SAMs. Whereas van der Waals attraction drives the assembly and ordering in typical SAMs, DNA immobilization is subject to strong electrostatic repulsion. Strands of ssDNA are also much longer and more flexible than typical molecules in SAMs therefore, lateral spacing is length-dependent, and long-range lateral ordering is not observed in DNA monolayers. The main type of local ordering that may be present in a DNA film is nucleobase stacking. Nucleobase stacking largely determines the structure and interactions of DNA including DNA hybridization therefore, development of methods to detect the associated orientational ordering is a major objective in characterization of DNA films. Such methods will also help to study other biointerfaces e.g., surface-bound proteins1 and to elucidate the correspondence of structures determined ex situ to those in aqueous solutions. We use thymine homo-oligonucleotides oligodT on polycrystalline

Subject Categories:

  • Biochemistry
  • Inorganic Chemistry
  • Numerical Mathematics

Distribution Statement:

APPROVED FOR PUBLIC RELEASE