The urgent need to develop revolutionary technologies, for sequencing large DNA molecules quickly and economically, has led to many experimental strategies. Chief among these are the nanopore-based electrophoretic experiments. In these experiments, translocation of single molecules of DNA is monitored as they pass through protein channels and solid-state nanopores under an external electric field. While the results from such experiments are extremely promising towards reaching $1000 genome target, there are many puzzles and the physics of these nanoscopic systems needs to be understood from a fundamental scientific point of view. The proposed research deals with a fundamental understanding of the behavior of DNA in nanopore environments under the influence of electrical and hydrodynamic forces. We will investigate the challenges underlying several key system components in the goal of reducing the cost of sequencing mammalian-sized genomes to $1000. The major challenges deal with the predictability of capture of the target molecule at the nanopore, efficient threading into the pore, and slowing down the translocating molecule through the pore. We will use a combination of statistical mechanics theory, computer simulations, and numerical computation of coupled nonlinear equations to address polymer statistics and dynamics, electrostatics, and hydrodynamics in the phenomena of DNA translocation. The proposed research, while being generally relevant to all nanopore-based experiments, will be hinged specifically on: (a) role of hybridization in translocation through a-hemolysin, MspA, and solid-state pores, (b) enzyme-modulated DNA translocation through channels, and (c) control of capture rate and successful translocation rate of DNA in protein channels and solid-state nanopores.

Public Health Relevance

Availability of low-cost technologies for DNA sequencing is vital in identifying the origins of diseases and maintenance of public health. The proposed research addresses the challenges in several key system components in the development of genome sequencing technologies at the cost of $1000 per a mammalian-sized genome.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
2R01HG002776-07
Application #
7978448
Study Section
Special Emphasis Panel (ZHG1-HGR-N (M1))
Program Officer
Schloss, Jeffery
Project Start
2003-06-06
Project End
2013-06-30
Budget Start
2010-09-01
Budget End
2011-06-30
Support Year
7
Fiscal Year
2010
Total Cost
$267,586
Indirect Cost
Name
University of Massachusetts Amherst
Department
Engineering (All Types)
Type
Schools of Arts and Sciences
DUNS #
153926712
City
Amherst
State
MA
Country
United States
Zip Code
01003
Katkar, H H; Muthukumar, M (2018) Role of non-equilibrium conformations on driven polymer translocation. J Chem Phys 148:024903
Katkar, H H; Muthukumar, M (2018) Single molecule electrophoresis of star polymers through nanopores: Simulations. J Chem Phys 149:163306
Jia, Di; Muthukumar, Murugappan (2018) Topologically frustrated dynamics of crowded charged macromolecules in charged hydrogels. Nat Commun 9:2248
Muthukumar, M (2017) 50th Anniversary Perspective: A Perspective on Polyelectrolyte Solutions. Macromolecules 50:9528-9560
Shojaei, H R; Muthukumar, M (2017) Adsorption and encapsulation of flexible polyelectrolytes in charged spherical vesicles. J Chem Phys 146:244901
Jou, Ining; Muthukumar, Murugappan (2017) Effects of Nanopore Charge Decorations on the Translocation Dynamics of DNA. Biophys J 113:1664-1672
Shojaei, Hamid R; Muthukumar, Murugappan (2016) Translocation of an Incompressible Vesicle through a Pore. J Phys Chem B 120:6102-9
Bell, Nicholas A W; Muthukumar, Murugappan; Keyser, Ulrich F (2016) Translocation frequency of double-stranded DNA through a solid-state nanopore. Phys Rev E 93:022401
Muthukumar, Murugappan (2016) Ordinary-extraordinary transition in dynamics of solutions of charged macromolecules. Proc Natl Acad Sci U S A 113:12627-12632
Mondal, Debasish; Muthukumar, M (2016) Stochastic resonance during a polymer translocation process. J Chem Phys 144:144901

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