1
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Zheng J, Zhang X, Yang Y, Cui J, Fang L, Zhou M, Chen Q. Highly Sensitive and Selective DNA Sequencing Device Using Metal Adatom Adsorption on 2D Phosphorene. ACS OMEGA 2023; 8:17768-17778. [PMID: 37251187 PMCID: PMC10210229 DOI: 10.1021/acsomega.3c00540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Two-dimensional (2D) material revolutionarily extends the technique capability of traditional nanopore/nanogap-based DNA sequencing devices. However, challenges associated with DNA sequencing on nanopores still remained in improving the sensitivity and specificity. Herein, by first-principles calculation, we theoretically studied the potential of transition-metal elements (Cr, Fe, Co, Ni, and Au) anchored on monolayer black phosphorene (BP) to act as all-electronic DNA sequencing devices. The spin-polarized band structures appeared in Cr-, Fe-, Co-, and Au-doped BP. Remarkably, the adsorption energy of nucleobases can be significantly enhanced on BP with Co, Fe, and Cr doping, which contribute to the enlarged current signal and lower noise levels. Furthermore, the order of nucleobases in terms of their adsorption energies onto the Cr@BP is C > A > G > T, which exhibits more distinct adsorption energies than Fe@BP or Co@BP. Therefore, Cr-doped BP is more effective to avoid ambiguity in recognizing various bases. We thus envisaged a possibility of a highly sensitive and selective DNA sequencing device based on phosphorene.
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Affiliation(s)
- Junfeng Zheng
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Xuan Zhang
- Department
of Pharmacology, College of Pharmacy and Laboratory Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Youhao Yang
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Jin Cui
- United
Microelectronics Center Co., Ltd. (CUMEC), Chongqing 401332, P. R. China
| | - Liang Fang
- Key
Laboratory of Optoelectronic Technology & Systems (Ministry of
Education), College of Optoelectronic Engineering, Chongqing University, Chongqing 400044, P. R. China
| | - Miao Zhou
- College
of Physics, Chongqing University, Chongqing 400044, P. R. China
| | - Qian Chen
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
- Key Laboratory
of Electromagnetic Radiation Protection, Ministry of Education, Army Medical University (Third Military Medical University), Chongqing 400038, China
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2
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Huang C, Li Z, Zhu X, Ma X, Li N, Fan J. Two Detection Modes of Nanoslit Sensing Based on Planar Heterostructure of Graphene/Hexagonal Boron Nitride. ACS NANO 2023; 17:3301-3312. [PMID: 36638059 DOI: 10.1021/acsnano.2c05002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the y and z directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.
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Affiliation(s)
- Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Na Li
- School of Chemistry and Materials Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials of Ministry of Education, Shanxi Normal University, Taiyuan030000, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
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3
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Recent Advances in Aptamer‐Based Nanopore Sensing at Single‐Molecule Resolution. Chem Asian J 2022; 17:e202200364. [DOI: 10.1002/asia.202200364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/20/2022] [Indexed: 11/07/2022]
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4
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Qiu H, Zhou W, Guo W. Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing. ACS NANO 2021; 15:18848-18864. [PMID: 34841865 DOI: 10.1021/acsnano.1c07960] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.
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Affiliation(s)
- Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanqi Zhou
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
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5
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Zolotoukhina T, Yamada M, Iwakura S. Vibrational Spectra of Nucleotides in the Presence of the Au Cluster Enhancer in MD Simulation of a SERS Sensor. BIOSENSORS 2021; 11:37. [PMID: 33572778 PMCID: PMC7911439 DOI: 10.3390/bios11020037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 11/29/2022]
Abstract
Surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in in vivo imaging. The development of single oligomer resolution in the SERS promotes experiments on DNA and protein identification using SERS as a nanobiosensor. As Raman scanners rely on a multiple spectrum acquisition, faster imaging in real-time is required. SERS weak signal requires averaging of the acquired spectra that erases information on conformation and interaction. To build spectral libraries, the simulation of measurement conditions and conformational variations for the nucleotides relative to enhancer nanostructures would be desirable. In the molecular dynamic (MD) model of a sensing system, we simulate vibrational spectra of the cytosine nucleotide in FF2/FF3 potential in the dynamic interaction with the Au20 nanoparticles (NP) (EAM potential). Fourier transfer of the density of states (DOS) was performed to obtain the spectra of bonds in reaction coordinates for nucleotides at a resolution of 20 to 40 cm-1. The Au20 was optimized by ab initio density functional theory with generalized gradient approximation (DFT GGA) and relaxed by MD. The optimal localization of nucleotide vs. NP was defined and the spectral modes of both components vs. interaction studied. Bond-dependent spectral maps of nucleotide and NP have shown response to interaction. The marker frequencies of the Au20-nucleotide interaction have been evaluated.
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Affiliation(s)
- Tatiana Zolotoukhina
- Department of Mechanical Engineering, University of Toyama, Toyama 930-8555, Japan
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6
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Huang C, Zhu X, Li N, Ma X, Li Z, Fan J. Simultaneous Sensing of Force and Current Signals to Recognize Proteinogenic Amino Acids at a Single-Molecule Level. J Phys Chem Lett 2021; 12:793-799. [PMID: 33411544 DOI: 10.1021/acs.jpclett.0c02989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The identification ability of nanopore sequencing is severely hindered by the diversity of amino acids in a protein. To tackle this problem, a graphene nanoslit sensor is adopted to collect force and current signals to distinguish 20 residues. Extensive molecular dynamics simulations are performed on sequencing peptides under pulling force and applied electric field. Results show that the signals of force and current can be simultaneously collected. Tailoring the geometry of the nanoslit sensor optimizes signal differences between tyrosine and alanine residues. Using the tailored geometry, the characteristic signals of 20 types of residues are detected, enabling excellent distinguishability so that the residues are well-grouped by their properties and signals. The signals reveal a trend in which the larger amino acids have larger pulling forces and lower ionic currents. Generally, the graphene nanoslit sensor can be employed to simultaneously sense two signals, thereby enhancing the identification ability and providing an effective mode of nanopore protein sequencing.
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Affiliation(s)
- Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Na Li
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao, Shandong 266580, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon 999077, Hong Kong, China
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7
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Zhao D, Chen H, Wang Y, Li B, Duan C, Li Z, Li L. Molecular dynamics simulation on DNA translocating through MoS2 nanopores with various structures. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-020-2004-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Perez A, Amorim RG, Villegas CEP, Rocha AR. Nanogap-based all-electronic DNA sequencing devices using MoS 2 monolayers. Phys Chem Chem Phys 2020; 22:27053-27059. [PMID: 33215614 DOI: 10.1039/d0cp04138f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The realization of nanopores in atom-thick materials may pave the way towards electrical detection of single biomolecules in a stable and scalable manner. In this work, we theoretically study the potential of different phases of MoS2 nanogaps to act as all-electronic DNA sequencing devices. We carry out simulations based on density functional theory and the non-equilibrium Green's function formalism to investigate the electronic transport across the device. Our results suggest that the 1T'-MoS2 nanogap structure is energetically more favorable than its 2H counterpart. At zero bias, the changes in the conductance of the 1T'-MoS2 device can be well distinguished, making possible the selectivity of the DNA nucleobases. Although the conductance fluctuates around the resonances, the overall results suggest that it is possible to distinguish the four DNA bases for energies close to the Fermi level.
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Affiliation(s)
- A Perez
- Instituto de Física Teórica, Universidade Estadual Paulista (UNESP), Rua Dr Bento T. Ferraz, 271, São Paulo, SP 01140-070, Brazil.
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9
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10
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Shepherd BA, Tanjil MRE, Jeong Y, Baloğlu B, Liao J, Wang MC. Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens. ACTA ACUST UNITED AC 2020; 5:2889-2906. [PMID: 33437534 PMCID: PMC7790041 DOI: 10.1557/adv.2020.402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
State-of-the-art nanopore sequencing enables rapid and real-time identification of novel pathogens, which has wide application in various research areas and is an emerging diagnostic tool for infectious diseases including COVID-19. Nanopore translocation enables de novo sequencing with long reads (> 10 kb) of novel genomes, which has advantages over existing short-read sequencing technologies. Biological nanopore sequencing has already achieved success as a technology platform but it is sensitive to empirical factors such as pH and temperature. Alternatively, ångström- and nano-scale solid-state nanopores, especially those based on two-dimensional (2D) membranes, are promising next-generation technologies as they can surpass biological nanopores in the variety of membrane materials, ease of defining pore morphology, higher nucleotide detection sensitivity, and facilitation of novel and hybrid sequencing modalities. Since the discovery of graphene, atomically-thin 2D materials have shown immense potential for the fabrication of nanopores with well-defined geometry, rendering them viable candidates for nanopore sequencing membranes. Here, we review recent progress and future development trends of 2D materials and their ångström- and nano-scale pore-based nucleic acid (NA) sequencing including fabrication techniques and current and emerging sequencing modalities. In addition, we discuss the current challenges of translocation-based nanopore sequencing and provide an outlook on promising future research directions.
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Affiliation(s)
- Britney A Shepherd
- Department of Medical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Md Rubayat-E Tanjil
- Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Yunjo Jeong
- Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Bilgenur Baloğlu
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1 Canada
| | - Jingqiu Liao
- Department of Systems Biology, Columbia University, 1130 St. Nicholas Avenue, New York, New York 10032 USA
| | - Michael Cai Wang
- Department of Medical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA.,Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
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11
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Kong Z, Hu W, Jiao F, Zhang P, Shen J, Cui B, Wang H, Liang L. Theoretical Evaluation of DNA Genotoxicity of Graphene Quantum Dots: A Combination of Density Functional Theory and Molecular Dynamics Simulations. J Phys Chem B 2020; 124:9335-9342. [PMID: 32870004 DOI: 10.1021/acs.jpcb.0c05882] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Owing to their unique morphology, ultrasmall lateral sizes, and exceptional properties, graphene quantum dots (GQDs) hold great potential in many applications, especially in the fields of electrochemical biosensors, bioimaging, drug delivery, gene delivery, etc. Their biosafety and potential genotoxicity to human and animal cells have been a growing concern in recent years. Especially, the potential DNA damage caused by GQDs is very crucial but still unclear. In this study, the effect of GQDs on DNA damage has been evaluated by a combination of molecular dynamics (MD) simulations and density functional theory. Our results demonstrate that the DNA damaging mechanism of GQDs depends on the size of GQDs. The small GQDs (seven benzene rings) tend to enter into the interior of DNA molecules and cause a DNA base mismatch. The relatively large GQDs (61 benzene rings) tend to adsorb onto the two ends of a DNA molecule and cause DNA unwinding. Due to the strong interaction between guanine (G) and GQDs, the effect of GQDs is much larger on G than on the other three bases (A, C, and T). In addition, the concentration of GQDs could also affect the results of DNA damaging.
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Affiliation(s)
- Zhe Kong
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China.,Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Wei Hu
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, People's Republic of China
| | - Fangfang Jiao
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, People's Republic of China
| | - Pengzhen Zhang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Jiawei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 311121, People's Republic of China
| | - Bo Cui
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Hongbo Wang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Lijun Liang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China.,College of Automation, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
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12
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Yuan Z, Liu Y, Dai M, Yi X, Wang C. Controlling DNA Translocation Through Solid-state Nanopores. NANOSCALE RESEARCH LETTERS 2020; 15:80. [PMID: 32297032 PMCID: PMC7158975 DOI: 10.1186/s11671-020-03308-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/24/2020] [Indexed: 05/14/2023]
Abstract
Compared with the status of bio-nanopores, there are still several challenges that need to be overcome before solid-state nanopores can be applied in commercial DNA sequencing. Low spatial and low temporal resolution are the two major challenges. Owing to restrictions on nanopore length and the solid-state nanopores' surface properties, there is still room for improving the spatial resolution. Meanwhile, DNA translocation is too fast under an electrical force, which results in the acquisition of few valid data points. The temporal resolution of solid-state nanopores could thus be enhanced if the DNA translocation speed is well controlled. In this mini-review, we briefly summarize the methods of improving spatial resolution and concentrate on controllable methods to promote the resolution of nanopore detection. In addition, we provide a perspective on the development of DNA sequencing by nanopores.
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Affiliation(s)
- Zhishan Yuan
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Youming Liu
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Min Dai
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Xin Yi
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Chengyong Wang
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
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13
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Liang L, Zhang Y, Kong Z, Liu F, Shen JW, He Z, Wang H. DNA fragment translocation through the lipid membrane assisted by carbon nanotube. Int J Pharm 2019; 574:118921. [PMID: 31812796 DOI: 10.1016/j.ijpharm.2019.118921] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/14/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022]
Abstract
DNA delivery through cell membrane is a fundamental step for efficiency gene therapy. As a potential DNA carrier, carbon nanotubes (CNTs) have been extensively studied due to its unique properties. However, the mechanism of DNA translocation with CNTs through cell membrane is still not well understood. In this study, the DNA translocation process through POPC (1-palmitoyl-2-oleoylphosphatidylcholine) membrane with the assistance of CNTs was explored by molecular dynamics (MD) simulation. Our simulation results demonstrated that the CNTs could insert steadily into the POPC membrane, and DNA molecules tends to insert into the inner space of CNTs. With the assistance of CNTs, the free energy of nucleotides passing through the POPC membrane decreases. Moreover, the free energy of nucleotides (DA (deoxyadenosine), DT (deoxythymidine), DC (deoxycytidine), and DG (deoxyguanosine)) passing through POPC membrane follows the order: DA (deoxyadenosine) > DG (deoxyguanosine) > DC (deoxycytidine) > DT (deoxythymidine). These results may promote the design and application of CNT-based gene delivery system.
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Affiliation(s)
- Lijun Liang
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Yujin Zhang
- School of Electronic and Information Engineering (Department of Physics), Qilu University of Technology, Jinan, Shandong 250353, People's Republic of China
| | - Zhe Kong
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Fei Liu
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 311121, People's Republic of China.
| | - Zhiwei He
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Hongbo Wang
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China.
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14
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Garoli D, Yamazaki H, Maccaferri N, Wanunu M. Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications. NANO LETTERS 2019; 19:7553-7562. [PMID: 31587559 DOI: 10.1021/acs.nanolett.9b02759] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Solid-state nanopore-based sensors are promising platforms for next-generation sequencing technologies, featuring label-free single-molecule sensitivity, rapid detection, and low-cost manufacturing. In recent years, solid-state nanopores have been explored due to their miscellaneous fabrication methods and their use in a wide range of sensing applications. Here, we highlight a novel family of solid-state nanopores which have recently appeared, namely plasmonic nanopores. The use of plasmonic nanopores to engineer electromagnetic fields around a nanopore sensor allows for enhanced optical spectroscopies, local control over temperature, thermophoresis of molecules and ions to/from the sensor, and trapping of entities. This Mini Review offers a comprehensive understanding of the current state-of-the-art plasmonic nanopores for single-molecule detection and biomolecular sequencing applications and discusses the latest advances and future perspectives on plasmonic nanopore-based technologies.
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Affiliation(s)
- Denis Garoli
- Istituto Italiano di Tecnologia , via Morego 30 , I-16163 , Genova , Italy
| | - Hirohito Yamazaki
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Nicolò Maccaferri
- Physics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Faïencerie , L-1511 Luxembourg , Luxembourg
| | - Meni Wanunu
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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15
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de Freitas Martins E, Troiano Feliciano G, Hendrik Scheicher R, Reily Rocha A. Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates. Molecules 2019; 24:E951. [PMID: 30857133 PMCID: PMC6429485 DOI: 10.3390/molecules24050951] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 11/16/2022] Open
Abstract
In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green's functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.
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Affiliation(s)
- Ernane de Freitas Martins
- Institute of Theoretical Physics, São Paulo State University (UNESP), Campus São Paulo, 01140-070 São Paulo, Brazil.
- Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, SE-751 20 Uppsala, Sweden.
| | - Gustavo Troiano Feliciano
- Institute of Chemistry, São Paulo State University (UNESP), Campus Araraquara, 14800-060 Araraquara, Brazil.
| | - Ralph Hendrik Scheicher
- Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, SE-751 20 Uppsala, Sweden.
| | - Alexandre Reily Rocha
- Institute of Theoretical Physics, São Paulo State University (UNESP), Campus São Paulo, 01140-070 São Paulo, Brazil.
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16
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Zhou M, Shen Q, Shen JW, Jin L, Zhang L, Sun Q, Hu Q, Liang L. Understanding the size effect of graphene quantum dots on protein adsorption. Colloids Surf B Biointerfaces 2018; 174:575-581. [PMID: 30502669 DOI: 10.1016/j.colsurfb.2018.11.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/18/2022]
Abstract
Due to the unique structural and mechanical properties, graphene quantum dots (GQDs) are considered as potential candidates in the field of biosensors, bioimaging, and drug delivery etc. In this work, the adsorption of protein villin headpiece (HP35) on GQDs with different sizes was investigated by molecular dynamics simulations. The simulation results identified the key role of the π-π stacking interactions between the aromatic residues of HP35 and GQDs as the binding site. More importantly, with the increase of GQD size, the amount and binding strength of adsorbed residues increase, and sequentially enhance the structure change of adsorbed protein, verified by various analysis of protein structures etc. These findings may improve the understanding of the cytotoxicity and biosafety of GQDs, and hence promote the design and application of GQDs-based biomedical devices.
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Affiliation(s)
- Mengdi Zhou
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Qiyin Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China.
| | - Lehong Jin
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Li Zhang
- Department of Chemistry, Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Education Ministry, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Quan Sun
- Department of ultrasound medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310015, People's Republic of China
| | - Quan Hu
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Lijun Liang
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, 310018, People's Republic of China.
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17
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Wasfi A, Awwad F, Ayesh AI. Graphene-based nanopore approaches for DNA sequencing: A literature review. Biosens Bioelectron 2018; 119:191-203. [DOI: 10.1016/j.bios.2018.07.072] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/20/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
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18
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Liang L, Liu F, Kong Z, Shen JW, Wang H, Wang H, Li L. Theoretical studies on key factors in DNA sequencing using atomically thin molybdenum disulfide nanopores. Phys Chem Chem Phys 2018; 20:28886-28893. [DOI: 10.1039/c8cp06167j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Applied voltage and MoS2 nanopore diameter affect the resolution of MoS2 nanopore-based DNA sequencing.
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Affiliation(s)
- Lijun Liang
- College of Life Information Science and Instrument Engineering
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Fei Liu
- College of Life Information Science and Instrument Engineering
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Zhe Kong
- College of Materials and Environmental Engineering
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Jia-Wei Shen
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016
- People's Republic of China
| | - Hongbo Wang
- College of Automation
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Haodong Wang
- College of Materials and Environmental Engineering
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Lihua Li
- College of Life Information Science and Instrument Engineering
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
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19
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Liang L, Kong Z, Kang Z, Wang H, Zhang L, Shen JW. Theoretical Evaluation on Potential Cytotoxicity of Graphene Quantum Dots. ACS Biomater Sci Eng 2016; 2:1983-1991. [PMID: 33440534 DOI: 10.1021/acsbiomaterials.6b00390] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Owing to unique morphology, ultrasmall lateral sizes, and exceptional properties, graphene quantum dots (GQDs) hold great potential in many applications, especially in the field of electrochemical biosensors, bioimaging, drug delivery, et cetera. Its biosafety and potential cytotoxicity to human and animal cells has been a growing concern in recent years. In this work, the potential cytotoxicity of GQDs was evaluated by molecular dynamics simulations. Our simulation demonstrates that small size GQDs could easily permeate into the lipid membrane in a vertical way. It is relatively difficult to permeate into the lipid membrane for GQDs that are larger than GQD61 on the nanosecond time-scale. The thickness of the POPC membrane could even be affected by the small size of GQDs. Free energy calculations revealed that the free energy barrier of GQD permeation through the lipid membrane could greatly change with the change of GQD size. Under high GQD concentration, the GQD molecules could rapidly aggregate in water but disaggregate after entering into the membrane interior. Moreover, high concentrations of GQDs could induce changes in the structure properties and diffusion properties of the lipid bilayer, and it may affect the cell signal transduction. However, GQDs with relatively small size are not large enough to mechanically damage the lipid membrane. Our results suggest that the cytotoxicity of GQDs with small size is low and may be appropriate for biomedical application.
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Affiliation(s)
- Lijun Liang
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, No. 1, Second Street, Jianggan District, Hangzhou, 310018, People's Republic of China
| | - Zhe Kong
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, No. 1, Second Street, Jianggan District, Hangzhou, 310018, People's Republic of China
| | - Zhengzhong Kang
- Department of Chemistry, Zhejiang University, Zheda Road 38, Hangzhou, 310028, People's Republic of China.,Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hongbo Wang
- College of Automation, Hangzhou Dianzi University, No. 1, Second Street, Jianggan District, Hangzhou 310018, People's Republic of China
| | - Li Zhang
- Department of Chemistry, Zhejiang Sci-Tech University, No. 2, Second Street, Jianggan District, Hangzhou, 310012, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Xuelin Street 16, Jianggan District, Hangzhou 310016, People's Republic of China
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