Structural Integrity of ssDNA on the Surface of Solid-state Nanopores

POSTER

Abstract

Self-assembly and 3D conformation of nucleic acid aptamers enable selective binding with biomarkers and cells. One mode of utilizing selective property of the aptamers is by grafting these in solid-state nanopores. Coating the inside walls of the nanopores with protein specific nucleic acid aptamers changes the energy landscape and affects the biomarker translocation. When the target protein passes through the nanopore, it interacts with surface-bound DNA and the process alters overall energy profile, which is essentially specific to the protein detected. The simulations showed that fundamental challenges in this process were to ensure these detection motifs held their structure and functionality under applied electric field and experimental conditions. The all-atom molecular dynamics simulation of the effects of external electric field on the 3D conformation of such ligand-DNA demonstrated how the grafted moieties affected the translocation time, velocity and the detection frequency of the target molecule. A novel case of protein translocation was also investigated for comparison where DNA was pre-bound to the protein.

Authors

  • Mohammed Arif Mahmood

    University of Texas at Arlington

  • Hanu Arava

    University of Houston, University of Texas at Brownsville, None, Univ of Texas, San Antonio, University of Texas at El Paso, Univ of Arizona, Department of Physics and Astronomy and Center for Gravitational Wave Astronomy, University of Texas at Brownsville, Laboratoire des Mat\'eriaux Avanc\'es, Universit\'e Claude Bernard Lyon 1, UTEP, University of Texas, Austin, University of Texas at Austin, Institute for Astronomy, Russian Academy of Sciences, University of Texas at Arlington, The University of Texas at Arlington, MIT, U. Mass. Dartmouth, Texas A{\&}M University, Texas Christian University, Laboratoire des Mat\'erieux Avanc\'es B\^atiment Virgo, Ion Beam Materials Laboratory, Los Alamos National Laboratory, Texas A\&M University, Accelerator Research Laboratory, University of Florida, The Ohio State University, Yale University, University of Guelph, Canada, Armagh Observatory, NASA-Ames, NASA-Goddard, Texas A\&M University-Commerce, Texas A\&M University, Hanyang University, Texas A\&M Univ, Department of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran, Physics Department, Texas State University at San Marcos

  • Hanu Arava

    University of Houston, University of Texas at Brownsville, None, Univ of Texas, San Antonio, University of Texas at El Paso, Univ of Arizona, Department of Physics and Astronomy and Center for Gravitational Wave Astronomy, University of Texas at Brownsville, Laboratoire des Mat\'eriaux Avanc\'es, Universit\'e Claude Bernard Lyon 1, UTEP, University of Texas, Austin, University of Texas at Austin, Institute for Astronomy, Russian Academy of Sciences, University of Texas at Arlington, The University of Texas at Arlington, MIT, U. Mass. Dartmouth, Texas A{\&}M University, Texas Christian University, Laboratoire des Mat\'erieux Avanc\'es B\^atiment Virgo, Ion Beam Materials Laboratory, Los Alamos National Laboratory, Texas A\&M University, Accelerator Research Laboratory, University of Florida, The Ohio State University, Yale University, University of Guelph, Canada, Armagh Observatory, NASA-Ames, NASA-Goddard, Texas A\&M University-Commerce, Texas A\&M University, Hanyang University, Texas A\&M Univ, Department of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran, Physics Department, Texas State University at San Marcos

  • Samir Iqbal

    Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX 76011, USA, University of Texas at Arlington, University of Texas at Arlington (UTA), Texas, USA