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Title: Electrostatic confinement and manipulation of DNA molecules for genome analysis

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,more » 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.« less

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3];  [3];  [3];  [3];  [4];  [3];  [5];  [6];  [3]
  1. Univ. of Nebraska, Kearney, NE (United States)
  2. Univ. Nacional de Colombia, Medellin (Columbia)
  3. Univ. of Wisconsin, Madison, WI (United States)
  4. Sogang Univ., Seoul (Korea, Republic of)
  5. Univ. of Leiden (Netherlands)
  6. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, IL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Institutes of Health (NIH); National Institutes of Health (NIH) - National Cancer Institute; National Institutes of Health (NIH) - National Human Genome Research Institute (NHGRI); National Institute of Standards and Technology (NIST) - Center for Hierarchical Materials Design (CHiMaD); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division
OSTI Identifier:
1557440
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 114; Journal Issue: 51; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; devices; genomics; nanofluidics; single DNA molecules

Citation Formats

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., and Schwartz, David C. Electrostatic confinement and manipulation of DNA molecules for genome analysis. United States: N. p., 2017. Web. doi: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. United States. doi: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., and Schwartz, David C. Mon . "Electrostatic confinement and manipulation of DNA molecules for genome analysis". United States. doi:10.1073/pnas.1711069114. https://www.osti.gov/servlets/purl/1557440.
@article{osti_1557440,
title = {Electrostatic confinement and manipulation of DNA molecules for genome analysis},
author = {Kounovsky-Shafer, Kristy L. and Hernandez-Ortiz, Juan P. and Potamousis, Konstantinos and Tsvid, Gene and Place, Michael and Ravindran, Prabu and Jo, Kyubong and Zhou, Shiguo and Odijk, Theo and de Pablo, Juan J. and Schwartz, David C.},
abstractNote = {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 Mesoplasmaflorum 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.},
doi = {10.1073/pnas.1711069114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 51,
volume = 114,
place = {United States},
year = {2017},
month = {12}
}

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