Nucleobase Orientation and Ordering in Films of Single-Stranded DNA on Gold
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 proteins)1 and to elucidate the correspondence of structures determined ex situ to those in aqueous solutions. We use thymine homo-oligonucleotides [oligo(dT)] on polycrystalline
Document Details
- Document Type
- Technical Report
- Publication Date
- Apr 01, 2005
- Accession Number
- ADA482470
Entities
People
- Aric Opdahl
- Dmitri Y. Petrovykh
- F. J. Himpsel
- Hiromi Kimura-suda
- J. M. Sullivan
- Lloyd J. Whitman
- Michael J. Tarlov
- V. Perez-dieste
Organizations
- University of Maryland