Kinetics of Diffusion-Mediated DNA Hybridization in Lipid Monolayer Films Determined by Single-Molecule Fluorescence Spectroscopy
Artikel i vetenskaplig tidskrift, 2013

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.

surface

simulations

DNA

monte-carlo

nanofluidics

fluorescence

cell-membranes

single-molecule

kinetics

diffusion

Författare

Jonas Hannestad

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Ralf Brune

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Ilja Czolkos

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Aldo Jesorka

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Afaf El-Sagheer

Suez Canal University

University of Southampton

T. Brown

University of Southampton

Bo Albinsson

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Owe Orwar

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

ACS Nano

1936-0851 (ISSN) 1936-086X (eISSN)

Vol. 7 1 308-315

Styrkeområden

Nanovetenskap och nanoteknik

Ämneskategorier

Fysikalisk kemi

DOI

10.1021/nn304010p