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Search: id:"swepub:oai:research.chalmers.se:96f56d8a-f385-49ae-8f04-1e2bb101d855" > Kinetics of Diffusi...

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

Hannestad, Jonas, 1981 (author)
Chalmers tekniska högskola,Chalmers University of Technology
Brune, Ralf, 1974 (author)
Chalmers tekniska högskola,Chalmers University of Technology
Czolkos, Ilja, 1980 (author)
Chalmers tekniska högskola,Chalmers University of Technology
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Jesorka, Aldo, 1967 (author)
Chalmers tekniska högskola,Chalmers University of Technology
El-Sagheer, Afaf (author)
Suez Canal University,University of Southampton
Brown, T. (author)
University of Southampton
Albinsson, Bo, 1963 (author)
Chalmers tekniska högskola,Chalmers University of Technology
Orwar, Owe, 1964 (author)
Chalmers tekniska högskola,Chalmers University of Technology
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 (creator_code:org_t)
2012-12-20
2013
English.
In: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851. ; 7:1, s. 308-315
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • 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.

Subject headings

NATURVETENSKAP  -- Kemi -- Fysikalisk kemi (hsv//swe)
NATURAL SCIENCES  -- Chemical Sciences -- Physical Chemistry (hsv//eng)

Keyword

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

Publication and Content Type

art (subject category)
ref (subject category)

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