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Issue 3, 2018
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Concentrating and labeling genomic DNA in a nanofluidic array

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Abstract

Nucleotide incorporation by DNA polymerase forms the basis of DNA sequencing-by-synthesis. In current platforms, either the single-stranded DNA or the enzyme is immobilized on a solid surface to locate the incorporation of individual nucleotides in space and/or time. Solid-phase reactions may, however, hinder the polymerase activity. We demonstrate a device and a protocol for the enzymatic labeling of genomic DNA arranged in a dense array of single molecules without attaching the enzyme or the DNA to a surface. DNA molecules accumulate in a dense array of pits embedded within a nanoslit due to entropic trapping. We then perform ϕ29 polymerase extension from single-strand nicks created on the trapped molecules to incorporate fluorescent nucleotides into the DNA. The array of entropic traps can be loaded with λ-DNA molecules to more than 90% of capacity at a flow rate of 10 pL min−1. The final concentration can reach up to 100 μg mL−1, and the DNA is eluted from the array by increasing the flow rate. The device may be an important preparative module for carrying out enzymatic processing on DNA extracted from single-cells in a microfluidic chip.

Graphical abstract: Concentrating and labeling genomic DNA in a nanofluidic array

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Publication details

The article was received on 14 Aug 2017, accepted on 04 Nov 2017 and first published on 04 Jan 2018


Article type: Paper
DOI: 10.1039/C7NR06016E
Citation: Nanoscale, 2018,10, 1376-1382
  • Open access: Creative Commons BY license
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    Concentrating and labeling genomic DNA in a nanofluidic array

    R. Marie, J. N. Pedersen, K. U. Mir, B. Bilenberg and A. Kristensen, Nanoscale, 2018, 10, 1376
    DOI: 10.1039/C7NR06016E

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