Electrostatic confinement and manipulation of DNA molecules for genome analysis

Kristy L. Kounovsky-Shafer, Juan P. Hernandez-Ortiz, Konstantinos Potamousis, Gene Tsvid, Michael Place, Prabu Ravindran, Kyubong Jo, Shiguo Zhou, Theo Odijk, Juan J. De Pablo, David C. Schwartz

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Very large DNA molecules enable comprehensive analysis of complex genomes, such as human, cancer, and plants because they span across sequence repeats and complex somatic events. When physically manipulated, or analyzed as single molecules, long polyelectrolytes are problematic because of mechanical considerations that include shear-mediated breakage, dealing with the massive size of these coils, or the length of stretched DNAs using common experimental techniques and fluidic devices. Accordingly, we harness analyte "issues" as exploitable advantages by our invention and characterization of the "molecular gate," which controls and synchronizes formation of stretched DNA molecules as DNA dumbbells within nanoslit geometries. Molecular gate geometries comprise micro- and nanoscale features designed to synergize very low ionic strength conditions in ways we show effectively create an "electrostatic bottle." This effect greatly enhances molecular confinement within large slit geometries and supports facile, synchronized electrokinetic loading of nanoslits, even without dumbbell formation. Device geometries were considered at the molecular and continuum scales through computer simulations, which also guided our efforts to optimize design and functionalities. In addition, we show that the molecular gate may govern DNA separations because DNA molecules can be electrokinetically triggered, by varying applied voltage, to enter slits in a size-dependent manner. Lastly, mapping the Mesoplasma florum genome, via synchronized dumbbell formation, validates our nascent approach as a viable starting point for advanced development that will build an integrated system capable of large-scale genome analysis.

Original languageEnglish (US)
Pages (from-to)13400-13405
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume114
Issue number51
DOIs
StatePublished - Dec 19 2017

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Static Electricity
Genome
DNA
Entomoplasmataceae
Equipment and Supplies
Computer Simulation
Osmolar Concentration
Neoplasms

Keywords

  • Devices
  • Genomics
  • Nanofluidics
  • Single DNA molecules

ASJC Scopus subject areas

  • General

Cite this

Electrostatic confinement and manipulation of DNA molecules for genome analysis. / Kounovsky-Shafer, Kristy L.; Hernandez-Ortiz, Juan P.; Potamousis, Konstantinos; Tsvid, Gene; Place, Michael; Ravindran, Prabu; Jo, Kyubong; Zhou, Shiguo; Odijk, Theo; De Pablo, Juan J.; Schwartz, David C.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 114, No. 51, 19.12.2017, p. 13400-13405.

Research output: Contribution to journalArticle

Kounovsky-Shafer, KL, Hernandez-Ortiz, JP, Potamousis, K, Tsvid, G, Place, M, Ravindran, P, Jo, K, Zhou, S, Odijk, T, De Pablo, JJ & Schwartz, DC 2017, 'Electrostatic confinement and manipulation of DNA molecules for genome analysis', Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 51, pp. 13400-13405. https://doi.org/10.1073/pnas.1711069114
Kounovsky-Shafer, Kristy L. ; Hernandez-Ortiz, Juan P. ; Potamousis, Konstantinos ; Tsvid, Gene ; Place, Michael ; Ravindran, Prabu ; Jo, Kyubong ; Zhou, Shiguo ; Odijk, Theo ; De Pablo, Juan J. ; Schwartz, David C. / Electrostatic confinement and manipulation of DNA molecules for genome analysis. In: Proceedings of the National Academy of Sciences of the United States of America. 2017 ; Vol. 114, No. 51. pp. 13400-13405.
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