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Côté S, Bouilly D, Mousseau N. The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:4174-4186. [PMID: 35113103 DOI: 10.1039/d1cp04626h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Field-effect biosensors (bioFETs) offer a novel way to measure the kinetics of biomolecular events such as protein function and DNA hybridization at the single-molecule level on a wide range of time scales. These devices generate an electrical current whose fluctuations are correlated to the kinetics of the biomolecule under study. BioFETs are indeed highly sensitive to changes in the electrostatic potential (ESP) generated by the biomolecule. Here, using all-atom solvent explicit molecular dynamics simulations, we further investigate the molecular origin of the variation of this ESP for two prototypical cases of proteins or nucleic acids attached to a carbon nanotube bioFET: the function of the lysozyme protein and the hybridization of a 10-nt DNA sequence, as previously done experimentally. Our results show that the ESP changes significantly on the surface of the carbon nanotube as the state of these two biomolecules changes. More precisely, the ESP distributions calculated for these molecular states explain well the magnitude of the conductance fluctuations measured experimentally. The dependence of the ESP with salt concentration is found to agree with the reduced conductance fluctuations observed experimentally for the lysozyme, but to differ for the case of DNA, suggesting that other mechanisms might be at play in this case. Furthermore, we show that the carbon nanotube does not impact significantly the structural stability of the lysozyme, corroborating that the kinetic rates measured using bioFETs are similar to those measured by other techniques. For DNA, we find that the structural ensemble of the single-stranded DNA is significantly impacted by the presence of the nanotube, which, combined with the ESP analysis, suggests a stronger DNA-device interplay. Overall, our simulations strengthen the comprehension of the inner working of field-effect biosensors used for single-molecule kinetics measurements on proteins and nucleic acids.
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Affiliation(s)
- Sébastien Côté
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada. .,Département de Physique, Cégep de Saint-Jérôme, Saint-Jérôme, Canada
| | - Delphine Bouilly
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada. .,Institut de recherche en immunologie et cancérologie (IRIC), Université de Montréal, Montréal, Canada.
| | - Normand Mousseau
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada.
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2
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Saikia N, Taha M, Pandey R. Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes. Phys Chem Chem Phys 2021; 23:219-228. [PMID: 33325925 DOI: 10.1039/d0cp05759b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The strategic approaches to the design of self-assembled hybrids of biomolecular systems at the nanoscale such as deoxyribonucleic acid (DNA) with single-wall carbon nanotubes (CNTs) and their structural analog, boron nitride nanotubes (BNNTs), rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface. In this paper, we consider peptide nucleic acid (PNA), which is a synthetic analog of DNA, and investigate its interaction with a zigzag CNT and BNNT of similar diameter. The results based on the molecular dynamics method find that PNA provides definitive contrasts in the adsorption on the tubular surface in aqueous solution: it prefers to wrap along the circumferential direction on a (11,0) CNT, whereas it binds along the axial direction adopting an extended configuration on a (11,0) BNNT. Moreover, gas-phase Monte Carlo simulations show a dependence of the nanotube diameter on the calculated adsorption energy, with BNNTs exhibiting higher adsorption energy compared to CNTs, and the largest-diameter (25,0) tubular configuration facilitates encapsulation of PNA rather than PNA being adsorbed on its sidewall. The results are expected to be of relevance in the design of novel PNA-based archetypal hybrid materials for nanoscale applications in health-related areas including biosensing.
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Affiliation(s)
- Nabanita Saikia
- Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA.
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Kumari I, Kaur N, Gupta S, Goel N. Nucleotide conjugated (ZnO) 3 cluster: Interaction and optical characteristics using TDDFT. J Mol Graph Model 2018; 87:211-219. [PMID: 30554067 DOI: 10.1016/j.jmgm.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/06/2018] [Accepted: 12/03/2018] [Indexed: 11/18/2022]
Abstract
Binding of four DNA nucleotide units with (ZnO)3 cluster in an aqueous phase has been investigated using density functional theory (DFT) and time dependent-density functional theory (TDDFT) method and the stability order for (ZnO)3-nucleobases/sugar/phosphate systems is predicted as phosphate > C > A > S > T ∼ G. The order of binding energy for (ZnO)3-nucleotide hybrid systems is observed to be (ZnO)3 + nuc-C ˃ (ZnO)3 + nuc-A ˃ (ZnO)3 + nuc-G ˃ (ZnO)3 + nuc-T. The binding of nucleotide units with the cluster has been explained on the basis of molecular electrostatic potential (MEP) plots, hydrogen bonding, glycosidic torsion angles, density of state (DOS) plots. The photophysical properties of (ZnO)3-nucleotide complexes have been studied using TDDFT approach. Among all (ZnO)3-nucleotide complexes, the absorption spectra of (ZnO)3 + nuc-A and (ZnO)3 + nuc-C complexes are seen to undergo red shift with respect to their bare nucleotide units that would be useful in the optical sensing of the respective nucleotides of DNA. It is interesting to note that binding of the nucleotide unit with the cluster makes it fluorescent, the study reports the fluorescence activity of (ZnO)3 + nuc-T complex.
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Affiliation(s)
- Indu Kumari
- Theoretical & Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Navjot Kaur
- Theoretical & Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Shuchi Gupta
- Department of Applied Sciences, University Institute of Engineering and Technology, Panjab University, Chandigarh, 160014, India
| | - Neetu Goel
- Theoretical & Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.
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He W, Dai J, Li T, Bao Y, Yang F, Zhang X, Uyama H. Novel Strategy for the Investigation on Chirality Selection of Single-Walled Carbon Nanotubes with DNA by Electrochemical Characterization. Anal Chem 2018; 90:12810-12814. [DOI: 10.1021/acs.analchem.8b03323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Wenya He
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Jianying Dai
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Tiantian Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Yunkai Bao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Fengchun Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Xin Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Hiroshi Uyama
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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Chehelamirani M, da Silva MC, Salahub DR. Electronic properties of carbon nanotubes complexed with a DNA nucleotide. Phys Chem Chem Phys 2018; 19:7333-7342. [PMID: 28239719 DOI: 10.1039/c6cp08376e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic properties of carbon nanotubes (CNTs) play an important role in their interactions with nano-structured materials. In this work, interactions of adenosine monophosphate (AMP), a DNA nucleotide, with metallic and semi-conducting CNTs are studied using the density functional tight binding (DFTB) method. The electronic structure of semi-conducting CNTs was found to be changed as they turned to metallic CNTs in a vacuum upon interaction with the nucleotide while metallic CNTs remain metallic. Specifically, the band gap of semi-conducting CNTs was decreased by 0.79 eV on average while nearly no change was found in the metallic tubes. However, our investigations showed that the presence of explicit water molecules prevents the metallicity change and only small changes in the CNT band gap occur. According to our charge analysis, the average negative charge accumulated on CNTs upon interaction with the AMP was determined to be 0.77 e in a vacuum while it was 0.03 e in solution. Therefore, it is essential to include explicit water molecules in simulating complexes formed by DNA nucleotides and CNTs which were ignored in several past studies performed using quantum mechanical approaches.
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Affiliation(s)
- Morteza Chehelamirani
- Department of Chemistry and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Maurício C da Silva
- Department of Chemistry and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Dennis R Salahub
- Department of Chemistry and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. and Institute for Quantum Science and Technology, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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Bezerra KS, Lima Neto JX, Oliveira JIN, Albuquerque EL, Caetano EWS, Freire VN, Fulco UL. Computational investigation of the α2β1 integrin–collagen triple helix complex interaction. NEW J CHEM 2018. [DOI: 10.1039/c8nj04175j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, quantum biochemistry methods have been used to describe important protein–protein interactions for the complex integrin–collagen.
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Affiliation(s)
- K. S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - J. X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - J. I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - E. L. Albuquerque
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - E. W. S. Caetano
- Instituto Federal de Educação
- Ciência e Tecnologia do Ceará
- Fortaleza-CE
- Brazil
| | - V. N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
| | - U. L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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Chehelamirani M, Tang T. Effect of charge redistribution on the binding of DNA nucleotide to carbon nanotube in molecular dynamics. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1279285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada
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Zarudnev ES, Stepanian SG, Adamowicz L, Leontiev VS, Karachevtsev VA. Comparison of noncovalent interactions of zigzag and armchair carbon nanotubes with heterocyclic and aromatic compounds: Imidazole and benzene, imidazophenazines, and tetracene. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
Minima of the electric field and positions of K+ and Na+ (zero of the x-coordinate is the center of the cavity).
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici
- ICCOM – UOS Pisa
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
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Arabi AA. Evaluating dispersion forces for optimization of van der Waals complexes using a non-empirical functional. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0145. [PMID: 27698041 PMCID: PMC5052729 DOI: 10.1098/rsta.2016.0145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/05/2016] [Indexed: 05/27/2023]
Abstract
Modelling dispersion interactions with traditional density functional theory (DFT) is a challenge that has been extensively addressed in the past decade. The exchange-dipole moment (XDM), among others, is a non-empirical add-on dispersion correction model in DFT. The functional PW86+PBE+XDM for exchange, correlation and dispersion, respectively, compromises an accurate functional for thermochemistry and for van der Waals (vdW) complexes at equilibrium and non-equilibrium geometries. To use this functional in optimizing vdW complexes, rather than computing single point energies, it is necessary to evaluate accurate forces. The purpose of this paper is to validate that, along the potential energy surface, the distance at which the energy is minimum is commensurate with the distance at which the forces vanish to zero. This test was validated for 10 rare gas diatomic molecules using various integration grids and different convergence criteria. It was found that the use of either convergence criterion, 10-6 or 10-8, in Gaussian09, does not affect the accuracy of computed optimal distances and binding energies. An ultra-fine grid needs to be used when computing accurate energies using generalized gradient approximation functionals.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Alya A Arabi
- College of Natural and Health Sciences, Zayed University, Abu Dhabi, PO Box 144534, United Arab Emirates
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11
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Kosevich MV, Zobnina VG, Stepanian SG, Karachevtsev VA, Adamowicz L. The effect of protonation of cytosine and adenine on their interactions with carbon nanotubes. J Mol Graph Model 2016; 70:77-84. [DOI: 10.1016/j.jmgm.2016.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 01/12/2023]
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Chehel Amirani M, Tang T. Electrostatics of DNA nucleotide-carbon nanotube hybrids evaluated from QM:MM simulations. NANOSCALE 2015; 7:19586-19595. [PMID: 26542447 DOI: 10.1039/c5nr03665h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Biomolecule-functionalized carbon nanotubes (CNTs) have been studied vastly in recent years due to their potential applications for instance in cancer detection, purification and separation of CNTs, and nanoelectronics. Studying the electrostatic potential generated by a biomolecule-CNT hybrid is important in predicting its interactions with the surrounding environment such as charged particles and surfaces. In this paper, we performed atomistic simulations using a QM:MM approach to evaluate the electrostatic potential and charge transfer for a hybrid structure formed by a DNA nucleotide and a CNT in solution. Four types of DNA nucleotides and two CNTs with chiralities of (4,4) and (7,0) were considered. The types of nucleotides and CNTs were both found to play important roles in the electrostatic potential and charge transfer of the hybrid. At the same distance from the CNT axis, the electrostatic potential for the nucleotide-(4,4) CNT hybrids was found to be stronger compared with that for the nucleotide-(7,0) CNT hybrids. Higher electric charge was also shown to be transferred from the DNA nucleotides to the (7,0) CNT compared with the (4,4) CNT. These results correlate with the previous finding that the nucleotides bound more tightly to the (7,0) CNT compared with the (4,4) CNT.
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Affiliation(s)
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada.
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