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For: 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)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Number Cited by Other Article(s)
1
Mou J, Zhang H, Zhang L, Zhang B, Liu J, Zheng S, Kou Q, Wang H, Su X, Guo S, Ke Y, Zhang Y. Simulation-Guided Rational Design of DNA Walker-Based Theranostic Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024;20:e2400963. [PMID: 38686696 DOI: 10.1002/smll.202400963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/11/2024] [Indexed: 05/02/2024]
2
Chwojnowska E, Kowalska AA, Kamińska A, Lewiński J. Direct Readout of Homo- vs Heterochiral Ligand Shell of Quantum Dots. ACS APPLIED MATERIALS & INTERFACES 2024;16:37308-37317. [PMID: 38973569 PMCID: PMC11261568 DOI: 10.1021/acsami.4c07648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
3
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] [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
4
Ratajczyk EJ, Šulc P, Turberfield AJ, Doye JPK, Louis AA. Coarse-grained modeling of DNA-RNA hybrids. J Chem Phys 2024;160:115101. [PMID: 38497475 DOI: 10.1063/5.0199558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 03/19/2024]  Open
5
DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024;7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
6
Centola M, Poppleton E, Ray S, Centola M, Welty R, Valero J, Walter NG, Šulc P, Famulok M. A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower. NATURE NANOTECHNOLOGY 2024;19:226-236. [PMID: 37857824 PMCID: PMC10873200 DOI: 10.1038/s41565-023-01516-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
7
Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023;14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023]  Open
8
Pfeifer WG, Huang CM, Poirier MG, Arya G, Castro CE. Versatile computer-aided design of free-form DNA nanostructures and assemblies. SCIENCE ADVANCES 2023;9:eadi0697. [PMID: 37494445 PMCID: PMC10371015 DOI: 10.1126/sciadv.adi0697] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
9
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] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
10
Mogheiseh M, Etemadi E, Hasanzadeh Ghasemi R. Design, molecular dynamics simulation, and investigation of the mechanical behavior of DNA origami nanotubes with auxetic and honeycomb structures. J Biomol Struct Dyn 2023;41:14822-14831. [PMID: 36889931 DOI: 10.1080/07391102.2023.2186719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/22/2023] [Indexed: 03/10/2023]
11
Büber E, Schröder T, Scheckenbach M, Dass M, Franquelim HG, Tinnefeld P. DNA Origami Curvature Sensors for Nanoparticle and Vesicle Size Determination with Single-Molecule FRET Readout. ACS NANO 2023;17:3088-3097. [PMID: 36735241 DOI: 10.1021/acsnano.2c11981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
12
Kucinic A, Huang CM, Wang J, Su HJ, Castro CE. DNA origami tubes with reconfigurable cross-sections. NANOSCALE 2023;15:562-572. [PMID: 36520453 DOI: 10.1039/d2nr05416g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
13
Doye JPK, Fowler H, Prešern D, Bohlin J, Rovigatti L, Romano F, Šulc P, Wong CK, Louis AA, Schreck JS, Engel MC, Matthies M, Benson E, Poppleton E, Snodin BEK. The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami. Methods Mol Biol 2023;2639:93-112. [PMID: 37166713 DOI: 10.1007/978-1-0716-3028-0_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
14
Kou Q, Wang L, Zhang L, Ma L, Fu S, Su X. Simulation-Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022;18:e2205191. [PMID: 36287076 DOI: 10.1002/smll.202205191] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/30/2022] [Indexed: 06/16/2023]
15
Deng Y, Tan Y, Zhang Y, Zhang L, Zhang C, Ke Y, Su X. Design of Uracil-Modified DNA Nanotubes for Targeted Drug Release via DNA-Modifying Enzyme Reactions. ACS APPLIED MATERIALS & INTERFACES 2022;14:34470-34479. [PMID: 35867518 DOI: 10.1021/acsami.2c09488] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
16
Kaufhold WT, Pfeifer W, Castro CE, Di Michele L. Probing the Mechanical Properties of DNA Nanostructures with Metadynamics. ACS NANO 2022;16:8784-8797. [PMID: 35580231 PMCID: PMC9245350 DOI: 10.1021/acsnano.1c08999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
17
Kaufhold WT, Pfeifer W, Castro CE, Di Michele L. Probing the Mechanical Properties of DNA Nanostructures with Metadynamics. ACS NANO 2022;16:8784-8797. [PMID: 35580231 DOI: 10.48550/arxiv.2110.01477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
18
The Free-Energy Landscape of a Mechanically Bistable DNA Origami. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12125875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
19
Sensale S, Sharma P, Arya G. Binding kinetics of harmonically confined random walkers. Phys Rev E 2022;105:044136. [PMID: 35590574 DOI: 10.1103/physreve.105.044136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
20
Wong CK, Tang C, Schreck JS, Doye JPK. Characterizing the free-energy landscapes of DNA origamis. NANOSCALE 2022;14:2638-2648. [PMID: 35129570 DOI: 10.1039/d1nr05716b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
21
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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
22
Huang CM, Kucinic A, Johnson JA, Su HJ, Castro CE. Integrated computer-aided engineering and design for DNA assemblies. NATURE MATERIALS 2021;20:1264-1271. [PMID: 33875848 DOI: 10.1038/s41563-021-00978-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 03/04/2021] [Indexed: 05/15/2023]
23
Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021;10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
24
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: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Indexed: 11/11/2022]
25
Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021;8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022]  Open
26
Li R, Chen H, Choi JH. Auxetic Two-Dimensional Nanostructures from DNA*. Angew Chem Int Ed Engl 2021;60:7165-7173. [PMID: 33403767 DOI: 10.1002/anie.202014729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/10/2020] [Indexed: 11/09/2022]
27
Li R, Chen H, Choi JH. Auxetic Two‐Dimensional Nanostructures from DNA**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
28
Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
29
DNA origami. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-020-00009-8] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
30
Berengut JF, Wong CK, Berengut JC, Doye JPK, Ouldridge TE, Lee LK. Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation. ACS NANO 2020;14:17428-17441. [PMID: 33232603 DOI: 10.1021/acsnano.0c07696] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
31
Wang W, Arias DS, Deserno M, Ren X, Taylor RE. Emerging applications at the interface of DNA nanotechnology and cellular membranes: Perspectives from biology, engineering, and physics. APL Bioeng 2020;4:041507. [PMID: 33344875 PMCID: PMC7725538 DOI: 10.1063/5.0027022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022]  Open
32
Chhabra H, Mishra G, Cao Y, Prešern D, Skoruppa E, Tortora MMC, Doye JPK. Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures. J Chem Theory Comput 2020;16:7748-7763. [PMID: 33164531 DOI: 10.1021/acs.jctc.0c00661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
33
Engel MC, Romano F, Louis AA, Doye JPK. Measuring Internal Forces in Single-Stranded DNA: Application to a DNA Force Clamp. J Chem Theory Comput 2020;16:7764-7775. [PMID: 33147408 DOI: 10.1021/acs.jctc.0c00286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
34
Suma A, Stopar A, Nicholson AW, Castronovo M, Carnevale V. Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure. Nucleic Acids Res 2020;48:4672-4680. [PMID: 32043111 PMCID: PMC7229852 DOI: 10.1093/nar/gkaa080] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 01/17/2023]  Open
35
Nummelin S, Shen B, Piskunen P, Liu Q, Kostiainen MA, Linko V. Robotic DNA Nanostructures. ACS Synth Biol 2020;9:1923-1940. [PMID: 32589832 PMCID: PMC7467825 DOI: 10.1021/acssynbio.0c00235] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Indexed: 12/25/2022]
36
Dastorani S, Mogheiseh M, Ghasemi RH, Soheilifard R. Modelling and structural investigation of a new DNA Origami based flexible bio-nano joint. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1797019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
37
Ban DK, Liu Y, Wang Z, Ramachandran S, Sarkar N, Shi Z, Liu W, Karkisaval AG, Martinez-Loran E, Zhang F, Glinsky G, Bandaru PR, Fan C, Lal R. Direct DNA Methylation Profiling with an Electric Biosensor. ACS NANO 2020;14:6743-6751. [PMID: 32407064 DOI: 10.1021/acsnano.9b10085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
38
Piskunen P, Nummelin S, Shen B, Kostiainen MA, Linko V. Increasing Complexity in Wireframe DNA Nanostructures. Molecules 2020;25:E1823. [PMID: 32316126 PMCID: PMC7221932 DOI: 10.3390/molecules25081823] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022]  Open
39
Kowalska AA, Berus S, Szleszkowski Ł, Kamińska A, Kmiecik A, Ratajczak-Wielgomas K, Jurek T, Zadka Ł. Brain tumour homogenates analysed by surface-enhanced Raman spectroscopy: Discrimination among healthy and cancer cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020;231:117769. [PMID: 31787534 DOI: 10.1016/j.saa.2019.117769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 05/13/2023]
40
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] [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
41
Bartnik K, Barth A, Pilo-Pais M, Crevenna AH, Liedl T, Lamb DC. A DNA Origami Platform for Single-Pair Förster Resonance Energy Transfer Investigation of DNA-DNA Interactions and Ligation. J Am Chem Soc 2020;142:815-825. [PMID: 31800234 DOI: 10.1021/jacs.9b09093] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
42
Yang S, Liu W, Wang R. Control of the stepwise assembly-disassembly of DNA origami nanoclusters by pH stimuli-responsive DNA triplexes. NANOSCALE 2019;11:18026-18030. [PMID: 31560004 DOI: 10.1039/c9nr05047g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
43
Roodhuizen JA, Hendrikx PJTM, Hilbers PAJ, de Greef TFA, Markvoort AJ. Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation. ACS NANO 2019;13:10798-10809. [PMID: 31502824 PMCID: PMC6764110 DOI: 10.1021/acsnano.9b05650] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/09/2019] [Indexed: 05/18/2023]
44
Snodin BEK, Schreck JS, Romano F, Louis AA, Doye JPK. Coarse-grained modelling of the structural properties of DNA origami. Nucleic Acids Res 2019;47:1585-1597. [PMID: 30605514 PMCID: PMC6379721 DOI: 10.1093/nar/gky1304] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/17/2018] [Accepted: 12/20/2018] [Indexed: 01/12/2023]  Open
45
Huang CM, Kucinic A, Le JV, Castro CE, Su HJ. Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis. NANOSCALE 2019;11:1647-1660. [PMID: 30519693 DOI: 10.1039/c8nr06377j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
46
Zhou L, Marras AE, Huang CM, Castro CE, Su HJ. Paper Origami-Inspired Design and Actuation of DNA Nanomachines with Complex Motions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018;14:e1802580. [PMID: 30369060 DOI: 10.1002/smll.201802580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/19/2018] [Indexed: 05/26/2023]
47
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] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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Dutta PK, Zhang Y, Blanchard A, Ge C, Rushdi M, Weiss K, Zhu C, Ke Y, Salaita K. Programmable Multivalent DNA-Origami Tension Probes for Reporting Cellular Traction Forces. NANO LETTERS 2018;18:4803-4811. [PMID: 29911385 PMCID: PMC6087633 DOI: 10.1021/acs.nanolett.8b01374] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Ijäs H, Nummelin S, Shen B, Kostiainen MA, Linko V. Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems. Int J Mol Sci 2018;19:E2114. [PMID: 30037005 PMCID: PMC6073283 DOI: 10.3390/ijms19072114] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022]  Open
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Liu Y, Kumar S, Taylor RE. Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018;10:e1518. [PMID: 29633568 DOI: 10.1002/wnan.1518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/23/2018] [Accepted: 02/14/2018] [Indexed: 01/04/2023]
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