1
|
Bošković F, Maffeo C, Patiño-Guillén G, Tivony R, Aksimentiev A, Keyser UF. Nanopore translocation reveals electrophoretic force on A- and B-form nucleic acids. bioRxiv 2023:2023.09.12.557357. [PMID: 37745457 PMCID: PMC10515835 DOI: 10.1101/2023.09.12.557357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Electrophoretic transport plays a pivotal role in advancing sensing technologies, with A-form nucleic acids, predominantly RNA-containing, emerging as the new frontier for nanopore sensing and sequencing. Here, we compare the less-explored dynamics of A-form electrophoretic transport with the well-researched transport of B-form DNA. Using DNA/RNA nanotechnology and solid-state nanopores, the translocation of RNA:DNA (RD) and DNA:DNA (DD) duplexes was examined. Notably, RD duplexes were found to translocate through nanopores up to 1.8 times faster than DD duplexes, despite containing the same number of base pairs. Our experiments reveal that A- and B-form duplex molecules with the same contour length move with comparable velocity through nanopores. We examined the physical characteristics of both duplex forms using atomic force microscopy, agarose gel electrophoresis, and dynamic light scattering measurements. With the help of coarse-grained and atomistic molecular dynamics simulations, we find the effective force applied by the electric field to a fragment of A-form or B-form duplex in a nanopore to be approximately the same. Our results shed light on the significance of helical form in nucleic acid translocation, with implications for RNA sensing, sequencing, and molecular understanding of electrophoretic transport.
Collapse
Affiliation(s)
- F. Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - C. Maffeo
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | | | - R. Tivony
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Current address: Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - A. Aksimentiev
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - U. F. Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| |
Collapse
|
2
|
Leitao SM, Navikas V, Miljkovic H, Drake B, Marion S, Pistoletti Blanchet G, Chen K, Mayer SF, Keyser UF, Kuhn A, Fantner GE, Radenovic A. Spatially multiplexed single-molecule translocations through a nanopore at controlled speeds. Nat Nanotechnol 2023; 18:1078-1084. [PMID: 37337057 DOI: 10.1038/s41565-023-01412-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/02/2023] [Indexed: 06/21/2023]
Abstract
In current nanopore-based label-free single-molecule sensing technologies, stochastic processes influence the selection of translocating molecule, translocation rate and translocation velocity. As a result, single-molecule translocations are challenging to control both spatially and temporally. Here we present a method using a glass nanopore mounted on a three-dimensional nanopositioner to spatially select molecules, deterministically tethered on a glass surface, for controlled translocations. By controlling the distance between the nanopore and glass surface, we can actively select the region of interest on the molecule and scan it a controlled number of times and at a controlled velocity. Decreasing the velocity and averaging thousands of consecutive readings of the same molecule increases the signal-to-noise ratio by two orders of magnitude compared with free translocations. We demonstrate the method's versatility by assessing DNA-protein complexes, DNA rulers and DNA gaps, achieving down to single-nucleotide gap detection.
Collapse
Affiliation(s)
- S M Leitao
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - V Navikas
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - H Miljkovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - B Drake
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - S Marion
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - G Pistoletti Blanchet
- Laboratory of Molecular Biology, Institute of Life Technologies, School of Engineering, HES-SO Valais-Wallis, Sion, Switzerland
- Central Environmental Laboratory, Institute of Environmental Engineering, ENAC, EPFL, Sion, Switzerland
| | - K Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - S F Mayer
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - U F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - A Kuhn
- Laboratory of Molecular Biology, Institute of Life Technologies, School of Engineering, HES-SO Valais-Wallis, Sion, Switzerland
| | - G E Fantner
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland.
| | - A Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland.
| |
Collapse
|
3
|
Abstract
Achieving a full understanding of the noise in resistive pulse sensing experiments is central to the development of this important single molecule technique. Here, we present a comprehensive study of the noise properties of conical glass nanopores as components in an ionic circuit by studying the power spectral density of the system in salt solutions at a range of concentrations. We begin by investigating the ionic current rectification of the pores, showing that it is only observed above a critical Dukhin number in agreement with theoretical predictions. We then investigate the noise properties of the pores and demonstrate that the fluctuations in the ionic current at no applied potential difference can be well modelled over four decades of frequency as thermal fluctuations over a complex impedance. Finally, we show that-when an ionic current flows-1/f noise dominates the power spectrum below ∼100 Hz. Fluctuations in the surface current govern the low-frequency 1/f noise, with the asymmetric shape of the pore leading the magnitude to scale with [Formula: see text], faster than predicted by Hooge's empirical relation.
Collapse
Affiliation(s)
- S F Knowles
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | | | | |
Collapse
|
4
|
Al Nahas K, Cama J, Schaich M, Hammond K, Deshpande S, Dekker C, Ryadnov MG, Keyser UF. A microfluidic platform for the characterisation of membrane active antimicrobials. Lab Chip 2019; 19:837-844. [PMID: 30698187 PMCID: PMC6404476 DOI: 10.1039/c8lc00932e] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/05/2018] [Indexed: 05/21/2023]
Abstract
The spread of bacterial resistance against conventional antibiotics generates a great need for the discovery of novel antimicrobials. Polypeptide antibiotics constitute a promising class of antimicrobial agents that favour attack on bacterial membranes. However, efficient measurement platforms for evaluating their mechanisms of action in a systematic manner are lacking. Here we report an integrated lab-on-a-chip multilayer microfluidic platform to quantify the membranolytic efficacy of such antibiotics. The platform is a biomimetic vesicle-based screening assay, which generates giant unilamellar vesicles (GUVs) in physiologically relevant buffers on demand. Hundreds of these GUVs are individually immobilised downstream in physical traps connected to separate perfusion inlets that facilitate controlled antibiotic delivery. Antibiotic efficacy is expressed as a function of the time needed for an encapsulated dye to leak out of the GUVs as a result of antibiotic treatment. This proof-of-principle study probes the dose response of an archetypal polypeptide antibiotic cecropin B on GUVs mimicking bacterial membranes. The results of the study provide a foundation for engineering quantitative, high-throughput microfluidics devices for screening antibiotics.
Collapse
Affiliation(s)
- K. Al Nahas
- Cavendish Laboratory
, Univ. of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
.
| | - J. Cama
- Cavendish Laboratory
, Univ. of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
.
| | - M. Schaich
- Cavendish Laboratory
, Univ. of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
.
| | - K. Hammond
- National Physical Laboratory
,
Hampton Road, Teddington
, Middlesex TW11 0LW
, UK
| | - S. Deshpande
- Kavli Institute of Nanoscience
, Delft Univ. of Technology
,
van der Maasweg 9
, Delft 2629 HZ
, Netherlands
| | - C. Dekker
- Kavli Institute of Nanoscience
, Delft Univ. of Technology
,
van der Maasweg 9
, Delft 2629 HZ
, Netherlands
| | - M. G. Ryadnov
- National Physical Laboratory
,
Hampton Road, Teddington
, Middlesex TW11 0LW
, UK
| | - U. F. Keyser
- Cavendish Laboratory
, Univ. of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
.
| |
Collapse
|
5
|
Abstract
We investigate general properties of nondeterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter can lead to self-limiting cluster growth. Furthermore, by adjusting the relative abundance of self-assembly particles in a two-particle mixture, we are able to tune the final sizes of these clusters. We show that this is a fundamental property of asymmetric interactions, which has potential applications in bioengineering, and provides insights into the study of diseases caused by protein aggregation.
Collapse
Affiliation(s)
- S Tesoro
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, CB3 0HE Cambridge, United Kingdom
| | - K Göpfrich
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, CB3 0HE Cambridge, United Kingdom
| | - T Kartanas
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, CB3 0HE Cambridge, United Kingdom
| | - U F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, CB3 0HE Cambridge, United Kingdom
| | - S E Ahnert
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, CB3 0HE Cambridge, United Kingdom
| |
Collapse
|
6
|
Cama J, Chimerel C, Pagliara S, Javer A, Keyser UF. A label-free microfluidic assay to quantitatively study antibiotic diffusion through lipid membranes. Lab Chip 2014; 14:2303-2308. [PMID: 24825393 DOI: 10.1039/c4lc00217b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
With the rise in antibiotic resistance amongst pathogenic bacteria, the study of antibiotic activity and transport across cell membranes is gaining widespread importance. We present a novel, label-free microfluidic assay that quantifies the permeability coefficient of a broad spectrum fluoroquinolone antibiotic, norfloxacin, across lipid membranes using the UV autofluorescence of the drug. We use giant lipid vesicles as highly controlled model systems to study the diffusion through lipid membranes. Our technique directly determines the permeability coefficient without requiring the measurement of the partition coefficient of the antibiotic.
Collapse
Affiliation(s)
- J Cama
- Biological and Soft Systems, Dept. of Physics, Univ. of Cambridge, Cavendish Laboratory, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | | | | | | | | |
Collapse
|
7
|
Otto O, Steinbock LJ, Wong DW, Gornall JL, Keyser UF. Note: Direct force and ionic-current measurements on DNA in a nanocapillary. Rev Sci Instrum 2011; 82:086102. [PMID: 21895280 DOI: 10.1063/1.3623502] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have developed optical tweezers, with force measurements based on fast video tracking, for analysis and control of DNA translocation through nanocapillaries. Nanocapillaries are single-molecule biosensors with very similar characteristics to solid-state nanopores. Our novel experimental setup allows for ionic-current measurements in which the nanocapillary is oriented perpendicular to the trapping laser. Using video-based particle tracking, we are able to measure the position of DNA coated colloids at sub-millisecond resolution and in real-time. We present the first electrophoretic force and simultaneous ionic-current measurements of a single DNA molecule inside the orifice of a nanocapillary.
Collapse
Affiliation(s)
- O Otto
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | |
Collapse
|
8
|
Gutsche C, Elmahdy MM, Kegler K, Semenov I, Stangner T, Otto O, Ueberschär O, Keyser UF, Krueger M, Rauscher M, Weeber R, Harting J, Kim YW, Lobaskin V, Netz RR, Kremer F. Micro-rheology on (polymer-grafted) colloids using optical tweezers. J Phys Condens Matter 2011; 23:184114. [PMID: 21508470 DOI: 10.1088/0953-8984/23/18/184114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Optical tweezers are experimental tools with extraordinary resolution in positioning (± 1 nm) a micron-sized colloid and in the measurement of forces (± 50 fN) acting on it-without any mechanical contact. This enables one to carry out a multitude of novel experiments in nano- and microfluidics, of which the following will be presented in this review: (i) forces within single pairs of colloids in media of varying concentration and valency of the surrounding ionic solution, (ii) measurements of the electrophoretic mobility of single colloids in different solvents (concentration, valency of the ionic solution and pH), (iii) similar experiments as in (i) with DNA-grafted colloids, (iv) the nonlinear response of single DNA-grafted colloids in shear flow and (v) the drag force on single colloids pulled through a polymer solution. The experiments will be described in detail and their analysis discussed.
Collapse
Affiliation(s)
- C Gutsche
- Institute of Experimental Physics I, Leipzig University, Linnéstrasse 5, D-04103, Leipzig, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Steinbock LJ, Otto O, Skarstam DR, Jahn S, Chimerel C, Gornall JL, Keyser UF. Probing DNA with micro- and nanocapillaries and optical tweezers. J Phys Condens Matter 2010; 22:454113. [PMID: 21339600 DOI: 10.1088/0953-8984/22/45/454113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We combine for the first time optical tweezer experiments with the resistive pulse technique based on capillaries. Quartz glass capillaries are pulled into a conical shape with tip diameters as small as 27 nm. Here, we discuss the translocation of λ-phage DNA which is driven by an electrophoretic force through the nanocapillary. The resulting change in ionic current indicates the folding state of single λ-phage DNA molecules. Our flow cell design allows for the straightforward incorporation of optical tweezers. We show that a DNA molecule attached to an optically trapped colloid is pulled into a capillary by electrophoretic forces. The detected electrophoretic force is in good agreement with measurements in solid-state nanopores.
Collapse
Affiliation(s)
- L J Steinbock
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | | | | | | | | | | | | |
Collapse
|
10
|
Wunderlich B, Leirer C, Idzko AL, Keyser UF, Wixforth A, Myles VM, Heimburg T, Schneider MF. Phase-state dependent current fluctuations in pure lipid membranes. Biophys J 2009; 96:4592-7. [PMID: 19486681 DOI: 10.1016/j.bpj.2009.02.053] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Revised: 01/20/2009] [Accepted: 02/20/2009] [Indexed: 10/20/2022] Open
Abstract
Current fluctuations in pure lipid membranes have been shown to occur under the influence of transmembrane electric fields (electroporation) as well as a result from structural rearrangements of the lipid bilayer during phase transition (soft perforation). We demonstrate that the ion permeability during lipid phase transition exhibits the same qualitative temperature dependence as the macroscopic heat capacity of a D15PC/DOPC vesicle suspension. Microscopic current fluctuations show distinct characteristics for each individual phase state. Although current fluctuations in the fluid phase show spikelike behavior of short timescales (approximately 2 ms) with a narrow amplitude distribution, the current fluctuations during lipid phase transition appear in distinct steps with timescales of approximately 20 ms. We propose a theoretical explanation for the origin of timescales and permeability based on a linear relationship between lipid membrane susceptibilities and relaxation times near the phase transition.
Collapse
Affiliation(s)
- B Wunderlich
- University of Augsburg, Experimental Physics I, Augsburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Abstract
The translocation of small molecules and polymers is an integral process for the functioning of living cells. Many of the basic physical, chemical, and biological interactions have not yet been studied because they are not directly experimentally accessible. We have shown that a combination of optical tweezers, single solid-state nanopores, and electrophysiological ionic current detection enable deeper insight into the behavior of polymers in confinement. Here we describe the experimental procedures that are necessary to manipulate single biopolymers in a single nanopore, not only by electrical fields, but also through mechanical forces using optical tweezers.
Collapse
Affiliation(s)
- U F Keyser
- University of Cambridge, JJ Thomson Avenue, 3 0HE, Cambridge, CB, UK.
| | | | | | | |
Collapse
|
12
|
Gutsche C, Keyser UF, Kegler K, Kremer F, Linse P. Forces between single pairs of charged colloids in aqueous salt solutions. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 76:031403. [PMID: 17930243 DOI: 10.1103/physreve.76.031403] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 06/29/2007] [Indexed: 05/25/2023]
Abstract
Forces between single pairs of negatively charged micrometer-sized colloids in aqueous solutions of monovalent, divalent, or trivalent counter-ions at varying concentrations have been measured by employing optical tweezers. The experimental data have been analyzed by using the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and a numerical solution of the Poisson-Boltzmann (PB) equation. With monovalent counterions, the data are well described by the DLVO and PB theories, suggesting that the DLVO theory is adequate to describe the colloidal forces at these conditions. At higher counter-ion valence, the approximations within the two theories become evident.
Collapse
Affiliation(s)
- C Gutsche
- Institut für Experimentelle Physik I der Universität Leipzig, Germany
| | | | | | | | | |
Collapse
|
13
|
Abstract
From conductance and noise studies, we infer that nanometer-sized gaseous bubbles (nanobubbles) are the dominant noise source in solid-state nanopores. We study the ionic conductance through solid-state nanopores as they are moved through the focus of an infrared laser beam. The resulting conductance profiles show strong variations in both the magnitude of the conductance and in the low-frequency noise when a single nanopore is measured multiple times. Differences up to 5 orders of magnitude are found in the current power spectral density. In addition, we measure an unexpected double-peak ionic conductance profile. A simple model of a cylindrical nanopore that contains a nanobubble explains the measured profile and accounts for the observed variations in the magnitude of the conductance.
Collapse
Affiliation(s)
- R M M Smeets
- Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, The Netherlands
| | | | | | | | | |
Collapse
|
14
|
Keyser UF, Fühner C, Borck S, Haug RJ, Bichler M, Abstreiter G, Wegscheider W. Kondo effect in a few-electron quantum ring. Phys Rev Lett 2003; 90:196601. [PMID: 12785965 DOI: 10.1103/physrevlett.90.196601] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2002] [Indexed: 05/24/2023]
Abstract
A small quantum ring with less than ten electrons was studied by transport spectroscopy. For strong coupling to the leads a Kondo effect is observed and used to characterize the spin structure of the system in a wide range of magnetic fields. At small magnetic fields Aharonov-Bohm oscillations influenced by Coulomb interaction appear. They exhibit phase jumps by pi at the Coulomb-blockade resonances. Inside Coulomb-blockade valleys the Aharonov-Bohm oscillations can also be studied due to the finite conductance caused by the Kondo effect. Astonishingly, the maxima of the oscillations show linear shifts with increasing magnetic field and gate voltage.
Collapse
Affiliation(s)
- U F Keyser
- Institut für Festkörperphysik, Universität Hannover, Germany.
| | | | | | | | | | | | | |
Collapse
|