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Bespalova M, Öz R, Westerlund F, Krishnan M. Single-Molecule Trapping and Measurement in a Nanostructured Lipid Bilayer System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13923-13934. [PMID: 36326814 PMCID: PMC9671048 DOI: 10.1021/acs.langmuir.2c02203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The repulsive electrostatic force between a biomolecule and a like-charged surface can be geometrically tailored to create spatial traps for charged molecules in solution. Using a parallel-plate system composed of silicon dioxide surfaces, we recently demonstrated single-molecule trapping and high precision molecular charge measurements in a nanostructured free energy landscape. Here we show that surfaces coated with charged lipid bilayers provide a system with tunable surface properties for molecular electrometry experiments. Working with molecular species whose effective charge and geometry are well-defined, we demonstrate the ability to quantitatively probe the electrical charge density of a supported lipid bilayer. Our findings indicate that the fraction of charged lipids in nanoslit lipid bilayers can be significantly different from that in the precursor lipid mixtures used to generate them. We also explore the temporal stability of bilayer properties in nanofluidic systems. Beyond their relevance in molecular measurement, such experimental systems offer the opportunity to examine lipid bilayer formation and wetting dynamics on nanostructured surfaces.
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Affiliation(s)
- Maria Bespalova
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
| | - Robin Öz
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Fredrik Westerlund
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Madhavi Krishnan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
- The
Kavli Institute for Nanoscience Discovery, Sherrington Road, OxfordOX1 3QU, United Kingdom
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Li S, Zeng S, Wen C, Barbe L, Tenje M, Zhang Z, Hjort K, Zhang SL. Dynamics of DNA Clogging in Hafnium Oxide Nanopores. J Phys Chem B 2020; 124:11573-11583. [PMID: 33315405 PMCID: PMC7770817 DOI: 10.1021/acs.jpcb.0c07756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Interfacing
solid-state nanopores with biological systems has been
exploited as a versatile analytical platform for analysis of individual
biomolecules. Although clogging of solid-state nanopores due to nonspecific
interactions between analytes and pore walls poses a persistent challenge
in attaining the anticipated sensing efficacy, insufficient studies
focus on elucidating the clogging dynamics. Herein, we investigate
the DNA clogging behavior by passing double-stranded (ds) DNA molecules
of different lengths through hafnium oxide(HfO2)-coated
silicon (Si) nanopore arrays, at different bias voltages and electrolyte
pH values. Employing stable and photoluminescent-free HfO2/Si nanopore arrays permits a parallelized visualization of DNA clogging
with confocal fluorescence microscopy. We find that the probability
of pore clogging increases with both DNA length and bias voltage.
Two types of clogging are discerned: persistent and temporary. In
the time-resolved analysis, temporary clogging events exhibit a shorter
lifetime at higher bias voltage. Furthermore, we show that the surface
charge density has a prominent effect on the clogging probability
because of electrostatic attraction between the dsDNA and the HfO2 pore walls. An analytical model based on examining the energy
landscape along the DNA translocation trajectory is developed to qualitatively
evaluate the DNA–pore interaction. Both experimental and theoretical
results indicate that the occurrence of clogging is strongly dependent
on the configuration of translocating DNA molecules and the electrostatic
interaction between DNA and charged pore surface. These findings provide
a detailed account of the DNA clogging phenomenon and are of practical
interest for DNA sensing based on solid-state nanopores.
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Affiliation(s)
- Shiyu Li
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Shuangshuang Zeng
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Chenyu Wen
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Laurent Barbe
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Maria Tenje
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Zhen Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Klas Hjort
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shi-Li Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
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