1
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DeLuca M, Duke D, Ye T, Poirier M, Ke Y, Castro C, Arya G. Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nat Commun 2024; 15:3015. [PMID: 38589344 PMCID: PMC11001925 DOI: 10.1038/s41467-024-46998-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA
| | - Daniel Duke
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA
| | - Tao Ye
- Department of Chemistry & Biochemistry, University of California, Merced, CA, 95343, USA
- Department of Materials and Biomaterials Science & Engineering, University of California, Merced, CA, 95343, USA
| | - Michael Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA.
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2
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Shi C, Yang D, Ma X, Pan L, Shao Y, Arya G, Ke Y, Zhang C, Wang F, Zuo X, Li M, Wang P. A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202320179. [PMID: 38288561 DOI: 10.1002/anie.202320179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Indexed: 02/17/2024]
Abstract
Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay named SPOT (sensitive loop-initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a catalytic DNAzyme of endonuclease capability into a unified one-stranded allosteric biosensor. SPOT is activated once a nucleic acid target of a specific sequence binds to its allosteric module to enable continuous cleavage of molecular reporters. SPOT provides a highly robust platform for sensitive, convenient and cost-effective detection of low-abundance nucleic acids. For clinical validation, we demonstrated that SPOT could detect serum miRNAs for the diagnostics of breast cancer, gastric cancer and prostate cancer. Furthermore, SPOT exhibits potent detection performance over SARS-CoV-2 RNA from clinical swabs with high sensitivity and specificity. Finally, SPOT is compatible with point-of-care testing modalities such as lateral flow assays. Hence, we envision that SPOT may serve as a robust assay for the sensitive detection of a variety of nucleic acid targets enabling molecular diagnostics in clinics.
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Affiliation(s)
- Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuanchuan Shao
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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3
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DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS Appl Bio Mater 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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4
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Wang S, Lin PA, DeLuca M, Zauscher S, Arya G, Ke Y. Controlling Silicification on DNA Origami with Polynucleotide Brushes. J Am Chem Soc 2024; 146:358-367. [PMID: 38117542 PMCID: PMC10785815 DOI: 10.1021/jacs.3c09310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single- or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarse-grained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic-inorganic nanomaterials.
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Affiliation(s)
- Shuang Wang
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Po-An Lin
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Marcello DeLuca
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Stefan Zauscher
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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5
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Roozbahani GM, Colosi P, Oravecz A, Sorokina EM, Pfeifer W, Shokri S, Wei Y, Didier P, DeLuca M, Arya G, Tora L, Lakadamyali M, Poirier MG, Castro CE. Piggybacking functionalized DNA nanostructures into live cell nuclei. bioRxiv 2024:2023.12.30.573746. [PMID: 38260628 PMCID: PMC10802371 DOI: 10.1101/2023.12.30.573746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
DNA origami (DO) are promising tools for in vitro or in vivo applications including drug delivery; biosensing, detecting biomolecules; and probing chromatin sub-structures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing visualizing and controlling important biological processes in live cells. Here we present an approach to deliver DO strucures into live cell nuclei. We show that labelled DOs do not undergo detectable structural degradation in cell culture media or human cell extracts for 24 hr. To deliver DO platforms into the nuclei of human U2OS cells, we conjugated 30 nm long DO nanorods with an antibody raised against the largest subunit of RNA Polymerase II (Pol II), a key enzyme involved in gene transcription. We find that DOs remain structurally intact in cells for 24hr, including within the nucleus. Using fluorescence microscopy we demonstrate that the electroporated anti-Pol II antibody conjugated DOs are efficiently piggybacked into nuclei and exihibit sub-diffusive motion inside the nucleus. Our results reveal that functionalizing DOs with an antibody raised against a nuclear factor is a highly effective method for the delivery of nanodevices into live cell nuclei.
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Affiliation(s)
- Golbarg M. Roozbahani
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Patricia Colosi
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Attila Oravecz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, 67404, France
- Université de Strasbourg, Illkirch, 67404, France
| | - Elena M. Sorokina
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wolfgang Pfeifer
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Siamak Shokri
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yin Wei
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Pascal Didier
- Université de Strasbourg, Illkirch, 67404, France
- Laboratoire de Biophotonique et Pharmacologie, Illkirch, 67401, France
| | - Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, United States
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, 67404, France
- Université de Strasbourg, Illkirch, 67404, France
| | - Melike Lakadamyali
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
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6
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Tang Q, Sensale S, Bond C, Xing J, Qiao A, Hugelier S, Arab A, Arya G, Lakadamyali M. Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets. Curr Biol 2023; 33:5169-5184.e8. [PMID: 37979580 PMCID: PMC10843832 DOI: 10.1016/j.cub.2023.10.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 08/03/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023]
Abstract
Microtubules in cells consist of functionally diverse subpopulations carrying distinct post-translational modifications (PTMs). Akin to the histone code, the tubulin code regulates a myriad of microtubule functions, ranging from intracellular transport to chromosome segregation. However, how individual PTMs only occur on subsets of microtubules to contribute to microtubule specialization is not well understood. In particular, microtubule detyrosination, the removal of the C-terminal tyrosine on α-tubulin subunits, marks the stable population of microtubules and modifies how microtubules interact with other microtubule-associated proteins to regulate a wide range of cellular processes. Previously, we found that in certain cell types, only ∼30% of microtubules are highly enriched with the detyrosination mark and that detyrosination spans most of the length of a microtubule, often adjacent to a completely tyrosinated microtubule. How the activity of a cytosolic detyrosinase, vasohibin (VASH), leads to only a small subpopulation of highly detyrosinated microtubules is unclear. Here, using quantitative super-resolution microscopy, we visualized nascent microtubule detyrosination events in cells consisting of 1-3 detyrosinated α-tubulin subunits after nocodazole washout. Microtubule detyrosination accumulates slowly and in a dispersed pattern across the microtubule length. By visualizing single molecules of VASH in live cells, we found that VASH engages with microtubules stochastically on a short timescale, suggesting limited removal of tyrosine per interaction, consistent with the super-resolution results. Combining these quantitative imaging results with simulations incorporating parameters from our experiments, we provide evidence for a stochastic model for cells to establish a subset of detyrosinated microtubules via a detyrosination-stabilization feedback mechanism.
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Affiliation(s)
- Qing Tang
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sebastian Sensale
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA; Department of Physics, Cleveland State University, Cleveland, OH 44115-2214, USA.
| | - Charles Bond
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiazheng Xing
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andy Qiao
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Siewert Hugelier
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arian Arab
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Yang Y, Lu Q, Chen Y, DeLuca M, Arya G, Ke Y, Zauscher S. Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures. Angew Chem Int Ed Engl 2023; 62:e202311727. [PMID: 37820028 DOI: 10.1002/anie.202311727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023]
Abstract
DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site-specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to "smart" functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.
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Affiliation(s)
- Yunqi Yang
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Qinyi Lu
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Yu Chen
- University Program in Materials Science and Engineering, Duke University, Durham, NC 27708, USA
| | - Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Stefan Zauscher
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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8
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Pfeifer WG, Huang CM, Poirier MG, Arya G, Castro CE. Versatile computer-aided design of free-form DNA nanostructures and assemblies. Sci Adv 2023; 9:eadi0697. [PMID: 37494445 PMCID: PMC10371015 DOI: 10.1126/sciadv.adi0697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables design of complex 3D DNA assemblies with many components; however, the design of structures with free-form features like vertices or curvature still required iterative design guided by simulation feedback and user intuition. Here, we present an updated design tool, MagicDNA 2.0, that automates the design of free-form 3D geometries, leveraging design models informed by coarse-grained molecular dynamics simulations. Our GUI-based, stepwise design approach integrates a high level of automation with versatile control over assembly and subcomponent design parameters. We experimentally validated this approach by fabricating a range of DNA origami assemblies with complex free-form geometries, including a 3D Nozzle, G-clef, and Hilbert and Trifolium curves, confirming excellent agreement between design input, simulation, and structure formation.
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Affiliation(s)
- Wolfgang G. Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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9
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Li WF, Arya G, Roques-Carmes C, Lin Z, Johnson SG, Soljačić M. Transcending shift-invariance in the paraxial regime via end-to-end inverse design of freeform nanophotonics. Opt Express 2023; 31:24260-24272. [PMID: 37475257 DOI: 10.1364/oe.492553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/28/2023] [Indexed: 07/22/2023]
Abstract
Traditional optical elements and conventional metasurfaces obey shift-invariance in the paraxial regime. For imaging systems obeying paraxial shift-invariance, a small shift in input angle causes a corresponding shift in the sensor image. Shift-invariance has deep implications for the design and functionality of optical devices, such as the necessity of free space between components (as in compound objectives made of several curved surfaces). We present a method for nanophotonic inverse design of compact imaging systems whose resolution is not constrained by paraxial shift-invariance. Our method is end-to-end, in that it integrates density-based full-Maxwell topology optimization with a fully iterative elastic-net reconstruction algorithm. By the design of nanophotonic structures that scatter light in a non-shift-invariant manner, our optimized nanophotonic imaging system overcomes the limitations of paraxial shift-invariance, achieving accurate, noise-robust image reconstruction beyond shift-invariant resolution.
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10
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Wang Y, Sensale S, Pedrozo M, Huang CM, Poirier MG, Arya G, Castro CE. Steric Communication between Dynamic Components on DNA Nanodevices. ACS Nano 2023; 17:8271-8280. [PMID: 37072126 PMCID: PMC10173695 DOI: 10.1021/acsnano.2c12455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex geometry, programmed motion, rapid actuation, force application, and various kinds of sensing modalities. Advanced robotic functions like feedback control, autonomy, or programmed routines also require the ability to transmit signals among subcomponents. Prior work in DNA nanotechnology has established approaches for signal transmission, for example through diffusing strands or structurally coupled motions. However, soluble communication is often slow and structural coupling of motions can limit the function of individual components, for example to respond to the environment. Here, we introduce an approach inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. These components undergo separate thermal fluctuations where certain conformations of one arm will sterically occlude conformations of the distal arm. We implement this approach in a DNA origami device consisting of two stiff arms each connected to a base platform via a flexible hinge joint. We demonstrate the ability for one arm to sterically regulate both the range of motion and the conformational state (latched or freely fluctuating) of the distal arm, results that are quantitatively captured by mesoscopic simulations using experimentally informed energy landscapes for hinge-angle fluctuations. We further demonstrate the ability to modulate signal transmission by mechanically tuning the range of thermal fluctuations and controlling the conformational states of the arms. Our results establish a communication mechanism well-suited to transmit signals between thermally fluctuating dynamic components and provide a path to transmitting signals where the input is a dynamic response to parameters like force or solution conditions.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sebastian Sensale
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Miguel Pedrozo
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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11
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DeLuca M, Pfeifer WG, Randoing B, Huang CM, Poirier MG, Castro CE, Arya G. Thermally reversible pattern formation in arrays of molecular rotors. Nanoscale 2023; 15:8356-8365. [PMID: 37092294 DOI: 10.1039/d2nr05813h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Control over the mesoscale to microscale patterning of materials is of great interest to the soft matter community. Inspired by DNA origami rotors, we introduce a 2D nearest-neighbor lattice of spinning rotors that exhibit discrete orientational states and interactions with their neighbors. Monte Carlo simulations of rotor lattices reveal that they exhibit a variety of interesting ordering behaviors and morphologies that can be modulated through rotor design parameters. The rotor arrays exhibit diverse patterns including closed loops, radiating loops, and bricklayer structures in their ordered states. They exhibit specific heat peaks at very low temperatures for small system sizes, and some systems exhibit multiple order-disorder transitions depending on inter-rotor interaction design. We devise an energy-based order parameter and show via umbrella sampling and histogram reweighting that this order parameter captures well the order-disorder transitions occurring in these systems. We fabricate real DNA origami rotors which themselves can order via programmable DNA base-pairing interactions and demonstrate both ordered and disordered phases, illustrating how rotor lattices may be realized experimentally and used for responsive organization. This work establishes the feasibility of realizing structural nanomaterials that exhibit locally mediated microscale patterns which could have applications in sensing and precision surface patterning.
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Affiliation(s)
- Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, USA.
| | - Wolfgang G Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, USA
- Department of Physics, The Ohio State University, USA
| | | | - Chao-Min Huang
- Department of Mechanical Engineering and Materials Science, Duke University, USA.
| | | | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, USA.
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12
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Barcus K, Lin PA, Zhou Y, Arya G, Cohen SM. Influence of Polymer Characteristics on the Self-Assembly of Polymer-Grafted Metal-Organic Framework Particles. ACS Nano 2022; 16:18168-18177. [PMID: 36252115 PMCID: PMC9706656 DOI: 10.1021/acsnano.2c05175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Polymer-grafted metal-organic frameworks (MOFs) can combine the properties of MOFs and polymers into a single, matrix-free composite material. Herein, we examine polymer-grafted MOF particles (using UiO-66 as a model system) to examine how the molecular weight, grafting density, and chemical functionality of the polymer graft affects the preparation of free-standing self-assembled MOF monolayers (SAMMs). The physical properties of the monolayers are influenced by the choice of polymer, and robust, flexible monolayers were achieved more readily with poly(methyl acrylate) when compared to poly(methyl methacrylate) or poly(benzyl methacrylate). Molecular dynamics simulations were carried out to provide insights into the orientation and ordering of MOFs in the monolayers with respect to MOF size, graft length, and hydrophobicity. The relationship between molecular weight and graft density of the polymer brush was investigated and related to polymer brush conformation, offering design rules for further optimizations to balance mechanical strength, MOF weight fraction, and processability for this class of hybrid materials.
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Affiliation(s)
- Kyle Barcus
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California92093, United States
| | - Po-An Lin
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27710, United States
| | - Yilong Zhou
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27710, United States
| | - Gaurav Arya
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27710, United States
| | - Seth M. Cohen
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California92093, United States
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13
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Zhou C, Yang D, Sensale S, Sharma P, Wang D, Yu L, Arya G, Ke Y, Wang P. A bistable and reconfigurable molecular system with encodable bonds. Sci Adv 2022; 8:eade3003. [PMID: 36399380 PMCID: PMC9674029 DOI: 10.1126/sciadv.ade3003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Molecular systems with ability to controllably transform between different conformations play pivotal roles in regulating biochemical functions. Here, we report the design of a bistable DNA origami four-way junction (DOJ) molecular system that adopts two distinct stable conformations with controllable reconfigurability by using conformation-controlled base stacking. Exquisite control over DOJ's conformation and transformation is realized by programming the stacking bonds (quasi-blunt-ends) within the junction to induce prescribed coaxial stacking of neighboring junction arms. A specific DOJ conformation may be achieved by encoding the stacking bonds with binary stacking sequences based on thermodynamic calculations. Dynamic transformations of DOJ between various conformations are achieved by using specific environmental and molecular stimulations to reprogram the stacking codes. This work provides a useful platform for constructing self-assembled DNA nanostructures and nanomachines and insights for future design of artificial molecular systems with increasing complexity and reconfigurability.
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Affiliation(s)
- Chunyang Zhou
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
- College of Life Sciences and Technology, Changchun University of Science and Technology, Changchun 130013, Jilin, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Sebastian Sensale
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Pranav Sharma
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Lei Yu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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14
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Pajak J, Arya G. Molecular dynamics of DNA translocation by FtsK. Nucleic Acids Res 2022; 50:8459-8470. [PMID: 35947697 PMCID: PMC9410874 DOI: 10.1093/nar/gkac668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 07/16/2022] [Accepted: 07/23/2022] [Indexed: 12/24/2022] Open
Abstract
The bacterial FtsK motor harvests energy from ATP to translocate double-stranded DNA during cell division. Here, we probe the molecular mechanisms underlying coordinated DNA translocation in FtsK by performing long timescale simulations of its hexameric assembly and individual subunits. From these simulations we predict signaling pathways that connect the ATPase active site to DNA-gripping residues, which allows the motor to coordinate its translocation activity with its ATPase activity. Additionally, we utilize well-tempered metadynamics simulations to compute free-energy landscapes that elucidate the extended-to-compact transition involved in force generation. We show that nucleotide binding promotes a compact conformation of a motor subunit, whereas the apo subunit is flexible. Together, our results support a mechanism whereby each ATP-bound subunit of the motor conforms to the helical pitch of DNA, and ATP hydrolysis/product release causes a subunit to lose grip of DNA. By ordinally engaging and disengaging with DNA, the FtsK motor unidirectionally translocates DNA.
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Affiliation(s)
- Joshua Pajak
- Dept. of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
- Dept. of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gaurav Arya
- Dept. of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
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15
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Abstract
Self-assembly of faceted nanoparticles is a promising route for fabricating nanomaterials; however, achieving low-dimensional assemblies of particles with tunable orientations is challenging. Here, we demonstrate that trapping surface-functionalized faceted nanoparticles at fluid-fluid interfaces is a viable approach for controlling particle orientation and facilitating their assembly into unique one- and two-dimensional superstructures. Using molecular dynamics simulations of polymer-grafted nanocubes in a polymer bilayer along with a particle-orientation classification method we developed, we show that the nanocubes can be induced into face-up, edge-up, or vertex-up orientations by tuning the graft density and differences in their miscibility with the two polymer layers. The orientational preference of the nanocubes is found to be governed by an interplay between the interfacial area occluded by the particle, the difference in interactions of the grafts with the two layers, and the stretching and intercalation of grafts at the interface. The resulting orientationally constrained nanocubes are then shown to assemble into a variety of unusual architectures, such as rectilinear strings, close-packed sheets, bilayer ribbons, and perforated sheets, which are difficult to obtain using other assembly methods. Our work thus demonstrates a versatile strategy for assembling freestanding arrays of faceted nanoparticles with possible applications in plasmonics, optics, catalysis, and membranes, where precise control over particle orientation and position is required.
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Affiliation(s)
- Yilong Zhou
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Tsung-Yeh Tang
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Brian Hyun-Jong Lee
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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16
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Simões V, Cizubu BK, Harley L, Zhou Y, Pajak J, Snyder NA, Bouvette J, Borgnia MJ, Arya G, Bartesaghi A, Silva GM. Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes. Cell Rep 2022; 39:110860. [PMID: 35613580 PMCID: PMC9215706 DOI: 10.1016/j.celrep.2022.110860] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 01/11/2023] Open
Abstract
Protein ubiquitination is an essential process that rapidly regulates protein synthesis, function, and fate in dynamic environments. Within its non-proteolytic functions, we showed that K63-linked polyubiquitinated conjugates heavily accumulate in yeast cells exposed to oxidative stress, stalling ribosomes at elongation. K63-ubiquitinated conjugates accumulate mostly because of redox inhibition of the deubiquitinating enzyme Ubp2; however, the role and regulation of ubiquitin-conjugating enzymes (E2) in this pathway remained unclear. Here, we show that the E2 Rad6 associates and modifies ribosomes during stress. We further demonstrate that Rad6 and its human homolog UBE2A are redox regulated by forming a reversible disulfide with the E1 ubiquitin-activating enzyme (Uba1). This redox regulation is part of a negative feedback regulation, which controls the levels of K63 ubiquitination under stress. Finally, we show that Rad6 activity is necessary to regulate translation, antioxidant defense, and adaptation to stress, thus providing an additional physiological role for this multifunctional enzyme.
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Affiliation(s)
- Vanessa Simões
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Lana Harley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Ye Zhou
- Department of Computer Science, Department of Biochemistry, and Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Nathan A Snyder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jonathan Bouvette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC 27709, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Department of Biochemistry, and Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA.
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17
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Abstract
Diffusion-mediated binding of molecules under the influence of discrete spatially confining potentials is a commonly encountered scenario in systems subjected to explicit fields or implicit fields arising from tethering restraints. Here, we derive analytical expressions for the mean binding time of two random walkers geometrically confined by means of two harmonic potentials in one- and two-dimensional systems, which show excellent agreement with Brownian dynamics simulations. As a demonstration of its utility, we use this theory to maximize the communication speed in existing DNA walkers, obtaining quantitative agreement with previously reported experimental findings. The analytical expressions derived in this paper are broadly applicable to diverse systems, providing ways to characterize communication processes and optimize the rate of signal propagation for sensing and computing applications at the nanoscale.
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Affiliation(s)
- Sebastian Sensale
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Pranav Sharma
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
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18
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Lee BHJ, Arya G. Assembly mechanism of surface-functionalized nanocubes. Nanoscale 2022; 14:3917-3928. [PMID: 35225318 DOI: 10.1039/d1nr07995f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Faceted nanoparticles can be used as building blocks to assemble nanomaterials with exceptional optical and catalytic properties. Recent studies have shown that surface functionalization of such nanoparticles with organic molecules, polymer chains, or DNA can be used to control the separation distance and orientation of particles within their assemblies. In this study, we computationally investigate the mechanism of assembly of nanocubes grafted with short-chain molecules. Our approach involves computing the interaction free energy landscape of a pair of such nanocubes via Monte Carlo simulations and using the Dijkstra algorithm to determine the minimum free energy pathway connecting key states in the landscape. We find that the assembly pathway of nanocubes is very rugged involving multiple energy barriers and metastable states. Analysis of nanocube configurations along the pathway reveals that the assembly mechanism is dominated by sliding motion of nanocubes relative to each other punctuated by their local dissociation at grafting points involving lineal separation and rolling motions. The height of energy barriers between metastable states depends on factors such as the interaction strength and surface roughness of the nanocubes and the steric repulsion from the grafts. These results imply that the observed assembly configuration of nanocubes depends not only on their globally stable minimum free energy state but also on the assembly pathway leading to this state. The free energy landscapes and assembly pathways presented in this study along with the proposed guidelines for engineering such pathways should be useful to researchers aiming to achieve uniform nanostructures from self-assembly of faceted nanoparticles.
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Affiliation(s)
- Brian Hyun-Jong Lee
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA.
| | - Gaurav Arya
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA.
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19
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Yang Y, Lu Q, Huang C, Qian H, Zhang Y, Deshpande S, Arya G, Ke Y, Zauscher S. Programmable Site‐Specific Functionalization of DNA Origami with Polynucleotide Brushes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yunqi Yang
- Department of Mechanical Engineering and Materials Science Duke University Durham NC 27708 USA
| | - Qinyi Lu
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Chao‐Min Huang
- Department of Mechanical Engineering and Materials Science Duke University Durham NC 27708 USA
| | - Hongji Qian
- Department of Biomedical Engineering Duke University Durham NC 27708 USA
| | - Yunlong Zhang
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Sonal Deshpande
- Department of Biomedical Engineering Duke University Durham NC 27708 USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science Duke University Durham NC 27708 USA
| | - Yonggang Ke
- Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | - Stefan Zauscher
- Department of Mechanical Engineering and Materials Science Duke University Durham NC 27708 USA
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20
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Abstract
Gold nanorods assembled in a side-by-side chiral configuration have potential applications in sensing due to their strong chiroptical surface plasmon resonances. Recent experiments have shown that dimers of gold nanorods bridged by double-stranded DNA exhibit variable chiral configurations depending on the chemical and ionic properties of the solvent medium. Here, we uncover the underlying physics governing this intriguing chiral behavior of such DNA-bridged nanorods by theoretically evaluating their configurational free energy landscape. Our results reveal how chiral configurations emerge from an interplay between the twist-stretch coupling of the intervening DNA and the intermolecular interactions between the nanorods, with dimers exhibiting left-handed chirality when the interparticle interactions are dominated by attractive depletion or van der Waals forces and right-handed chirality when dominated by repulsive electrostatic or steric forces. We demonstrate how changes in the depletant or ion concentration of the solvent medium lead to different classes of configurational responses by the dimers, including chirality-switching behavior, in good agreement with experimental observations. Based on extensive analyses of how material properties like nanorod aspect ratio, DNA length, and graft height modulate the free energy landscape, we propose strategies for tuning the environmentally responsive reconfigurability of the nanorod dimers. Overall, this work should help control the chirality and related optical activity of nanoparticle dimers and higher-order assemblies for various applications.
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Affiliation(s)
- Brian Hyun-Jong Lee
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas A Kotov
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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21
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Yang Y, Lu Q, Huang CM, Qian H, Zhang Y, Deshpande S, Arya G, Ke Y, Zauscher S. Programmable site-specific functionalization of DNA origami with polynucleotide brushes. Angew Chem Int Ed Engl 2021; 60:23241-23247. [PMID: 34302317 DOI: 10.1002/anie.202107829] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Indexed: 11/11/2022]
Abstract
Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush-functionalized origami nanostructures. We demonstrate that SI-TcEP can site-specifically pattern DONs with brushes containing both natural and non-natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes. The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.
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Affiliation(s)
- Yunqi Yang
- Duke University, Mechanical Engineering and Materials Science, 101 Science Dr, Hudson Hall Room 144, 27708, Durham, UNITED STATES
| | - Qinyi Lu
- Emory University, Chemistry, UNITED STATES
| | - Chao-Min Huang
- Duke University, Mechanical Engineering and Materials Science, UNITED STATES
| | - Hongji Qian
- Duke University, Biomedical Engineering, UNITED STATES
| | | | | | - Gaurav Arya
- Duke University, Mechanical Engineering and Materials Science, UNITED STATES
| | - Yonggang Ke
- Georgia Tech: Georgia Institute of Technology, Biomedical Engineering, UNITED STATES
| | - Stefan Zauscher
- Duke University, Mechanical Engineering and Materials Science, 144 Hudson Hall, Box 90300, 27708, Durham, UNITED STATES
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22
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Pajak J, Dill E, Reyes-Aldrete E, White MA, Kelch BA, Jardine P, Arya G, Morais M. Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor. Nucleic Acids Res 2021; 49:6474-6488. [PMID: 34050764 PMCID: PMC8216284 DOI: 10.1093/nar/gkab372] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/20/2021] [Accepted: 05/28/2021] [Indexed: 01/16/2023] Open
Abstract
Double-stranded DNA viruses package their genomes into pre-assembled capsids using virally-encoded ASCE ATPase ring motors. We present the first atomic-resolution crystal structure of a multimeric ring form of a viral dsDNA packaging motor, the ATPase of the asccφ28 phage, and characterize its atomic-level dynamics via long timescale molecular dynamics simulations. Based on these results, and previous single-molecule data and cryo-EM reconstruction of the homologous φ29 motor, we propose an overall packaging model that is driven by helical-to-planar transitions of the ring motor. These transitions are coordinated by inter-subunit interactions that regulate catalytic and force-generating events. Stepwise ATP binding to individual subunits increase their affinity for the helical DNA phosphate backbone, resulting in distortion away from the planar ring towards a helical configuration, inducing mechanical strain. Subsequent sequential hydrolysis events alleviate the accumulated mechanical strain, allowing a stepwise return of the motor to the planar conformation, translocating DNA in the process. This type of helical-to-planar mechanism could serve as a general framework for ring ATPases.
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Affiliation(s)
- Joshua Pajak
- Dept. of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Erik Dill
- Dept. of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Emilio Reyes-Aldrete
- Dept. of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mark A White
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Brian A Kelch
- Dept. of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul J Jardine
- Dept. of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gaurav Arya
- Dept. of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Marc C Morais
- Dept. of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
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23
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Woodson M, Pajak J, Mahler BP, Zhao W, Zhang W, Arya G, White MA, Jardine PJ, Morais MC. A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. Sci Adv 2021; 7:7/19/eabc1955. [PMID: 33962953 PMCID: PMC8104870 DOI: 10.1126/sciadv.abc1955] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Molecular segregation and biopolymer manipulation require the action of molecular motors to do work by applying directional forces to macromolecules. The additional strand conserved E (ASCE) ring motors are an ancient family of molecular motors responsible for diverse biological polymer manipulation tasks. Viruses use ASCE segregation motors to package their genomes into their protein capsids and provide accessible experimental systems due to their relative simplicity. We show by cryo-EM-focused image reconstruction that ASCE ATPases in viral double-stranded DNA (dsDNA) packaging motors adopt helical symmetry complementary to their dsDNA substrates. Together with previous data, our results suggest that these motors cycle between helical and planar configurations, providing a possible mechanism for directional translocation of DNA. Similar changes in quaternary structure have been observed for proteasome and helicase motors, suggesting an ancient and common mechanism of force generation that has been adapted for specific tasks over the course of evolution.
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Affiliation(s)
- Michael Woodson
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Bryon P Mahler
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wei Zhao
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Characterization Facility, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Mark A White
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Marc C Morais
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
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24
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Pajak J, Atz R, Hilbert BJ, Morais MC, Kelch BA, Jardine PJ, Arya G. Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation. Proc Natl Acad Sci U S A 2021; 118:e2024928118. [PMID: 33888587 PMCID: PMC8092589 DOI: 10.1073/pnas.2024928118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate-switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases. Using free-energy landscapes computed through molecular dynamics simulations, we determined the stable conformational state of the ATPase active site in ATP- and ADP-bound states. Our results show that the catalytic glutamate residue transitions from an active to an inactive pose upon ATP hydrolysis and that a residue assigned as the glutamate switch is necessary for regulating this transition. Furthermore, we identified via mutual information analyses the intramolecular signaling pathway mediated by the glutamate switch that is responsible for coupling ATP binding to conformational transitions of DNA-gripping motifs. We corroborated these predictions with both structural and functional experimental measurements. Specifically, we showed that the crystal structure of the ADP-bound P74-26 packaging ATPase is consistent with the structural coupling predicted from simulations, and we further showed that disrupting the predicted signaling pathway indeed decouples ATPase activity from DNA translocation activity in the φ29 DNA packaging motor. Our work thus establishes a signaling pathway that couples chemical and mechanical events in viral DNA packaging motors.
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Affiliation(s)
- Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708
| | - Rockney Atz
- Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455
| | - Brendan J Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708;
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25
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Abstract
Dynamic DNA origami has been employed for generating a rich repository of molecular nanomachines that are capable of sensing various cues and changing their conformations accordingly. The common design principle of the existing DNA origami nanomachines is that each dynamic DNA origami is programmed to transform in a specific manner, and the nanomachine needs to be redesigned to achieve a different form of transformation. However, it remains challenging to enable a multitude of controlled transformations in a single design of dynamic DNA nanomachine. Here we report a modular design method to programmatically tune the shapes of a DNA origami nanomachine. The DNA origami consists of small, modular DNA units, and the length of each unit can be selectively changed by toehold-mediated strand displacement. By use of different combinations of trigger DNA strands, modular DNA units can be selectively transformed, leading to the programmable reconfiguration of the overall dimensions and curvatures of DNA origami. The modular design of programmable shape transformation of DNA origami can find potential applications in more sophisticated molecular nanorobots and smart drug delivery nanocarriers.
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Affiliation(s)
- Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Chao-Min Huang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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26
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Wang D, Yu L, Huang CM, Arya G, Chang S, Ke Y. Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units. J Am Chem Soc 2021; 143:2256-2263. [DOI: 10.1021/jacs.0c10576] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Chao-Min Huang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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27
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Abstract
Our ability to synthesize faceted nanoparticles of tunable shapes and sizes has opened up many intriguing applications of such particles. However, our progress in understanding, modeling, and simulating their collective rheology, phase behavior, and self-assembly has been hindered by the lack of analytical interparticle interaction potentials. Here, we present one of the first analytical models for the van der Waals interaction energy between faceted nanoparticles. The model was derived through various approximations that reduce the usual six-dimensional integral over particle volumes to a series of two-dimensional integrals over particle interaction areas with closed-form solutions. Comparison and analyses of energies obtained from the analytical model with those computed from exact atomistic calculations show that the model approximations lead to insignificant errors in predicted energies across all relevant particle configurations. We demonstrate that the model yields accurate energies for diverse particle shapes including nanocubes, triangular prisms, faceted rods, and square pyramids, while yielding many orders of magnitude improvement in computational efficiency compared to atomistic calculations. To make the model more accessible and to demonstrate its applicability, an open-source graphical user interface application implementing the model for nanocubes in arbitrary configurations has been developed. We expect that the analytical model will accelerate future investigations of faceted nanoparticles that require accurate calculation of interparticle interactions.
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Affiliation(s)
- Brian Hyun-Jong Lee
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
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28
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Meluzzi D, Arya G. Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. Methods 2020; 181-182:24-34. [PMID: 31470090 PMCID: PMC7044057 DOI: 10.1016/j.ymeth.2019.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/24/2019] [Accepted: 08/23/2019] [Indexed: 02/08/2023] Open
Abstract
Chromosome conformation capture (3C) and its variants are powerful experimental techniques for probing intra- and inter-chromosomal interactions within cell nuclei at high resolution and in a high-throughput, quantitative manner. The contact maps derived from such experiments provide an avenue for inferring the 3D spatial organization of the genome. This review provides an overview of the various computational methods developed in the past decade for addressing the very important but challenging problem of deducing the detailed 3D structure or structure population of chromosomal domains, chromosomes, and even entire genomes from 3C contact maps.
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Affiliation(s)
- Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, United States.
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29
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Shi Z, Arya G. Free energy landscape of salt-actuated reconfigurable DNA nanodevices. Nucleic Acids Res 2020; 48:548-560. [PMID: 31799631 PMCID: PMC6954428 DOI: 10.1093/nar/gkz1137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/15/2019] [Accepted: 12/02/2019] [Indexed: 12/11/2022] Open
Abstract
Achieving rapid, noninvasive actuation of DNA structures is critical to expanding the functionality of DNA nanotechnology. A promising actuation approach involves introducing multiple, short pairs of single-stranded DNA overhangs to components of the structure and triggering hybridization or dissociation of the overhangs via changes in solution ionic conditions to drive structural transitions. Here, we reveal the underlying basis of this new approach by computing via molecular simulations the free energy landscape of DNA origami hinges actuated between open and closed states. Our results reveal how the overhangs collectively introduce a sharp free-energy minimum at the closed state and a broad energy barrier between open and closed states and how changes in ionic conditions modulate these features of the landscape to drive actuation towards the open or closed state. We demonstrate the critical role played by hinge confinement in stabilizing the hybridized state of the overhangs and magnifying the energy barrier to dissociation. By analyzing how the distribution of overhangs and their length and sequence modulate the energy landscape, we obtain design rules for tuning the actuation behavior. The molecular insights obtained here should be applicable to a broad range of systems involving DNA hybridization within confined systems.
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Affiliation(s)
- Ze Shi
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
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30
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Wang J, Lee BHJ, Arya G. Kinetically assembled binary nanoparticle networks. Nanoscale 2020; 12:5091-5102. [PMID: 32068755 DOI: 10.1039/c9nr09900j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Embedding percolating networks of nanoparticles (NPs) within polymers is a promising approach for mechanically reinforcing polymers and for introducing novel electronic, transport, and catalytic properties into otherwise inert polymers. While such networks may be obtained through kinetic assembly of unary system of NPs, the ensuing structures exhibit limited morphologies. Here, we investigate the possibility of increasing the diversity of NP networks through kinetic assembly of multiple species of NPs. Using lattice Monte Carlo simulations we show that networks obtained from co-assembly of two NP species of different sizes exhibit significantly more diverse morphology than those assembled from a single species. In particular, we achieved considerable variations in the particle spatial distribution, proportions of intra- and interspecies contacts, fractal dimension, and pore sizes of the networks by simply modulating the stoichiometry of the two species and their intra and inter-species affinities. We classified these distinct morphologies into "integrated", "coated", "leaved", and "blocked" phases, and provide relevant phase diagrams for achieving them. Our findings are relevant to controlled and predictable assembly of particle networks for creating multifunctional composites with improved properties.
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Affiliation(s)
- Jiuling Wang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA.
| | - Brian Hyun-Jong Lee
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA.
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA.
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31
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delToro D, Ortiz D, Ordyan M, Pajak J, Sippy J, Catala A, Oh CS, Vu A, Arya G, Smith DE, Catalano CE, Feiss M. Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif. J Mol Biol 2019; 431:4455-4474. [PMID: 31473160 PMCID: PMC7416571 DOI: 10.1016/j.jmb.2019.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 11/30/2022]
Abstract
Many viruses employ ATP-powered motors for genome packaging. We combined genetic, biochemical, and single-molecule techniques to confirm the predicted Walker-B ATP-binding motif in the phage λ motor and to investigate the roles of the conserved residues. Most changes of the conserved hydrophobic residues resulted in >107-fold decrease in phage yield, but we identified nine mutants with partial activity. Several were cold-sensitive, suggesting that mobility of the residues is important. Single-molecule measurements showed that the partially active A175L exhibits a small reduction in motor velocity and increase in slipping, consistent with a slowed ATP binding transition, whereas G176S exhibits decreased slipping, consistent with an accelerated transition. All changes to the conserved D178, predicted to coordinate Mg2+•ATP, were lethal except conservative change D178E. Biochemical interrogation of the inactive D178N protein found no folding or assembly defects and near-normal endonuclease activity, but a ∼200-fold reduction in steady-state ATPase activity, a lag in the single-turnover ATPase time course, and no DNA packaging, consistent with a critical role in ATP-coupled DNA translocation. Molecular dynamics simulations of related enzymes suggest that the aspartate plays an important role in enhancing the catalytic activity of the motor by bridging the Walker motifs and precisely contributing its charged group to help polarize the bound nucleotide. Supporting this prediction, single-molecule measurements revealed that change D178E reduces motor velocity without increasing slipping, consistent with a slowed hydrolysis step. Our studies thus illuminate the mechanistic roles of Walker-B residues in ATP binding, hydrolysis, and DNA translocation by this powerful motor.
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Affiliation(s)
- Damian delToro
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Ortiz
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Mariam Ordyan
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Jean Sippy
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Alexis Catala
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Choon-Seok Oh
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Amber Vu
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Carlos E Catalano
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Michael Feiss
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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32
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Ranjan RS, Arya G, Yadav VK. Acute encephalopathy with biphasic seizures and late reduced diffusion (central sparing type)—MRI and MR spectroscopy findings. Indian J Radiol Imaging 2019; 29:426-430. [PMID: 31949346 PMCID: PMC6958896 DOI: 10.4103/ijri.ijri_235_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/26/2019] [Accepted: 11/30/2019] [Indexed: 11/04/2022] Open
Abstract
Acute encephalopathy with biphasic seizure and late reduced diffusion (AESD) is a clinico-radiologic syndrome of acute encephalopathy characterized by biphasic seizure and altered consciousness in acute phase followed by restricted diffusion in bilateral cerebral parenchyma on magnetic resonance imaging (MRI) in the subacute stage. Here, we present the MRI and magnetic resonance spectroscopy (MRS) findings in a case of AESD presenting in 4-year child and diagnosed based on clinico-radiological correlation.
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Affiliation(s)
- Rahul S Ranjan
- Departments of Radiodiagnosis, Rama Medical College, Mandhana, Kanpur, Uttar Pradesh
| | - Gaurav Arya
- Departments of Paediatrics, Rama Medical College, Mandhana, Kanpur, Uttar Pradesh
| | - Vikas K Yadav
- Consultant Radiologist at Maxcure Hospital, Hyderabad, Telangana, India
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33
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Abstract
Surface functionalization of nanoparticles with polymer grafts was recently shown to be a viable strategy for controlling the relative orientation of shaped nanoparticles in their higher-order assemblies. In this study, we investigated in silico the orientational phase behavior of coplanar polymer-grafted nanocubes confined in a thin film. We first used Monte Carlo simulations to compute the two-particle interaction free-energy landscape of the nanocubes and identify their globally stable configurations. The nanocubes were found to exhibit four stable phases: those with edge-edge and face-face orientations, and those exhibiting partially overlapped slanted and parallel faces previously assumed to be metastable. Moreover, the edge-edge configuration originally thought to involve kissing edges instead displayed partly overlapping edges, where the extent of the overlap depends on the attachment positions of the grafts. We next formulated analytical scaling expressions for the free energies of the identified configurations, which were used for constructing a comprehensive phase diagram of nanocube orientation in a multidimensional parameter space comprising of the size and interaction strength of the nanocubes and the Kuhn length and surface density of the grafts. The morphology of the phase diagram was shown to arise from an interplay between polymer- and surface-mediated interactions, especially differences in their scalings with respect to nanocube size and grafting density across the four phases. The phase diagram provided insights into tuning these interactions through the various parameters of the system for achieving target configurations. Overall, this work provides a framework for predicting and engineering interparticle configurations, with possible applications in plasmonic nanocomposites where control over particle orientation is critical.
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Affiliation(s)
- Brian Hyun-Jong Lee
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
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34
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Ortiz D, delToro D, Ordyan M, Pajak J, Sippy J, Catala A, Oh CS, Vu A, Arya G, Feiss M, Smith DE, Catalano CE. Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor. Nucleic Acids Res 2019; 47:1404-1415. [PMID: 30541105 PMCID: PMC6379665 DOI: 10.1093/nar/gky1217] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/09/2018] [Accepted: 12/06/2018] [Indexed: 01/09/2023] Open
Abstract
ASCE ATPases include ring-translocases such as cellular helicases and viral DNA packaging motors (terminases). These motors have conserved Walker A and B motifs that bind Mg2+-ATP and a catalytic carboxylate that activates water for hydrolysis. Here we demonstrate that Glu179 serves as the catalytic carboxylate in bacteriophage λ terminase and probe its mechanistic role. All changes of Glu179 are lethal: non-conservative changes abrogate ATP hydrolysis and DNA translocation, while the conservative E179D change attenuates ATP hydrolysis and alters single molecule translocation dynamics, consistent with a slowed chemical hydrolysis step. Molecular dynamics simulations of several homologous terminases suggest a novel mechanism, supported by experiments, wherein the conserved Walker A arginine ‘toggles’ between interacting with a glutamate residue in the ‘lid’ subdomain and the catalytic glutamate upon ATP binding; this switch helps mediate a transition from an ‘open’ state to a ‘closed’ state that tightly binds nucleotide and DNA, and also positions the catalytic glutamate next to the γ-phosphate to align the hydrolysis transition state. Concomitant reorientation of the lid subdomain may mediate mechanochemical coupling of ATP hydrolysis and DNA translocation. Given the strong conservation of these structural elements in terminase enzymes, this mechanism may be universal for viral packaging motors.
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Affiliation(s)
- David Ortiz
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Damian delToro
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariam Ordyan
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Jean Sippy
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Alexis Catala
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Choon-Seok Oh
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Amber Vu
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Michael Feiss
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carlos E Catalano
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
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35
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Kajal S, Dhankhar M, Mukherjee S, Arya G. Non traditional method of endotracheal tube fixation in bearded patients undergoing facial and occipital surgeries. Egyptian Journal of Anaesthesia 2019. [DOI: 10.1016/j.egja.2015.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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36
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Abstract
We propose a strategy for assembling spherical nanoparticles (NPs) into anisotropic architectures in a polymer matrix. The approach takes advantage of the interfacial tension between two mutually immiscible polymers forming a bilayer and differences in the compatibility of the two polymer layers with polymer grafts on particles to trap NPs within two-dimensional planes parallel to the interface. The ability to precisely tune the location of the entrapment planes via the NP grafting density, and to trap multiple interacting particles within distinct planes, can then be used to assemble NPs into unconventional arrangements near the interface. We carry out molecular dynamics simulations of polymer-grafted NPs in a polymer bilayer to demonstrate the viability of the proposed approach in both trapping NPs at tunable distances from the interface and assembling them into a variety of unusual nanostructures. We illustrate the assembly of NP clusters, such as dimers with tunable tilt relative to the interface and trimers with tunable bending angle, as well as anisotropic macroscopic phases, including serpentine and branched structures, ridged hexagonal monolayers, and square-ordered bilayers. We also develop a theoretical model to predict the preferred positions and free energies of NPs trapped at or near the interface that could help guide the design of polymer-grafted NPs for achieving target NP architectures. Overall, this work suggests that interfacial assembly of NPs could be a promising approach for fabricating next-generation polymer nanocomposites with potential applications in plasmonics, electronics, optics, and catalysis where precise arrangement of polymer-embedded NPs is required for function.
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Affiliation(s)
- Tsung-Yeh Tang
- Department of NanoEngineering , University of California, San Diego , La Jolla , California 92093 , United States
| | - Yilong Zhou
- Department of Mechanical Engineering and Materials Science , Duke University , Durham , North Carolina 27708 , United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science , Duke University , Durham , North Carolina 27708 , United States
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37
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Song JJ, Bhattacharya R, Kim H, Chang J, Tang TY, Guo H, Ghosh SK, Yang Y, Jiang Z, Kim H, Russell TP, Arya G, Narayanan S, Sinha SK. One-Dimensional Anomalous Diffusion of Gold Nanoparticles in a Polymer Melt. Phys Rev Lett 2019; 122:107802. [PMID: 30932658 DOI: 10.1103/physrevlett.122.107802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Indexed: 06/09/2023]
Abstract
We investigated the dynamics of polymer-grafted gold nanoparticles loaded into polymer melts using x-ray photon correlation spectroscopy. For low molecular weight host matrix polymer chains, normal isotropic diffusion of the gold nanoparticles is observed. For larger molecular weights, anomalous diffusion of the nanoparticles is observed that can be described by ballistic motion and generalized Lévy walks, similar to those often used to discuss the dynamics of jammed systems. Under certain annealing conditions, the diffusion is one-dimensional and related to the direction of heat flow during annealing and is associated with an dynamic alignment of the host polymer chains. Molecular dynamics simulations of a single gold nanoparticle diffusing in a partially aligned polymer network semiquantitatively reproduce the experimental results to a remarkable degree. The results help to showcase how nanoparticles can under certain circumstances move rapidly in polymer networks.
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Affiliation(s)
- Jing-Jin Song
- Department of Materials Science & Engineering, University of California San Diego, 9500 Gilman Dr. La Jolla, California 92093, USA
| | - Rupak Bhattacharya
- Department of Physics, University of California San Diego, 9500 Gilman Dr. La Jolla, California 92093, USA
| | - Hyunki Kim
- Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst Massachusetts 01003, USA
| | - Jooyoung Chang
- Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst Massachusetts 01003, USA
| | - Tsung-Yeh Tang
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr. La Jolla, California 92093, USA
| | - Hongyu Guo
- National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, Maryland 20899-6102, USA
| | - Sajal K Ghosh
- Department of Physics, University of California San Diego, 9500 Gilman Dr. La Jolla, California 92093, USA
| | - Yi Yang
- Department of Physics, University of California San Diego, 9500 Gilman Dr. La Jolla, California 92093, USA
| | - Zhang Jiang
- Advanced Photon Source, Argonne National Laboratory, 9700 Cass Ave, Lemont, Illinois 60439, USA
| | - Hyeyoung Kim
- Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst Massachusetts 01003, USA
| | - Thomas P Russell
- Polymer Science and Engineering Department, University of Massachusetts Amherst, Amherst Massachusetts 01003, USA
| | - Gaurav Arya
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr. La Jolla, California 92093, USA
| | - Suresh Narayanan
- Advanced Photon Source, Argonne National Laboratory, 9700 Cass Ave, Lemont, Illinois 60439, USA
| | - Sunil K Sinha
- Department of Physics, University of California San Diego, 9500 Gilman Dr. La Jolla, California 92093, USA
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38
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Pajak J, Arya G. Novel Regulatory Mechanisms Identified in Viral DNA Packaging Proteins using Molecular Dynamics Simulations. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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39
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Marras AE, Shi Z, Lindell MG, Patton RA, Huang CM, Zhou L, Su HJ, Arya G, Castro CE. Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices. ACS Nano 2018; 12:9484-9494. [PMID: 30169013 DOI: 10.1021/acsnano.8b04817] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability to design and control DNA nanodevices with programmed conformational changes has established a foundation for molecular-scale robotics with applications in nanomanufacturing, drug delivery, and controlling enzymatic reactions. The most commonly used approach for actuating these devices, DNA binding and strand displacement, allows devices to respond to molecules in solution, but this approach is limited to response times of minutes or greater. Recent advances have enabled electrical and magnetic control of DNA structures with sub-second response times, but these methods utilize external components with additional fabrication requirements. Here, we present a simple and broadly applicable actuation method based on the avidity of many weak base-pairing interactions that respond to changes in local ionic conditions to drive large-scale conformational transitions in devices on sub-second time scales. To demonstrate such ion-mediated actuation, we modified a DNA origami hinge with short, weakly complementary single-stranded DNA overhangs, whose hybridization is sensitive to cation concentrations in solution. We triggered conformational changes with several different types of ions including mono-, di-, and trivalent ions and also illustrated the ability to engineer the actuation response with design parameters such as number and length of DNA overhangs and hinge torsional stiffness. We developed a statistical mechanical model that agrees with experimental data, enabling effective interpretation and future design of ion-induced actuation. Single-molecule Förster resonance energy-transfer measurements revealed that closing and opening transitions occur on the millisecond time scale, and these transitions can be repeated with time resolution on the scale of one second. Our results advance capabilities for rapid control of DNA nanodevices, expand the range of triggering mechanisms, and demonstrate DNA nanomachines with tunable analog responses to the local environment.
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Affiliation(s)
| | - Ze Shi
- Department of NanoEngineering , University of California San Diego , La Jolla , California 92093 , United States
| | | | | | | | | | | | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science , Duke University , Durham , North Carolina 27708 , United States
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40
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Affiliation(s)
- Su-Wen Hsu
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, MC 0448, La Jolla, California 92039-0448, United States
| | - Andrea L. Rodarte
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, MC 0448, La Jolla, California 92039-0448, United States
| | - Madhura Som
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, MC 0448, La Jolla, California 92039-0448, United States
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, MC 0448, La Jolla, California 92039-0448, United States
| | - Andrea R. Tao
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, MC 0448, La Jolla, California 92039-0448, United States
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Kilic S, Felekyan S, Doroshenko O, Boichenko I, Dimura M, Vardanyan H, Bryan LC, Arya G, Seidel CAM, Fierz B. Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. Nat Commun 2018; 9:235. [PMID: 29339721 PMCID: PMC5770380 DOI: 10.1038/s41467-017-02619-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/11/2017] [Indexed: 01/17/2023] Open
Abstract
The dynamic architecture of chromatin fibers, a key determinant of genome regulation, is poorly understood. Here, we employ multimodal single-molecule Förster resonance energy transfer studies to reveal structural states and their interconversion kinetics in chromatin fibers. We show that nucleosomes engage in short-lived (micro- to milliseconds) stacking interactions with one of their neighbors. This results in discrete tetranucleosome units with distinct interaction registers that interconvert within hundreds of milliseconds. Additionally, we find that dynamic chromatin architecture is modulated by the multivalent architectural protein heterochromatin protein 1α (HP1α), which engages methylated histone tails and thereby transiently stabilizes stacked nucleosomes. This compacted state nevertheless remains dynamic, exhibiting fluctuations on the timescale of HP1α residence times. Overall, this study reveals that exposure of internal DNA sites and nucleosome surfaces in chromatin fibers is governed by an intrinsic dynamic hierarchy from micro- to milliseconds, allowing the gene regulation machinery to access compact chromatin. Chromatin fibers undergo continuous structural rearrangements but their dynamic architecture is poorly understood. Here, the authors use single-molecule FRET to determine the structural states and interconversion kinetics of chromatin fibers, monitoring their effector protein-dependent dynamic motions.
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Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Olga Doroshenko
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Iuliia Boichenko
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Mykola Dimura
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hayk Vardanyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Gaurav Arya
- Pratt School of Engineering, Duke University, 144 Hudson Hall, Box 90300, Durham, NC, 27708, USA
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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42
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Tsung-Yeh Tang
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0448, La Jolla, California 92093, United States
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0448, La Jolla, California 92093, United States
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Arya G. Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments. Molecular Simulation 2016. [DOI: 10.1080/08927022.2015.1123257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Root SE, Savagatrup S, Pais CJ, Arya G, Lipomi DJ. Predicting the Mechanical Properties of Organic Semiconductors Using Coarse-Grained Molecular Dynamics Simulations. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00204] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Samuel E. Root
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, Mail Code 0448, La Jolla, California 92093-0448, United States
| | - Suchol Savagatrup
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, Mail Code 0448, La Jolla, California 92093-0448, United States
| | - Christopher J. Pais
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, Mail Code 0448, La Jolla, California 92093-0448, United States
| | - Gaurav Arya
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, Mail Code 0448, La Jolla, California 92093-0448, United States
| | - Darren J. Lipomi
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, Mail Code 0448, La Jolla, California 92093-0448, United States
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46
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Nam GM, Arya G. Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes. Phys Rev E 2016; 93:032406. [PMID: 27078389 DOI: 10.1103/physreve.93.032406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 06/05/2023]
Abstract
The nucleosome represents the basic unit of eukaryotic genome organization, and its conformational fluctuations play a crucial role in various cellular processes. Here we provide insights into the flipping transition of a nucleosome by computing its free-energy landscape as a function of the linking number and nucleosome orientation using the density-of-states Monte Carlo approach. To investigate how the energy landscape is affected by the presence of neighboring nucleosomes in a chromatin fiber, we also compute the free-energy landscape for a dinucleosome array. We find that the mononucleosome is bistable between conformations with negatively and positively crossed linkers while the conformation with open linkers appears as a transition state. The dinucleosome exhibits a markedly different energy landscape in which the conformation with open linkers populates not only the transition state but also the global minimum. This enhanced stability of the open state is attributed to increased rotational flexibility of nucleosomes arising from their mechanical coupling with neighboring nucleosomes. Our results provide a possible mechanism by which chromatin may enhance the accessibility of its DNA and facilitate the propagation and mitigation of DNA torsional stresses.
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Affiliation(s)
- Gi-Moon Nam
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, USA
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, USA
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Zaretski AV, Root SE, Savchenko A, Molokanova E, Printz AD, Jibril L, Arya G, Mercola M, Lipomi DJ. Metallic Nanoislands on Graphene as Highly Sensitive Transducers of Mechanical, Biological, and Optical Signals. Nano Lett 2016; 16:1375-80. [PMID: 26765039 PMCID: PMC4751512 DOI: 10.1021/acs.nanolett.5b04821] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/08/2016] [Indexed: 05/28/2023]
Abstract
This article describes an effect based on the wetting transparency of graphene; the morphology of a metallic film (≤20 nm) when deposited on graphene by evaporation depends strongly on the identity of the substrate supporting the graphene. This control permits the formation of a range of geometries, such as tightly packed nanospheres, nanocrystals, and island-like formations with controllable gaps down to 3 nm. These graphene-supported structures can be transferred to any surface and function as ultrasensitive mechanical signal transducers with high sensitivity and range (at least 4 orders of magnitude of strain) for applications in structural health monitoring, electronic skin, measurement of the contractions of cardiomyocytes, and substrates for surface-enhanced Raman scattering (SERS, including on the tips of optical fibers). These composite films can thus be treated as a platform technology for multimodal sensing. Moreover, they are low profile, mechanically robust, semitransparent and have the potential for reproducible manufacturing over large areas.
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Affiliation(s)
- Aliaksandr V. Zaretski
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, United States
| | - Samuel E. Root
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, United States
| | - Alex Savchenko
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Sanford Burnham Prebys Medical Discovery
Institute, 10901 North
Torrey Pines Road., La Jolla, California 92037, United States
| | | | - Adam D. Printz
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, United States
| | - Liban Jibril
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, United States
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, United States
| | - Mark Mercola
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Sanford Burnham Prebys Medical Discovery
Institute, 10901 North
Torrey Pines Road., La Jolla, California 92037, United States
| | - Darren J. Lipomi
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, United States
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48
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Hamed MY, Arya G. Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases. J Biomol Struct Dyn 2016. [PMID: 26196228 DOI: 10.1080/07391102.2015.1068224] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Energy calculations based on MM-GBSA were employed to study various zinc finger protein (ZF) motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between binding energy and affinity of ZF motifs to their sites on DNA. ΔG values were -15.82(12), -3.66(12), and -12.14(11.6) kcal/mol for finger one, finger two, and finger three, respectively. The mutations in the DNA bases reduced the value of the negative energies of binding (maximum value for ΔΔG = 42Kcal/mol for F1 when GCG mutated to GGG, and ΔΔG = 22 kcal/mol for F2, the loss in total energy of binding originated in the loss in electrostatic energies upon mutation (r = .98). The mutations in key amino acids in the ZF motif in positions-1, 2, 3, and 6 showed reduced binding energies to DNA with correlation coefficients between total free energy and electrostatic was .99 and with Van der Waal was .93. Results agree with experimentally found selectivity which showed that Arginine in position-1 is specific to G, while Aspartic acid (D) in position 2 plays a complicated role in binding. There is a correlation between the MD calculated free energies of binding and those obtained experimentally for prepared ZF motifs bound to triplet bases in other reports (), our results may help in the design of ZF motifs based on the established recognition codes based on energies and contributing energies to the total energy.
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Affiliation(s)
- Mazen Y Hamed
- a Department of Chemistry , Birzeit University , P. O. Box 14 Birzeit, Palestine
| | - Gaurav Arya
- b Department of Nanoengineering , University of California , San Diego, 9500 Gilman Dr., MC-0448, La Jolla , CA 92093-0448 , USA
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49
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Murthy CR, Gao B, Tao AR, Arya G. Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites. Phys Rev E 2016; 93:022501. [PMID: 26986370 DOI: 10.1103/physreve.93.022501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 06/05/2023]
Abstract
Understanding how nanoparticles (NPs) diffuse, stick, and assemble into larger structures within polymers is key to the design and fabrication of NP-polymer composites. Here we describe an approach for inferring the dynamic parameters of NP assembly from spatially and temporally disjointed images of composites. The approach involves iterative adjustment of the parameters of a kinetic model of assembly until the computed size statistics of NP clusters match those obtained from high-throughput analysis of the experimental images. Application of this approach to the assembly of shaped, metal NPs in polymer films suggests that NP structures grow via a cluster-cluster aggregation mechanism, where NPs and their clusters diffuse with approximately Stokes-Einstein diffusivity and stick to other NPs or clusters with a probability that depends strongly on the size and shape of the NPs and the molecular weight of the polymer.
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Affiliation(s)
- Chaitanya R Murthy
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Bo Gao
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Andrea R Tao
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
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50
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Meluzzi D, Arya G. Quantification of DNA cleavage specificity in Hi-C experiments. Nucleic Acids Res 2016; 44:e4. [PMID: 26264668 PMCID: PMC4705682 DOI: 10.1093/nar/gkv820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 08/02/2015] [Indexed: 11/14/2022] Open
Abstract
Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin with a restriction endonuclease. Although this cleavage should happen specifically at the enzyme's recognition sequence, an unknown proportion of cleavage events may involve other sequences, owing to the enzyme's star activity or to random DNA breakage. A quantitative estimation of these non-specific cleavages may enable simulating realistic Hi-C read pairs for validation of downstream analyses, monitoring the reproducibility of experimental conditions and investigating biophysical properties that correlate with DNA cleavage patterns. Here we describe a computational method for analyzing Hi-C read pairs to estimate the fractions of cleavages at different possible targets. The method relies on expressing an observed local target distribution downstream of aligned reads as a linear combination of known conditional local target distributions. We validated this method using Hi-C read pairs obtained by computer simulation. Application of the method to experimental Hi-C datasets from murine cells revealed interesting similarities and differences in patterns of cleavage across the various experiments considered.
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Affiliation(s)
- Dario Meluzzi
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Gaurav Arya
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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