1
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Mandal S, Ganesh KN, Maiti PK. Dynamics of terminal fraying-peeling and hydrogen bonds dictates the sequential vs. cooperative melting pathways of nanoscale DNA and PNA triplexes. NANOSCALE 2024; 16:13029-13040. [PMID: 38904319 DOI: 10.1039/d4nr01104j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral synthetic DNA/RNA analogues. In many aspects of biology and biotechnology, the details of DNA and PNA melting reaction coordinates are crucial, and their associative/dissociative details remain inadequately understood. In the current study, we have attempted to gain insights into comparative melting pathways and binding affinity of iso-sequences of an 18-mer PNA-DNA-PNA triplex and the analogous DNA-DNA-DNA triplex, and DNA-DNA and PNA-DNA duplexes. It is intriguing that while the DNA-DNA-DNA triplex melts in two sequential steps, the PNA-DNA-PNA triplex melts in a single step and the mechanistic aspects for this difference are still not clear. We report an all-atom molecular dynamics simulation of both complexes in the temperature range of 300 to 500 K with 20 K intervals. Based on the trajectory analysis, we provide evidence that the association and dissociation are dictated by the differences in fraying-peeling effects from either terminus to the center in a zipper pattern among the PNA-DNA-PNA triplex and DNA-DNA-DNA triplexes. These are shown to be governed by the different characteristics of H-bonding, RMSD, and Free Energy Landscape (FEL) as analyzed by PCA, leading to the DNA-DNA-DNA triplex exhibiting sequential melting, while the PNA-DNA-PNA triplex shows cooperative melting of the whole fragment in a single-step. The PNA-DNA-PNA triplex base pairs are thermodynamically more stable than the DNA-DNA-DNA triplex, with the binding affinity of PNA-TFO to the PNA : DNA duplex being higher than that of DNA-TFO to the DNA : DNA duplex. The investigation of the association/dissociation of PNA-TFO to the PNA-DNA duplex has relevance and importance in the emerging effective applications of oligonucleotide therapy.
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Affiliation(s)
- Sandip Mandal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Krishna N Ganesh
- Jawaharlal Nehru Center for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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2
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Torkan E, Salmani-Tehrani M. Conformational dynamics and mechanical properties of biomimetic RNA, DNA, and RNA-DNA hybrid nanotubes: an atomistic molecular dynamics study. Phys Chem Chem Phys 2023. [PMID: 37309220 DOI: 10.1039/d3cp01028g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With the nanotechnology boom, artificially designed nucleic acid nanotubes have aroused interest due to their practical applications in nanorobotics, vaccine design, membrane channels, drug delivery, and force sensing. In this paper, computational study was performed to investigate the structural dynamics and mechanical properties of RNA nanotubes (RNTs), DNA nanotubes (DNTs), and RNA-DNA hybrid nanotubes (RDHNTs). So far, the structural and mechanical properties of RDHNTs have not been examined in experiments or theoretical calculations, and there is limited knowledge regarding these properties for RNTs. Here, the simulations were carried out using the equilibrium molecular dynamics (MD) and steered molecular dynamics (SMD) approaches. Using in-house scripting, we modeled hexagonal nanotubes composed of six double-stranded molecules connected by four-way Holliday junctions. Classical MD analyses were performed on the collected trajectory data to investigate structural properties. Analyses of the microscopic structural parameters of RDHNT indicated a structural transition from the A-form to a conformation between the A- and B-forms, which may be attributable to the increased rigidity of RNA scaffolds compared to DNA staples. Comprehensive research on the elastic mechanical properties was also conducted based on spontaneous thermal fluctuations of nanotubes and employing the equipartition theorem. The Young's modulus of RDHNT (E = 165 MPa) and RNT (E = 144 MPa) was found to be almost the same and nearly half of that found for DNT (E = 325 MPa). Furthermore, the results showed that RNT was more resistant to bending, torsional, and volumetric deformations than DNT and RDHNT. We also used non-equilibrium SMD simulations to acquire comprehensive knowledge of the mechanical response of nanotubes to tensile stress.
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Affiliation(s)
- Ehsan Torkan
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Mehdi Salmani-Tehrani
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
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3
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Naskar S, Bhatia D, Lin ST, Maiti PK. Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars. Phys Chem Chem Phys 2023; 25:7847-7858. [PMID: 36857659 DOI: 10.1039/d2cp04683k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504-512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly.
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Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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4
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Joshi H, Li CY, Aksimentiev A. All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores. Methods Mol Biol 2023; 2639:113-128. [PMID: 37166714 DOI: 10.1007/978-1-0716-3028-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Building on the recent technological advances, all-atom molecular dynamics (MD) simulations have become an indispensable tool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, and mechanical and electrical properties of DNA origami objects. In this chapter we describe a method to build all-atom model of lipid-spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.
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Affiliation(s)
- Himanshu Joshi
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Chen-Yu Li
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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5
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Chhetri KB, Sharma A, Naskar S, Maiti PK. Nanoscale structures and mechanics of peptide nucleic acids. NANOSCALE 2022; 14:6620-6635. [PMID: 35421892 DOI: 10.1039/d1nr04239d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral polyamide oligomers having extremely favorable thermal stability and high affinity to cell membranes when coupled with cationic cell-penetrating peptides (CPPs), as well as the encouraging antisense and antigene activity in cell-free systems. The study of the mechanical properties of short PNA molecules is rare both in experiments and theoretical calculations. Here, we studied the microscopic structures and elastic properties; namely, persistence length, stretch modulus, twist-stretch coupling, and structural crookedness of double-stranded PNA (dsPNA) and their hybrid derivatives using all-atom MD simulation and compared them with those of double-stranded DNA (dsDNA) and double-stranded RNA (dsRNA). The stretch modulus of the dsPNA is found to be ∼160 pN, an order of magnitude lower than that of dsDNA and smaller than dsRNA, respectively. Similarly, the persistence length of dsPNA is found to be ∼35 nm, significantly smaller than those of dsDNA and dsRNA. The PNA-DNA and PNA-RNA hybrid duplexes have elastic properties lying between that of dsPNA and dsDNA/dsRNA. We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA molecules. Measurement of structural crookedness and principal component analysis additionally support the bending flexibility of dsPNA. Detailed analysis of the helical-rise coupled to helical-twist indicates that the PNA-DNA hybrid over-winds like dsDNA, while PNA-PNA and PNA-RNA unwind like dsRNA upon stretching. Because of the highly flexible nature of PNA, it can bind other biomolecules by adopting a wide range of conformations and is believed to be crucial for future nanobiotechnology research studies.
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Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Nepal
| | - Akshara Sharma
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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6
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Fadaei F, Tortora M, Gessini A, Masciovecchio C, Catalini S, Vigna J, Mancini I, Mele A, Vacek J, Reha D, Minofar B, Rossi B. Structural specificity of groove binding mechanism between imidazolium-based ionic liquids and DNA revealed by synchrotron-UV Resonance Raman spectroscopy and molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Mei L, Chen B, Fan R, Wu M, Weng C, Tong A, Zou B, Yang H, Nie C, Guo G. Magic of Architecting Oligo‐DNAs: 3D Structure‐Dependent Stability and Programmable Specificity to Tumor Cells. ADVANCED FUNCTIONAL MATERIALS 2022. [DOI: 10.1002/adfm.202112544] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Lan Mei
- State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu 610041 China
| | - Bo Chen
- State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu 610041 China
| | - Rangrang Fan
- State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu 610041 China
| | - Min Wu
- State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu 610041 China
| | - Chengxin Weng
- Department of Vascular Surgery West China Hospital Sichuan University Chengdu 610041 China
| | - Aiping Tong
- State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu 610041 China
| | - Bingwen Zou
- State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu 610041 China
| | - Hui Yang
- Department of Otorhiolaryngology Head and Neck Surgery West China Hospital Sichuan University Chengdu 610041 China
| | - Chunlai Nie
- State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu 610041 China
| | - Gang Guo
- State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Collaborative Innovation Center for Biotherapy Chengdu 610041 China
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8
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Naskar S, Maiti PK. Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, Martini and oxDNA models. J Mater Chem B 2021; 9:5102-5113. [PMID: 34127998 DOI: 10.1039/d0tb02970j] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The flexibility and stiffness of small DNA molecules play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) with lengths ranging from 12 base-pairs (bp) to 56 bp, paranemic crossover (PX) DNA and hexagonal DNA nanotubes (DNTs) using two widely used coarse-grained models - Martini and oxDNA. To calculate the persistence length (Lp) and the stretch modulus (γ) of the dsDNA, we incorporate the worm-like chain and elastic rod model, while for the DNTs, we implement our previously developed theoretical framework. We compare and contrast all of the results with previously reported all-atom molecular dynamics (MD) simulations and experimental results. The mechanical properties of dsDNA (Lp ∼ 50 nm, γ ∼ 800-1500 pN), PX DNA (γ ∼ 1600-2000 pN) and DNTs (Lp ∼ 1-10 μm, γ ∼ 6000-8000 pN) estimated using the Martini soft elastic network and oxDNA are in very good agreement with the all-atom MD and experimental values, while the stiff elastic network Martini reproduces values of Lp and γ which are an order of magnitude higher. The high flexibility of small dsDNA is also depicted in our calculations. However, Martini models proved inadequate to capture the salt concentration effects on the mechanical properties with increasing salt molarity. oxDNA captures the salt concentration effect on the small dsDNA mechanics. But it is found to be ineffective for reproducing the salt-dependent mechanical properties of DNTs. Also, unlike Martini, the time evolved PX DNA and DNT structures from the oxDNA models are comparable to the all-atom MD simulated structures. Our findings provide a route to study the mechanical properties of DNA and DNA based nanostructures with increased time and length scales and has a remarkable implication in the context of DNA nanotechnology.
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Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
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9
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Chhabra H, Mishra G, Cao Y, Prešern D, Skoruppa E, Tortora MMC, Doye JPK. Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures. J Chem Theory Comput 2020; 16:7748-7763. [PMID: 33164531 DOI: 10.1021/acs.jctc.0c00661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persistence lengths and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a wormlike chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase nonlinearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths that we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origamis have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.
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Affiliation(s)
- Hemani Chhabra
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Garima Mishra
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Yijing Cao
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Maxime M C Tortora
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.,Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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10
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What do we know about DNA mechanics so far? Curr Opin Struct Biol 2020; 64:42-50. [DOI: 10.1016/j.sbi.2020.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/17/2020] [Indexed: 12/14/2022]
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11
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Bag S, Maiti PK. Tuning molecular fluctuation to boost the conductance in DNA based molecular wires. Phys Chem Chem Phys 2019; 21:23514-23520. [PMID: 31617554 DOI: 10.1039/c9cp03589c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherent molecular fluctuations are known to have a significant influence on the charge transport properties of biomolecules like DNA, PNA and proteins. In this work, we show ways to control these fluctuations and further demonstrate their use to enhance the conductance of two widely studied molecular wires, namely dsDNA (DNA) and G4 Quadruplex (G4-Quad). We quantify the molecular fluctuation in terms of the root mean square deviation (RMSD) of the molecule. In the case of DNA, we use temperature to control the fluctuations, while in the case of G4-Quad the fluctuations are tuned by the ions inside the pore. The electronic coupling between the bases of dsDNA and G4-Quad, which measures the conductance of these molecular wires, shows a non-monotonic behaviour with the increase in fluctuation. We find values of fluctuation which give rise to maximum electronic coupling and hence high conductivity for both the cases. In the case of DNA, these optimal fluctuations (∼2.5 Å) are achieved at a temperature of 210 K, which gives rise to an electronic coupling of 0.135 eV between the DNA bases. The optimal fluctuations in G4-Quad are achieved (∼7 Å) in a 4 base pair long system with 2 Na+ ions inside the pore, giving rise to an electronic coupling of 0.09 eV.
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Affiliation(s)
- Saientan Bag
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, India.
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12
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Naskar S, Joshi H, Chakraborty B, Seeman NC, Maiti PK. Atomic structures of RNA nanotubes and their comparison with DNA nanotubes. NANOSCALE 2019; 11:14863-14878. [PMID: 31355845 DOI: 10.1039/c9nr00786e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.
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Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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13
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetische DNA‐Nanoröhren: Gezielte Synthese und Anwendung nanoskopischer Kanäle. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
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14
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications. Angew Chem Int Ed Engl 2019; 58:8996-9011. [PMID: 30290046 DOI: 10.1002/anie.201807779] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/25/2018] [Indexed: 01/04/2023]
Abstract
Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter-cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom-up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel-aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site-specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.
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Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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15
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Garai A, Ghoshdastidar D, Senapati S, Maiti PK. Ionic liquids make DNA rigid. J Chem Phys 2018; 149:045104. [PMID: 30068211 DOI: 10.1063/1.5026640] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Persistence length of double-stranded DNA (dsDNA) is known to decrease with an increase in ionic concentration of the solution. In contrast to this, here we show that the persistence length of dsDNA increases dramatically as a function of ionic liquid (IL) concentration. Using all atom explicit solvent molecular dynamics simulations and theoretical models, we present, for the first time, a systematic study to determine the mechanical properties of dsDNA in various hydrated ILs at different concentrations. We find that dsDNA in 50 wt % ILs have lower persistence length and stretch modulus in comparison to 80 wt % ILs. We further observe that both the persistence length and stretch modulus of dsDNA increase as we increase the concentration of ILs. The present trend of the stretch modulus and persistence length of dsDNA with IL concentration supports the predictions of the macroscopic elastic theory, in contrast to the behavior exhibited by dsDNA in monovalent salt. Our study further suggests the preferable ILs that can be used for maintaining DNA stability during long-term storage.
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Affiliation(s)
- Ashok Garai
- Department of Physics, Centre for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Debostuti Ghoshdastidar
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sanjib Senapati
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Prabal K Maiti
- Department of Physics, Centre for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
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16
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Liu P, Zhao Y, Liu X, Sun J, Xu D, Li Y, Li Q, Wang L, Yang S, Fan C, Lin J. Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes. Angew Chem Int Ed Engl 2018; 57:5418-5422. [PMID: 29528530 PMCID: PMC6142180 DOI: 10.1002/anie.201801498] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 12/29/2022]
Abstract
Reconfiguration of membrane protein channels for gated transport is highly regulated under physiological conditions. However, a mechanistic understanding of such channels remains challenging owing to the difficulty in probing subtle gating-associated structural changes. Herein, we show that charge neutralization can drive the shape reconfiguration of a biomimetic 6-helix bundle DNA nanotube (6HB). Specifically, 6HB adopts a compact state when its charge is neutralized by Mg2+ ; whereas Na+ switches it to the expanded state, as revealed by MD simulations, small-angle X-ray scattering (SAXS), and FRET characterization. Furthermore, partial neutralization of the DNA backbone charges by chemical modification renders 6HB compact and insensitive to ions, suggesting an interplay between electrostatic and hydrophobic forces in the channels. This system provides a platform for understanding the structure-function relationship of biological channels and designing rules for the shape control of DNA nanostructures in biomedical applications.
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Affiliation(s)
- Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China); Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 (China)
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Xiaoguo Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Dede Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China)
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition Case Western Reserve University 10900 Euclid Ave, Cleveland, OH 44106-4988 (USA)
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences Shanghai 201800 (China)
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University Tianjin 300353 (China); Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 (China)
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17
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Pfeifer W, Saccà B. Synthetic DNA filaments: from design to applications. Biol Chem 2018; 399:773-785. [DOI: 10.1515/hsz-2018-0110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/25/2018] [Indexed: 01/06/2023]
Abstract
Abstract
Natural filaments, such as microtubules and actin filaments, are fundamental components of the cell. Despite their relatively simple linear structure, filaments play a number of crucial roles in living organisms, from scaffolding to cellular adhesion and motility. The mechanical properties of natural filaments mostly rely on the structural features of the component units and on the way they are connected together, thus providing an ideal molecular model for emulation purposes. In this review, we describe the progresses done in this field using DNA for the rational design of synthetic filamentous-like materials with tailored structural and physical characteristics. We firstly survey the strategies that have been adopted until now for the construction of individual DNA building components and their programmable self-assembly into linear oligomeric structures. We then describe the theoretical models of polymer elasticity applied to calculate the bending strength of DNA filaments, expressed in terms of persistence length. Finally, we report some of the most exciting examples of truly biomimetic DNA filaments, which are capable of mimicking not only the sophisticated structural features of their natural counterparts but also their responsiveness to external stimuli, thus resulting in active motion and growing networks between distant loci.
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Affiliation(s)
- Wolfgang Pfeifer
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE) , University of Duisburg-Essen, Universitätstraße 2 , D-45117 Essen , Germany
| | - Barbara Saccà
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE) , University of Duisburg-Essen, Universitätstraße 2 , D-45117 Essen , Germany
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18
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Liu P, Zhao Y, Liu X, Sun J, Xu D, Li Y, Li Q, Wang L, Yang S, Fan C, Lin J. Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiaoguo Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Dede Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition; Case Western Reserve University; 10900 Euclid Ave Cleveland OH 44106-4988 USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin 300353 China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
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19
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Joshi H, Maiti PK. Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes. Nucleic Acids Res 2018; 46:2234-2242. [PMID: 29136243 PMCID: PMC5861442 DOI: 10.1093/nar/gkx1078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/25/2017] [Accepted: 11/03/2017] [Indexed: 01/18/2023] Open
Abstract
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 μs long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane. Further, we explore the effect of ionic concentrations to the in-solution structure and stability of the lipid-DNT complex. Transmembrane ionic current measurements for the constant electric field MD simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. With increasing salt concentrations, the measured values of transmembrane ionic conductance of the porous DNT lumen vary from 4.3 to 20.6 nS. Simulations of the DNTs with ssDNA and dsDNA overhangs at the mouth of the pore show gating effect with remarkable difference in the transmembrane ionic conductivities for open and close state nanopores.
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Affiliation(s)
- Himanshu Joshi
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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20
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Park S, Lansac Y, Jang YH. Sub-nanometer pore formation in single-molecule-thick polyurea molecular-sieving membrane: a computational study. Phys Chem Chem Phys 2018; 20:16463-16468. [DOI: 10.1039/c8cp01580e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The surprisingly narrow sub-nm-pore-size distribution and urea-versus-glucose selectivity of a single-molecule-thick polyurea membrane are explained by Monte Carlo simulations on simple molecular models.
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Affiliation(s)
- Seongjin Park
- Department of Energy Science and Engineering
- DGIST
- Daegu 42988
- Korea
| | - Yves Lansac
- GREMAN
- UMR 7347
- CNRS
- Université de Tours
- 37200 Tours
| | - Yun Hee Jang
- Department of Energy Science and Engineering
- DGIST
- Daegu 42988
- Korea
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21
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Chen J, Liu B, Gao X, Xu D. A review of the interfacial characteristics of polymer nanocomposites containing carbon nanotubes. RSC Adv 2018; 8:28048-28085. [PMID: 35542749 PMCID: PMC9083916 DOI: 10.1039/c8ra04205e] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/26/2018] [Indexed: 12/17/2022] Open
Abstract
This paper provides an overview of recent advances in research on the interfacial characteristics of carbon nanotube–polymer nanocomposites. The state of knowledge about the chemical functionalization of carbon nanotubes as well as the interaction at the interface between the carbon nanotube and the polymer matrix is presented. The primary focus of this paper is on identifying the fundamental relationship between nanocomposite properties and interfacial characteristics. The progress, remaining challenges, and future directions of research are discussed. The latest developments of both microscopy and scattering techniques are reviewed, and their respective strengths and limitations are briefly discussed. The main methods available for the chemical functionalization of carbon nanotubes are summarized, and particular interest is given to evaluation of their advantages and disadvantages. The critical issues related to the interaction at the interface are discussed, and the important techniques for improving the properties of carbon nanotube–polymer nanocomposites are introduced. Additionally, the mechanism responsible for the interfacial interaction at the molecular level is briefly described. Furthermore, the mechanical, electrical, and thermal properties of the nanocomposites are discussed separately, and their influencing factors are briefly introduced. Finally, the current challenges and opportunities for efficiently translating the remarkable properties of carbon nanotubes to polymer matrices are summarized in the hopes of facilitating the development of this emerging area. Potential topics of oncoming focus are highlighted, and several suggestions concerning future research needs are also presented. The state of research on the characteristics at the interface in polymer nanocomposites is reviewed. Special emphasis is placed on the recent advances in the fundamental relationship between interfacial characteristics and nanocomposite properties.![]()
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Affiliation(s)
- Junjie Chen
- Department of Energy and Power Engineering
- School of Mechanical and Power Engineering
- Henan Polytechnic University
- Jiaozuo
- China
| | - Baofang Liu
- Department of Energy and Power Engineering
- School of Mechanical and Power Engineering
- Henan Polytechnic University
- Jiaozuo
- China
| | - Xuhui Gao
- Department of Energy and Power Engineering
- School of Mechanical and Power Engineering
- Henan Polytechnic University
- Jiaozuo
- China
| | - Deguang Xu
- Department of Energy and Power Engineering
- School of Mechanical and Power Engineering
- Henan Polytechnic University
- Jiaozuo
- China
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22
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Garai A, Mogurampelly S, Bag S, Maiti PK. Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA. J Chem Phys 2017; 147:225102. [DOI: 10.1063/1.4991862] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ashok Garai
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
- Department of Physics, The LNM Institute of Information Technology, Jamdoli, Jaipur 302031, India
| | - Santosh Mogurampelly
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K. Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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23
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Shi Z, Castro CE, Arya G. Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. ACS NANO 2017; 11:4617-4630. [PMID: 28423273 DOI: 10.1021/acsnano.7b00242] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures-DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles. The simulations reproduce the experimentally measured equilibrium angles between hinge arms for a range of hinge designs. The hinges are found to be structurally stable, except for some fraying of the open ends of the DNA helices comprising the hinge arms and some loss of base-pairing interactions in the joint regions coinciding with the crossover junctions, especially in hinges designed to exhibit a small bending angle that exhibit large local stresses resulting in strong kinks in their joints. Principal component analysis reveals that while the hinge dynamics are dominated by bending motion, some twisting and sliding of hinge arms relative to each other also exists. Forced deformation of the hinges reveals distinct bending mechanisms for hinges with short, inextensible springs versus those with longer, more extensible springs. Lastly, we introduce an approach for rapidly predicting equilibrium hinge angles from individual force-deformation behaviors of its single- and double-stranded DNA components. Taken together, these results demonstrate that coarse-grained modeling is a promising approach for designing, predicting, and studying the dynamics of compliant DNA nanostructures, where conformational fluctuations become important, multiple deformation mechanisms exist, and continuum approaches may not yield accurate properties.
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Affiliation(s)
- Ze Shi
- Department of NanoEngineering, University of California, San Diego , La Jolla, California 92093, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego , La Jolla, California 92093, United States
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24
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Joshi H, Bhatia D, Krishnan Y, Maiti PK. Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations. NANOSCALE 2017; 9:4467-4477. [PMID: 28304019 DOI: 10.1039/c6nr08036g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems. We study the structure and dynamics of this DNA icosahedron using fully atomistic molecular dynamics (MD) simulation in explicit water and ions. The major modes of internal motion have been identified using principal component analysis. We provide a quantitative estimate of the radius of gyration (Rg), solvent accessible surface area (SASA) and volume of the icosahedron which is essential to estimate its maximal cargo carrying capacity. Importantly, our simulation of gold nanoparticles (AuNPs) encapsulated within DNA icosahedra revealed enhanced stability of the AuNP loaded DNA icosahedra compared to empty icosahedra. This is consistent with the experimental results that show high yields of cargo-encapsulated DNA icosahedra that have led to its diverse applications for precision targeting. These studies reveal that the stabilizing interactions between the cargo and the DNA scaffold powerfully position DNA polyhedra as targetable nanocapsules for payload delivery. These insights can be exploited for precise molecular display for diverse biological applications.
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Affiliation(s)
- Himanshu Joshi
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Dhiraj Bhatia
- Institut Curie, PSL Research University, Chemical Biology of Membranes and Therapeutic Delivery unit, INSERM, U 1143, CNRS, UMR 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA and Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, Illinois 60637, USA
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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25
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Maingi V, Burns JR, Uusitalo JJ, Howorka S, Marrink SJ, Sansom MSP. Stability and dynamics of membrane-spanning DNA nanopores. Nat Commun 2017; 8:14784. [PMID: 28317903 PMCID: PMC5364398 DOI: 10.1038/ncomms14784] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/31/2017] [Indexed: 01/05/2023] Open
Abstract
Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine. Although DNA nanopores are widely explored as synthetic membrane proteins, it is still unclear how the anionic DNA assemblies stably reside within the hydrophobic core of a lipid bilayer. Here, the authors use molecular dynamics simulations to reveal the key dynamic interactions and energetics stabilizing the nanopore-membrane interaction.
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Affiliation(s)
- Vishal Maingi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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