AVS 52nd International Symposium
    DNA Topical Conference Monday Sessions
       Session DN+BI-MoA

Paper DN+BI-MoA8
Probing DNA-DNA Interactions between Cytosine (dC) Homo-Oligonucleotides Immobilized on Gold

Monday, October 31, 2005, 4:20 pm, Room 311

Session: DNA Detection and Sensing
Presenter: A.M. Opdahl, National Institute of Standards and Technology
Authors: A.M. Opdahl, National Institute of Standards and Technology
D.Y. Petrovykh, University of Maryland and Naval Research Laboratory
H. Kimura-Suda, National Institute of Standards and Technology
L.J. Whitman, Naval Research Laboratory
M.J. Tarlov, National Institute of Standards and Technology
Correspondent: Click to Email
We present experimental evidence for strong interactions between cytosine (dC) homo-oligonucleotides immobilized on gold surfaces. It is known that in neutral and acidic pH solutions (dC)-rich oligos can form multistrand structures [e.g. parallel strand, i-motif] via hemiprotonated (C+)(C) base pairing. For surface-immobilized DNA, we find evidence for the existence of these structures by probing the susceptibility of oligo(dC) films to displacement by 1-mercapto-6-hexanol (MCH) as a function of the buffer solution pH and ion composition. The premise of the method is that MCH is less effective at displacing any individual oligos within a film when strong DNA-DNA interactions are present. The structures and coverages of alkanethiol modified (-SH) and unmodified oligo(dC) films were characterized by Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). Specifically, we find that (dC)@sub 25@-SH films are not displaced by MCH in neutral and acidic pH conditions that favor base-base (C+)(C) interactions, but are readily removed by MCH in mildly basic conditions. Both thiol modified and unmodified (dC) films exhibit higher resistance to MCH displacement in the presence of divalent buffer cations. This additional stability is attributed in part to electrostatic crosslinking of the negatively charged phosphate backbones. These results will be discussed along with the possibility of using (C+)(C) base pairing for stabilizing thiol-tethered DNA strands on gold.