Presentation of large DNA molecules for analysis as nanoconfined dumbbells

Kristy L. Kounovsky-Shafer, Juan P. Hernández-Ortiz, Kyubong Jo, Theo Odijk, Juan J. De Pablo, David C. Schwartz

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multipronged approach that marshaled molecular confinement, ionic environment, and DNA elastic properties - buttressed by molecular simulations - we have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green's function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the "Odijk regime" does indeed start when the confinement dimensions are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics.

Original languageEnglish (US)
Pages (from-to)8356-8368
Number of pages13
JournalMacromolecules
Volume46
Issue number20
DOIs
StatePublished - Nov 1 2013

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DNA
Molecules
Conformations
Hydrodynamics
Green's function
Optical microscopy
Electrostatics
Polymers
Genes

ASJC Scopus subject areas

  • Organic Chemistry
  • Polymers and Plastics
  • Inorganic Chemistry
  • Materials Chemistry

Cite this

Kounovsky-Shafer, K. L., Hernández-Ortiz, J. P., Jo, K., Odijk, T., De Pablo, J. J., & Schwartz, D. C. (2013). Presentation of large DNA molecules for analysis as nanoconfined dumbbells. Macromolecules, 46(20), 8356-8368. https://doi.org/10.1021/ma400926h

Presentation of large DNA molecules for analysis as nanoconfined dumbbells. / Kounovsky-Shafer, Kristy L.; Hernández-Ortiz, Juan P.; Jo, Kyubong; Odijk, Theo; De Pablo, Juan J.; Schwartz, David C.

In: Macromolecules, Vol. 46, No. 20, 01.11.2013, p. 8356-8368.

Research output: Contribution to journalArticle

Kounovsky-Shafer, KL, Hernández-Ortiz, JP, Jo, K, Odijk, T, De Pablo, JJ & Schwartz, DC 2013, 'Presentation of large DNA molecules for analysis as nanoconfined dumbbells', Macromolecules, vol. 46, no. 20, pp. 8356-8368. https://doi.org/10.1021/ma400926h
Kounovsky-Shafer KL, Hernández-Ortiz JP, Jo K, Odijk T, De Pablo JJ, Schwartz DC. Presentation of large DNA molecules for analysis as nanoconfined dumbbells. Macromolecules. 2013 Nov 1;46(20):8356-8368. https://doi.org/10.1021/ma400926h
Kounovsky-Shafer, Kristy L. ; Hernández-Ortiz, Juan P. ; Jo, Kyubong ; Odijk, Theo ; De Pablo, Juan J. ; Schwartz, David C. / Presentation of large DNA molecules for analysis as nanoconfined dumbbells. In: Macromolecules. 2013 ; Vol. 46, No. 20. pp. 8356-8368.
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