nl7b01829_si_001.pdf (3.72 MB)
A DNA Walker as a Fluorescence Signal Amplifier
journal contribution
posted on 2017-07-28, 00:00 authored by Dongfang Wang, Carolin Vietz, Tim Schröder, Guillermo Acuna, Birka Lalkens, Philip TinnefeldSensing
nucleic acids typically involves the recognition of a specific
sequence and reporting by, for example, a fluorogenic reaction yielding
one activated dye molecule per detected nucleic acid. Here, we show
that after binding to a DNA origami track a bound DNA target (a “DNA
walker”) can release the fluorescence of many molecules by
acting as the catalyst of an enzymatic nicking reaction. As the walking
kinetics sensitively depends on the walker sequence, the resulting
brightness distribution of DNA origamis is a sequence fingerprint
with single-nucleotide sensitivity. Using Monte Carlo simulations,
we rationalize that the random self-avoiding walk is mainly terminated
when steps to nearest neighbors are exhausted. Finally, we demonstrate
that the DNA walker is also active in a plasmonic hotspot for fluorescence
enhancement, indicating the potential of combining different amplification
mechanisms enabled by the modularity of DNA nanotechnology.
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Keywords
DNA walkerdye moleculeMonte Carlo simulationssingle-nucleotide sensitivityDNA nanotechnologywalker sequenceDNA origamisnicking reactionplasmonic hotspotDNA origami trackfluorogenic reactionfluorescence enhancementDNA Walkeramplification mechanismsbrightness distributionDNA targetFluorescence Signal Amplifiersequence fingerprint
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