title: Nucleobase orientation and ordering in films of single-stranded DNA on gold.
abstract: We demonstrate how the orientation and ordering of DNA bases in ultrahigh vacuum (UHV) and ambient environments can be determined using complementary spectroscopic methods. Near-edge X-ray absorption fine structure (NEXAFS) with fluorescence detection, X-ray photoelectron (XPS), and Fourier transform infrared (FTIR) spectroscopies are used to quantify the coverage, chemical composition, orientation, and ordering of thymine bases in model self-assembled monolayers of thymine homo-oligonucleotides [oligo(dT)] on gold. We find that, in monolayers of thiol-modified oligo(dT), thymine bases tend to orient parallel to the Au substrate, and this preferential orientation is significantly more pronounced in monolayers of thiolated 5-mers compared to 25-mers. We interpret this preferential orientation as a signature of significant correlations (local ordering) between individual nuleobases, which offers a way to quantify and compare nucleobase interactions in films under both ambient and UHV conditions.
authors.affiliation: Physics Department, University of Maryland, College Park, MD 20742, USA. dmitri.petrovykh@nrl.navy.mil
authors.forename: Dmitri Y
authors.initials: DY
authors.lastname: Petrovykh
authors.forename: V
authors.initials: V
authors.lastname: Pérez-Dieste
authors.forename: Aric
authors.initials: A
authors.lastname: Opdahl
authors.forename: Hiromi
authors.initials: H
authors.lastname: Kimura-Suda
authors.forename: J M
authors.initials: JM
authors.lastname: Sullivan
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Tarlov
authors.forename: F J
authors.initials: FJ
authors.lastname: Himpsel
authors.forename: Lloyd J
authors.initials: LJ
authors.lastname: Whitman
mesh_terms: D004277:DNA, Single-Stranded / Q000737:chemistry*; D006046:Gold / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods; D013057:Spectrum Analysis / Q000379:methods; D013941:Thymine / Q000737:chemistry; D014965:X-Rays
chemical_list: D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; C027903:oligo (dT); D006046:Gold; D013941:Thymine