Journal
ACS SENSORS
Volume 3, Issue 7, Pages 1308-1315Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acssensors.8b00165
Keywords
solid-state nanopore; structured DNA constructs; single molecule detection; molecular substructure identification; sensor
Funding
- Natural Sciences and Engineering Research Council of Canada (NSERC)
- province of Ontario through their Early Researcher Award
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The challenge when employing solid-state nano pores as single-molecule sensors in a given assay is the specificity of the ionic current signal during the translocation of target molecules. Here we present the capture and translocation characteristics of short structurally defined DNA molecules that could serve as effective surrogate labels in biosensing applications. We produced T-shaped or Y-shaped DNA molecules with a 50 bp double-stranded DNA (dsDNA) backbone and a 25 bp dsDNA branch in the middle, as improved labels over short linear DNA fragments. We show that molecular topologies can be distinguished from linear DNA by analyzing ionic current blockades produced as these DNA labels translocate through nanopores fabricated by controlled breakdown on 10-nm-thick SiN membranes and ranging in diameter from 4 to 10 nm. Event signatures are shown to be a direct result of the structure of the label and lead to an increased signal-to-noise ratio over that of short linear dsDNA, in addition to well resolved dwell times for the pore size in this range. These results show that structurally defined branched DNA molecules can be robustly detected for a broad range of pore size, and thus represent promising candidates as surrogate labels in a variety of nanopore-based molecular or immunoassay schemes.
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