title: Kinetics of diffusion-mediated DNA hybridization in lipid monolayer films determined by single-molecule fluorescence spectroscopy.
abstract: We use single-molecule fluorescence microscopy to monitor individual hybridization reactions between membrane-anchored DNA strands, occurring in nanofluidic lipid monolayer films deposited on Teflon AF substrates. The DNA molecules are labeled with different fluorescent dyes, which make it possible to simultaneously monitor the movements of two different molecular species, thus enabling tracking of both reactants and products. We employ lattice diffusion simulations to determine reaction probabilities upon interaction. The observed hybridization rate of the 40-mer DNA was more than 2-fold higher than that of the 20-mer DNA. Since the lateral diffusion coefficient of the two different constructs is nearly identical, the effective molecule radius determines the overall kinetics. This implies that when two DNA molecules approach each other, hydrogen bonding takes place distal from the place where the DNA is anchored to the surface. Strand closure then propagates bidirectionally through a zipper-like mechanism, eventually bringing the lipid anchors together. Comparison with hybridization rates for corresponding DNA sequences in solution reveals that hybridization rates are lower for the lipid-anchored strands and that the dependence on strand length is stronger.
authors.affiliation: Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96, Göteborg, Sweden.
authors.forename: Jonas K
authors.initials: JK
authors.lastname: Hannestad
authors.forename: Ralf
authors.initials: R
authors.lastname: Brune
authors.forename: Ilja
authors.initials: I
authors.lastname: Czolkos
authors.forename: Aldo
authors.initials: A
authors.lastname: Jesorka
authors.forename: Afaf H
authors.initials: AH
authors.lastname: El-Sagheer
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: Bo
authors.initials: B
authors.lastname: Albinsson
authors.forename: Owe
authors.initials: O
authors.lastname: Orwar
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004058:Diffusion; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D007700:Kinetics; D008051:Lipid Bilayers / Q000737:chemistry*; D008567:Membranes, Artificial; D057054:Molecular Imaging / Q000379:methods*; D013050:Spectrometry, Fluorescence / Q000379:methods*
chemical_list: D008051:Lipid Bilayers; D008567:Membranes, Artificial; D004247:DNA