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Kinetics of Diffusion-Mediated DNA Hybridization in Lipid Monolayer Films Determined by Single-Molecule Fluorescence Spectroscopy

Jonas K. Hannestad (Institutionen för kemi- och bioteknik, Fysikalisk kemi) ; Ralf Brune (Institutionen för kemi- och bioteknik, Fysikalisk kemi) ; Ilja Czolkos (Institutionen för kemi- och bioteknik, Fysikalisk kemi) ; Aldo Jesorka (Institutionen för kemi- och bioteknik, Fysikalisk kemi) ; A. H. El-Sagheer ; T. Brown ; Bo Albinsson (Institutionen för kemi- och bioteknik, Fysikalisk kemi) ; Owe Orwar (Institutionen för kemi- och bioteknik, Fysikalisk kemi)
Acs Nano (1936-0851). Vol. 7 (2013), 1, p. 308-315.
[Artikel, refereegranskad vetenskaplig]

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.

Nyckelord: single-molecule, nanofluidics, kinetics, fluorescence, DNA, diffusion, cell-membranes, monte-carlo, surface, simulations

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Denna post skapades 2013-04-08. Senast ändrad 2013-04-08.
CPL Pubid: 175490


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Institutioner (Chalmers)

Institutionen för kemi- och bioteknik, Fysikalisk kemi (2005-2014)


Nanovetenskap och nanoteknik
Fysikalisk kemi

Chalmers infrastruktur