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Waduge P, Hu R, Bandarkar P, Yamazaki H, Cressiot B, Zhao Q, Whitford PC, Wanunu M. Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes. ACS NANO 2017; 11:5706-5716. [PMID: 28471644 DOI: 10.1021/acsnano.7b01212] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Proteins are structurally dynamic macromolecules, and it is challenging to quantify the conformational properties of their native state in solution. Nanopores can be efficient tools to study proteins in a solution environment. In this method, an electric field induces electrophoretic and/or electro-osmotic transport of protein molecules through a nanopore slightly larger than the protein molecule. High-bandwidth ion current measurement is used to detect the transit of each protein molecule. First, our measurements reveal a correlation between the mean current blockade amplitude and the radius of gyration for each protein. Next, we find a correlation between the shape of the current signal amplitude distributions and the protein fluctuation as obtained from molecular dynamics simulations. Further, the magnitude of the structural fluctuations, as probed by experiments and simulations, correlates with the ratio of α-helix to β-sheet content. We highlight the resolution of our measurements by resolving two states of calmodulin, a canonical protein that undergoes a conformational change in response to calcium binding.
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Affiliation(s)
| | - Rui Hu
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
| | | | - Hirohito Yamazaki
- Graduate School of Science and Technology, Keio University , 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | | | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
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A new sight for detecting the ADRB1 gene mutation to guide a therapeutic regimen for hypertension based on a CeO 2 -doped nanoprobe. Biosens Bioelectron 2017; 92:402-409. [DOI: 10.1016/j.bios.2016.10.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/12/2016] [Accepted: 10/28/2016] [Indexed: 01/17/2023]
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53
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Abdolvahab RH. Chaperone-driven polymer translocation through nanopore: Spatial distribution and binding energy. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:41. [PMID: 28389823 DOI: 10.1140/epje/i2017-11528-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/10/2017] [Indexed: 06/07/2023]
Abstract
Chaperones are binding proteins working as a driving force in biopolymer translocation. They bind to the biopolymer near the pore and prevent its backsliding. Chaperones may have different spatial distributions. Recently, we showed the importance of their spatial distribution in translocation and its effects on the sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. Because of the exponential distribution of chaperones, the energy dependency of the translocation time will change. Here we find a minimum in translocation time versus binding effective energy (EBE) curve. The same trend can be seen in the scaling exponent of time versus polymer length, [Formula: see text] ([Formula: see text]), when plotted against EBE. Interestingly in some special cases, e.g. chaperones of size [Formula: see text] and with an exponential distribution rate of [Formula: see text], the minimum even reaches to an amount of less than 1 ([Formula: see text]). We explain the possibility of this rare result. Moreover, based on a theoretical discussion we show that, by taking into account the velocity dependency of the translocation on polymer length, one can truly predict the value of this minimum.
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55
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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56
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Menais T, Mossa S, Buhot A. Polymer translocation through nano-pores in vibrating thin membranes. Sci Rep 2016; 6:38558. [PMID: 27934936 PMCID: PMC5146916 DOI: 10.1038/srep38558] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/10/2016] [Indexed: 01/31/2023] Open
Abstract
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer can accommodate several bases at the same time, making difficult accurate sequencing applications. More recently, the use of graphene membranes has paved the way to new sequencing capabilities, with the possibility to measure transverse currents, among other advances. The reduced thickness of these new membranes poses new questions on the effect of deformability and vibrations of the membrane on the translocation process, two features which are not taken into account in the well established theoretical frameworks. Here, we make a first step forward in this direction. We report numerical simulation work on a model system simple enough to allow gathering significant insight on the effect of these features on the average translocation time, with appropriate statistical significance. We have found that the interplay between thermal fluctuations and the deformability properties of the nano-pore play a crucial role in determining the process. We conclude by discussing new directions for further work.
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Affiliation(s)
- Timothée Menais
- Univ. Grenoble Alpes, INAC-SYMMES, F-38000 Grenoble, France
- CNRS, INAC-SYMMES, F-38000 Grenoble, France
- CEA, INAC-SYMMES, F-38000 Grenoble, France
| | - Stefano Mossa
- Univ. Grenoble Alpes, INAC-SYMMES, F-38000 Grenoble, France
- CNRS, INAC-SYMMES, F-38000 Grenoble, France
- CEA, INAC-SYMMES, F-38000 Grenoble, France
| | - Arnaud Buhot
- Univ. Grenoble Alpes, INAC-SYMMES, F-38000 Grenoble, France
- CNRS, INAC-SYMMES, F-38000 Grenoble, France
- CEA, INAC-SYMMES, F-38000 Grenoble, France
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57
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Squires AH, Gilboa T, Torfstein C, Varongchayakul N, Meller A. Single-Molecule Characterization of DNA-Protein Interactions Using Nanopore Biosensors. Methods Enzymol 2016; 582:353-385. [PMID: 28062042 DOI: 10.1016/bs.mie.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Detection and characterization of nucleic acid-protein interactions, particularly those involving DNA and proteins such as transcription factors, enzymes, and DNA packaging proteins, remain significant barriers to our understanding of genetic regulation. Nanopores are an extremely sensitive and versatile sensing platform for label-free detection of single biomolecules. Analyte molecules are drawn to and through a nanoscale aperture by an electrophoretic force, which acts upon their native charge while in the sensing region of the pore. When the nanopore's diameter is only slightly larger than the biopolymer's cross section (typically a few nm); the latter must translocate through the pore in a linear fashion due to the constricted geometry in this region. These features allow nanopores to interrogate protein-nucleic acids in multiple sensing modes: first, by scanning and mapping the locations of binding sites along an analyte molecule, and second, by probing the strength of the bond between a protein and nucleic acid, using the native charge of the nucleic acid to apply an electrophoretic force to the complex while the protein is geometrically prevented from passing through the nanopore. In this chapter, we describe progress toward nanopore sensing of protein-nucleic acid complexes in the context of both mapping binding sites and performing force spectroscopy to determine the strength of interactions. We conclude by reviewing the strengths and challenges of the nanopore technique in the context of studying DNA-protein interactions.
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Affiliation(s)
- A H Squires
- Stanford University, Stanford, CA, United States
| | | | | | | | - A Meller
- The Technion, Haifa, Israel; Boston University, Boston, MA, United States.
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58
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Vollmer SC, de Haan HW. Translocation is a nonequilibrium process at all stages: Simulating the capture and translocation of a polymer by a nanopore. J Chem Phys 2016; 145:154902. [DOI: 10.1063/1.4964630] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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The Semiflexible Polymer Translocation into Laterally Unbounded Region between Two Parallel Flat Membranes. Polymers (Basel) 2016; 8:polym8090332. [PMID: 30974609 PMCID: PMC6431992 DOI: 10.3390/polym8090332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 11/17/2022] Open
Abstract
Using the dynamic Monte Carlo method, we investigate dynamics of semiflexible polymer translocation through a nanopore into laterally unbounded region between two parallel flat membranes with separation R in presence of an electric field inside the pore. The average translocation time τ initially decreases rapidly with increase of R in the range of R < 10 and then almost keeps constant for R ≥ 10, and the decline range increases with increase of dimensionless bending stiffness κ. We mainly study the effect of chain length N, κ and electric field strength E on the translocation process for R = 5. The translocation dynamics is significantly altered in comparison to an unconfined environment. We find τ ~ Nα, where the exponent α increases with increase of E for small κ. α initially increases slowly with increase of E and then keeps constant for moderate κ. α decreases with increase of E for large κ. However, α decreases with increase of κ under various E. In addition, we find τ ~ κβ. β decreases with increase of N under various E. These behaviors are interpreted in terms of the probability distribution of translocation time and the waiting time of an individual monomer segment passing through the pore during translocation.
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60
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Tanaka S, Tsutsui M, Theodore H, Yuhui H, Arima A, Tsuji T, Doi K, Kawano S, Taniguchi M, Kawai T. Tailoring particle translocation via dielectrophoresis in pore channels. Sci Rep 2016; 6:31670. [PMID: 27527126 PMCID: PMC4985646 DOI: 10.1038/srep31670] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/21/2016] [Indexed: 11/25/2022] Open
Abstract
Understanding and controlling electrophoretic motions of nanoscopic objects in fluidic channels are a central challenge in developing nanopore technology for molecular analyses. Although progress has been made in slowing the translocation velocity to meet the requirement for electrical detections of analytes via picoampere current measurements, there exists no method useful for regulating particle flows in the transverse directions. Here, we report the use of dielectrophoresis to manipulate the single-particle passage through a solid-state pore. We created a trap field by applying AC voltage between electrodes embedded in a low-aspect-ratio micropore. We demonstrated a traffic control of particles to go through center or near side surface via the voltage frequency. We also found enhanced capture efficiency along with faster escaping speed of particles by virtue of the AC-mediated electroosmosis. This method is compatible with nanopore sensing and would be widely applied for reducing off-axis effects to achieve single-molecule identification.
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Affiliation(s)
- Shoji Tanaka
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Hu Theodore
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Luo Yu Road, Wuhan 430074, China
| | - He Yuhui
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Luo Yu Road, Wuhan 430074, China
| | - Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Tsuji
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Satoyuki Kawano
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
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61
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Rems L, Kawale D, Lee LJ, Boukany PE. Flow of DNA in micro/nanofluidics: From fundamentals to applications. BIOMICROFLUIDICS 2016; 10:043403. [PMID: 27493701 PMCID: PMC4958106 DOI: 10.1063/1.4958719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 05/26/2023]
Abstract
Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new single-molecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena, which were previously unachievable with conventional methods such as bulk rheometry tests. For instance, the field of polymer rheology is at a turning point to relate the complex molecular conformations to the nonlinear viscoelasticity of polymeric fluids (such as coil-stretch transition, shear thinning, and stress overshoot in startup shear). In addition, nanofluidic devices provided a starting point for manipulating single DNA molecules by applying basic principles of polymer physics, which is highly relevant to numerous processes in biosciences. In this article, we review recent progress regarding the flow and deformation of DNA in micro/nanofluidic systems from both fundamental and application perspectives. We particularly focus on advances in the understanding of polymer rheology and identify the emerging research trends and challenges, especially with respect to future applications of nanofluidics in the biomedical field.
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Affiliation(s)
- Lea Rems
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - Durgesh Kawale
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - L James Lee
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, Ohio 43210, USA
| | - Pouyan E Boukany
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
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62
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Li Q, Yu C, Gao R, Xia C, Yuan G, Li Y, Zhao Y, Chen Q, He J. A novel DNA biosensor integrated with Polypyrrole/streptavidin and Au-PAMAM-CP bionanocomposite probes to detect the rs4839469 locus of the vangl1 gene for dysontogenesis prediction. Biosens Bioelectron 2016; 80:674-681. [DOI: 10.1016/j.bios.2016.02.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/31/2016] [Accepted: 02/09/2016] [Indexed: 10/22/2022]
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63
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Sivaraman G, Amorim RG, Scheicher RH, Fyta M. Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides. NANOSCALE 2016; 8:10105-10112. [PMID: 27121677 DOI: 10.1039/c6nr00500d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Modified tiny hydrogen-terminated diamond structures, known as diamondoids, show a high efficiency in sensing DNA molecules. These diamond cages, as recently proposed, could offer functionalization possibilities for gold junction electrodes. In this investigation, we report on diamondoid-functionalized electrodes, showing that such a device would have a high potential in sensing and sequencing DNA. The smallest diamondoid including an amine modification was chosen for the functionalization. Here, we report on the quantum tunneling signals across diamondoid-functionalized Au(111) electrodes. Our work is based on quantum-transport calculations and predicts the expected signals arising from different DNA units within the break junctions. Different gating voltages are proposed in order to tune the sensitivity of the functionalized electrodes with respect to specific nucleotides. The relation of this sensitivity to the coupling or decoupling of the electrodes is discussed. Our results also shed light on the sensing capability of such a device in distinguishing the DNA nucleotides, in their natural and mutated forms.
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Affiliation(s)
- Ganesh Sivaraman
- Institute for Computational Physics, Universität Stuttgart, Germany.
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64
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Zhu Y, Ruan Y, Zhang Y, Lu L, Lu X. Nanomaterial-oriented molecular simulations of ion behaviour in aqueous solution under nanoconfinement. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1161189] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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65
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Paulechka E, Wassenaar TA, Kroenlein K, Kazakov A, Smolyanitsky A. Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing. NANOSCALE 2016; 8:1861-1867. [PMID: 26731166 DOI: 10.1039/c5nr07061a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics (MD) simulations, we study sensor operation at ambient conditions. We combine simulated data with theoretical arguments to estimate the levels of measurable electrical signal variation in response to strains and determine that the proposed sensing mechanism shows significant promise for realistic DNA sensing devices without the need for advanced data processing, or highly restrictive operational conditions.
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Affiliation(s)
- Eugene Paulechka
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80301, USA.
| | - Tsjerk A Wassenaar
- Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Kenneth Kroenlein
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80301, USA.
| | - Andrei Kazakov
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80301, USA.
| | - Alex Smolyanitsky
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80301, USA.
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66
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Johnson RP, Fleming AM, Beuth LR, Burrows CJ, White HS. Base Flipping within the α-Hemolysin Latch Allows Single-Molecule Identification of Mismatches in DNA. J Am Chem Soc 2016; 138:594-603. [PMID: 26704521 PMCID: PMC4828915 DOI: 10.1021/jacs.5b10710] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A method for identifying and differentiating DNA duplexes containing the mismatched base pairs CC and CA at single molecule resolution with the protein pore α-hemolysin (αHL) is presented. Unique modulating current signatures are observed for duplexes containing the CC and CA mismatches when the mismatch site in the duplex is situated in proximity to the latch constriction of αHL during DNA residence inside the pore. The frequency and current amplitude of the modulation states are dependent on the mismatch type (CC or CA) permitting easy discrimination of these mismatches from one another, and from a fully complementary duplex that exhibits no modulation. We attribute the modulating current signatures to base flipping and subsequent interaction with positively charged lysine residues at the latch constriction of αHL. Our hypothesis is supported by the extended residence times of DNA duplexes within the pore when a mismatch is in proximity to the latch constriction, and by the loss of the two-state current signature in low pH buffers (<6.3), where the protonation of one of the cytosine bases increases the stability of the intrahelical state.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Laura R Beuth
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Henry S White
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
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67
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Henley RY, Carson S, Wanunu M. Studies of RNA Sequence and Structure Using Nanopores. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 139:73-99. [PMID: 26970191 DOI: 10.1016/bs.pmbts.2015.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nanopores are powerful single-molecule sensors with nanometer scale dimensions suitable for detection, quantification, and characterization of nucleic acids and proteins. Beyond sequencing applications, both biological and solid-state nanopores hold great promise as tools for studying the biophysical properties of RNA. In this review, we highlight selected landmark nanopore studies with regards to RNA sequencing, microRNA detection, RNA/ligand interactions, and RNA structural/conformational analysis.
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Affiliation(s)
- Robert Y Henley
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts, USA; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA.
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68
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Liang L, Shen JW, Zhang Z, Wang Q. DNA sequencing by two-dimensional materials: As theoretical modeling meets experiments. Biosens Bioelectron 2015; 89:280-292. [PMID: 26711358 DOI: 10.1016/j.bios.2015.12.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Owing to their extraordinary electrical, chemical, optical, mechanical and structural properties, two-dimensional (2D) materials (mainly including graphene, boron nitride, MoS2 etc.) have stimulated exploding interests in sensor applications. 2D-material based nanoscale DNA sequencing is a single-molecule technique with revolutionary potential. In this paper, we review the methodology of DNA sequencing based on the measurements of ionic current, force peak, and transverse electrical currents etc. by 2D materials. The advantages and disadvantages of DNA sequencing by 2D materials are discussed. Besides the recent development of experiments, we will focus on the theoretical calculations of DNA sequencing, which have been played a critical role in the development of this field. Special emphasis will focus on the disagreements between experiments and theoretical calculations, and the explanations for the discrepancy will be highlighted. Finally, some new plausible sequencing methods from computational studies will be discussed, which may be applied in the realistic DNA sequencing experiments in future.
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Affiliation(s)
- Lijun Liang
- Department of Chemistry and §Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Zhisen Zhang
- Research Institute for Soft Matter and Biomimetics, Department of Physics, Xiamen University, Xiamen 361005, People' s Republic of China
| | - Qi Wang
- Department of Chemistry and §Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
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69
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Qiu H, Sarathy A, Leburton JP, Schulten K. Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores. NANO LETTERS 2015; 15:8322-30. [PMID: 26581231 PMCID: PMC4676420 DOI: 10.1021/acs.nanolett.5b03963] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/17/2015] [Indexed: 05/24/2023]
Abstract
We investigate by means of molecular dynamics simulations stretch-induced stepwise translocation of single-stranded DNA (ssDNA) through graphene nanopores. The intrinsic stepwise DNA motion, found to be largely independent of size and shape of the graphene nanopore, is brought about through alternating conformational changes between spontaneous adhesion of DNA bases to the rim of the graphene nanopore and unbinding due to mechanical force or electric field. The adhesion reduces the DNA bases' vertical conformational fluctuations, facilitating base detection and recognition. A graphene membrane shaped as a quantum point contact permits, by means of transverse electronic conductance measurement, detection of the stepwise translocation of the DNA as predicted through quantum mechanical Green's function-based transport calculations. The measurement scheme described opens a route to enhance the signal-to-noise ratio not only by slowing down DNA translocation to provide sufficient time for base recognition but also by stabilizing single DNA bases and, thereby, reducing thermal noise.
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Affiliation(s)
- Hu Qiu
- Beckman Institute for Advanced Science and
Technology, Department of Electrical and Computer Engineering, Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
| | - Aditya Sarathy
- Beckman Institute for Advanced Science and
Technology, Department of Electrical and Computer Engineering, Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
| | - Jean-Pierre Leburton
- Beckman Institute for Advanced Science and
Technology, Department of Electrical and Computer Engineering, Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
| | - Klaus Schulten
- Beckman Institute for Advanced Science and
Technology, Department of Electrical and Computer Engineering, Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
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70
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Feng J, Liu K, Bulushev RD, Khlybov S, Dumcenco D, Kis A, Radenovic A. Identification of single nucleotides in MoS2 nanopores. NATURE NANOTECHNOLOGY 2015; 10:1070-6. [PMID: 26389660 DOI: 10.1038/nnano.2015.219] [Citation(s) in RCA: 288] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/20/2015] [Indexed: 05/19/2023]
Abstract
The size of the sensing region in solid-state nanopores is determined by the size of the pore and the thickness of the pore membrane, so ultrathin membranes such as graphene and single-layer molybdenum disulphide could potentially offer the necessary spatial resolution for nanopore DNA sequencing. However, the fast translocation speeds (3,000-50,000 nt ms(-1)) of DNA molecules moving across such membranes limit their usability. Here, we show that a viscosity gradient system based on room-temperature ionic liquids can be used to control the dynamics of DNA translocation through MoS2 nanopores. The approach can be used to statistically detect all four types of nucleotide, which are identified according to current signatures recorded during their transient residence in the narrow orifice of the atomically thin MoS2 nanopore. Our technique, which exploits the high viscosity of room-temperature ionic liquids, provides optimal single nucleotide translocation speeds for DNA sequencing, while maintaining a signal-to-noise ratio higher than 10.
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Affiliation(s)
- Jiandong Feng
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Ke Liu
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Sergey Khlybov
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Dumitru Dumcenco
- Laboratory of Nanoscale Electronics and Structure, Institute of Electrical Engineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Andras Kis
- Laboratory of Nanoscale Electronics and Structure, Institute of Electrical Engineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
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71
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Carson S, Wilson J, Aksimentiev A, Weigele PR, Wanunu M. Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA. Nucleic Acids Res 2015; 44:2085-92. [PMID: 26578595 PMCID: PMC4797264 DOI: 10.1093/nar/gkv1199] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA molecules, which may account for the differences observed in our nanopore translocation experiments. The altered physico-chemical properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins.
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Affiliation(s)
- Spencer Carson
- Department of Physics, Northeastern University, Boston, MA, USA
| | - James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
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72
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Demming A. DNA sequencing: nanotechnology unravels the code for life. NANOTECHNOLOGY 2015; 26:310201. [PMID: 26180041 DOI: 10.1088/0957-4484/26/31/310201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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73
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Ding Y, Fleming AM, He L, Burrows CJ. Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH. J Am Chem Soc 2015; 137:9053-60. [PMID: 26110559 PMCID: PMC4513840 DOI: 10.1021/jacs.5b03912] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Cytosine
(C)-rich DNA can adopt i-motif folds under acidic conditions,
with the human telomere i-motif providing a well-studied example.
The dimensions of this i-motif are appropriate for capture in the
nanocavity of the α-hemolysin (α-HL) protein pore under
an electrophoretic force. Interrogation of the current vs time (i–t) traces when the i-motif interacts
with α-HL identified characteristic signals that were pH dependent.
These features were evaluated from pH 5.0 to 7.2, a region surrounding
the transition pH of the i-motif (6.1). When the i-motif without polynucleotide
tails was studied at pH 5.0, the folded structure entered the nanocavity
of α-HL from either the top or bottom face to yield characteristic
current patterns. Addition of a 5′ 25-mer poly-2′-deoxyadensosine
tail allowed capture of the i-motif from the unfolded terminus, and
this was used to analyze the pH dependency of unfolding. At pH values
below the transition point, only folded strands were observed, and
when the pH was increased above the transition pH, the number of folded
events decreased, while the unfolded events increased. At pH 6.8 and
7.2 4% and 2% of the strands were still folded, respectively. The
lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms,
respectively, at 160 mV electrophoretic force. These lifetimes are
sufficiently long to affect enzymes operating on DNA. Furthermore,
these transient lifetimes are readily obtained using the α-HL
nanopore, a feature that is not easily achievable by other methods.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Lidong He
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
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74
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Mathwig K, Albrecht T, Goluch ED, Rassaei L. Challenges of Biomolecular Detection at the Nanoscale: Nanopores and Microelectrodes. Anal Chem 2015; 87:5470-5. [DOI: 10.1021/acs.analchem.5b01167] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Klaus Mathwig
- Pharmaceutical
Analysis, Groningen Research Institute of Pharmacy, University of Groningen, P.O. Box 196, 9700 AD Groningen, The Netherlands
| | - Tim Albrecht
- Department
of Chemistry, Imperial College London, Exhibition Road, South Kensington
Campus, London, SW7 2AZ, U.K
| | - Edgar D. Goluch
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 313SN, Boston, Massachusetts 02115, United States
| | - Liza Rassaei
- Department
of Chemical Engineering, Delft University of Technology, Julianalaan
136, 2628 BL Delft, The Netherlands
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75
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Harrer S, Kim SC, Schieber C, Kannam S, Gunn N, Moore S, Scott D, Bathgate R, Skafidas S, Wagner JM. Label-free screening of single biomolecules through resistive pulse sensing technology for precision medicine applications. NANOTECHNOLOGY 2015; 26:182502. [PMID: 25875197 DOI: 10.1088/0957-4484/26/18/182502] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Employing integrated nano- and microfluidic circuits for detecting and characterizing biological compounds through resistive pulse sensing technology is a vibrant area of research at the interface of biotechnology and nanotechnology. Resistive pulse sensing platforms can be customized to study virtually any particle of choice which can be threaded through a fluidic channel and enable label-free single-particle interrogation with the primary read-out signal being an electric current fingerprint. The ability to perform label-free molecular screening with single-molecule and even single binding site resolution makes resistive pulse sensing technology a powerful tool for analyzing the smallest units of biological systems and how they interact with each other on a molecular level. This task is at the core of experimental systems biology and in particular 'omics research which in combination with next-generation DNA-sequencing and next-generation drug discovery and design forms the foundation of a novel disruptive medical paradigm commonly referred to as personalized medicine or precision medicine. DNA-sequencing has approached the 1000-Dollar-Genome milestone allowing for decoding a complete human genome with unmatched speed and at low cost. Increased sequencing efficiency yields massive amounts of genomic data. Analyzing this data in combination with medical and biometric health data eventually enables understanding the pathways from individual genes to physiological functions. Access to this information triggers fundamental questions for doctors and patients alike: what are the chances of an outbreak for a specific disease? Can individual risks be managed and if so how? Which drugs are available and how should they be applied? Could a new drug be tailored to an individual's genetic predisposition fast and in an affordable way? In order to provide answers and real-life value to patients, the rapid evolvement of novel computing approaches for analyzing big data in systems genomics has to be accompanied by an equally strong effort to develop next-generation DNA-sequencing and next-generation drug screening and design platforms. In that context lab-on-a-chip devices utilizing nanopore- and nanochannel based resistive pulse-sensing technology for DNA-sequencing and protein screening applications occupy a key role. This paper describes the status quo of resistive pulse sensing technology for these two application areas with a special focus on current technology trends and challenges ahead.
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Affiliation(s)
- S Harrer
- IBM Research-Australia, 204 Lygon Street, 3053 Carlton, VIC, Australia. University of Melbourne, 3010 Parkville, VIC, Australia
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76
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Polson JM. Polymer translocation into and out of an ellipsoidal cavity. J Chem Phys 2015; 142:174903. [DOI: 10.1063/1.4919642] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- James M. Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada
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77
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Kong Z, Zheng W, Wang Q, Wang H, Xi F, Liang L, Shen JW. Charge-tunable absorption behavior of DNA on graphene. J Mater Chem B 2015; 3:4814-4820. [DOI: 10.1039/c5tb00635j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Charge-tunable absorption behavior of DNA on graphene: 0 is uncharged; − is negative charge; + is positive charge.
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Affiliation(s)
- Zhe Kong
- College of Materials and Environmental Engineering
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Wei Zheng
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016
- People's Republic of China
| | - Qi Wang
- Soft Matter Research Center and Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- People's Republic of China
| | - Hongbo Wang
- College of Automation
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Fengna Xi
- Department of Chemistry
- Zhejiang Sci-Tech University
- Hangzhou
- Zhejiang 310018
- China
| | - Lijun Liang
- Soft Matter Research Center and Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- People's Republic of China
- Department of Polymer Science and Engineering
| | - Jia-Wei Shen
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016
- People's Republic of China
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