A microfluidic device that generates hydroxyl radicals to probe the solvent accessible surface of nucleic acids

Christopher D. Jones, Jörg C. Schlatterer, Michael Brenowitz, Lois Pollack

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

We describe a microfluidic device containing a mineral matrix capable of rapidly generating hydroxyl radicals that enables high-resolution structural studies of nucleic acids. Hydroxyl radicals cleave the solvent accessible backbone of DNA and RNA; the cleavage products can be detected with as fine as single nucleotide resolution. Protection from hydroxyl radical cleavage (footprinting) can identify sites of protein binding or the presence of tertiary structure. Here we report preparation of micron sized particles of iron sulfide (pyrite) and fabrication of a microfluidic prototype that together generate enough hydroxyl radicals within 20 ms to cleave DNA sufficiently for a footprinting analysis to be conducted. This prototype enables the development of high-throughput and/or rapid reaction devices with which to probe nucleic acid folding dynamics and ligand binding.

Original languageEnglish (US)
Pages (from-to)3458-3464
Number of pages7
JournalLab on a Chip
Volume11
Issue number20
DOIs
StatePublished - Oct 21 2011

ASJC Scopus subject areas

  • Bioengineering
  • Biochemistry
  • Chemistry(all)
  • Biomedical Engineering

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