1
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Janowski J, Pham VAB, Vecchioni S, Woloszyn K, Lu B, Zou Y, Erkalo B, Perren L, Rueb J, Madnick J, Mao C, Saito M, Ohayon YP, Jonoska N, Sha R. Engineering tertiary chirality in helical biopolymers. Proc Natl Acad Sci U S A 2024; 121:e2321992121. [PMID: 38684000 PMCID: PMC11087804 DOI: 10.1073/pnas.2321992121] [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: 12/15/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Tertiary chirality describes the handedness of supramolecular assemblies and relies not only on the primary and secondary structures of the building blocks but also on topological driving forces that have been sparsely characterized. Helical biopolymers, especially DNA, have been extensively investigated as they possess intrinsic chirality that determines the optical, mechanical, and physical properties of the ensuing material. Here, we employ the DNA tensegrity triangle as a model system to locate the tipping points in chirality inversion at the tertiary level by X-ray diffraction. We engineer tensegrity triangle crystals with incremental rotational steps between immobile junctions from 3 to 28 base pairs (bp). We construct a mathematical model that accurately predicts and explains the molecular configurations in both this work and previous studies. Our design framework is extendable to other supramolecular assemblies of helical biopolymers and can be used in the design of chiral nanomaterials, optically active molecules, and mesoporous frameworks, all of which are of interest to physical, biological, and chemical nanoscience.
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Affiliation(s)
- Jordan Janowski
- Department of Chemistry, New York University, New York, NY10003
| | - Van A. B. Pham
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL33620
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, NY10003
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY10003
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY10003
| | - Yijia Zou
- Department of Chemistry, New York University, New York, NY10003
| | - Betel Erkalo
- Department of Chemistry, New York University, New York, NY10003
| | - Lara Perren
- Department of Chemistry, New York University, New York, NY10003
| | - Joe Rueb
- Department of Chemistry, New York University, New York, NY10003
| | - Jesse Madnick
- Department of Mathematics, University of Oregon, Eugene, OR97403
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN47907
| | - Masahico Saito
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL33620
| | - Yoel P. Ohayon
- Department of Chemistry, New York University, New York, NY10003
| | - Nataša Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL33620
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY10003
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2
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Wu WD, Gong S, Lei W, Wang SM, Huang BH, Yuan LJ, Wang Q, Sha R, Xie AT, Liang GB, Tao YQ. [The efficacy analysis of neurosurgical robot-assisted DBS in the treatment of elderly Parkinson's disease]. Zhonghua Yi Xue Za Zhi 2023; 103:3816-3821. [PMID: 38123222 DOI: 10.3760/cma.j.cn112137-20231006-00642] [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] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Objective: To investigate the surgical efficacy of neurosurgery robot deep brain stimulation(DBS) in the treatment of elderly Parkinson's disease(PD). Methods: The clinical data of elderly patients (≥75 years) with PD who underwent neurosurgical robot-assisted DBS surgery in the Department of Neurosurgery of the General Hospital of Northern Theater Command from September 2016 to September 2022 were collected retrospectively. Operation time, electrode implantation duration, postoperative pneumocephalus volume, electrode implantation accuracy, the Tao's DBS surgery scale, perioperative complications were analyzed.The unified Parkinson's disease rating scales (UPDRS), UPDRS-Ⅲ, tremor, rigidity, bradykinesia, axial, Barthel Activities of Daily Living (ADL-Barthel), Levodopa Equivalent Daily Dose (LEDD), Montreal Cognitive Assessment (MoCA), Hamilton Anxiety Scale (HAMA) and Hamilton Depression Scale (HAMD) scores and mortality were assessed respectively before operation, 6, 12 and 24 months after operation and last follow-up. Results: A total of 25 elderly patients were enrolled, including 14 males and 11 females, aged(78.3±3.2) years. Nine patients had underlying diseases. Nine patients (36%) underwent bilateral Globus Pallidus pars Interna deep brain stimulation (GPi-DBS) and 16 patients (64%) underwent bilateral subthalamic nucleus deep brain stimulation (STN-DBS).The operation time was (1.56±0.19) hours, the electrode implantation duration was (1.01±0.19) hours, the pneumocephalus volume was 9.8(4.7, 23.3) cm3, and the electrode implantation accuracy was (0.84±0.24) mm, the Tao's DBS surgery scale was (80.2±6.2).The follow-up time [M(Q1, Q3)] was 57.3(27.9, 75.7) months. No serious complications such as intracranial hemorrhage, infection or poor wound healing occurred during the perioperative period. The improvement rate of UPDRS, UPDRS-Ⅲ, rigidity, bradykinesia, and LEDD at 6 months after surgery was significantly higher than that at 24 months after surgery and at the last follow-up (all P<0.05); the improvement rate of axial symptoms, ADL-Barthel score, and MoCA score at 6 months after surgery was significantly higher than that at the last follow-up (P<0.05). HAMD and HAMA scores showed no significant improvement during follow-up after surgery (both P>0.05). At the last follow-up, 12 patients died, with death time of (35.1±20.2) months after operation, and the death age of [M(Q1, Q3)] 80(79, 83)years. Conclusions: Robot-assisted DBS surgery for elderly patients with PD is accurate and safe, and the postoperative symptoms are significantly improved, and they can benefit from neuromodulation for long term, and the risks are controllable.
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Affiliation(s)
- W D Wu
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - S Gong
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - W Lei
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - S M Wang
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - B H Huang
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - L J Yuan
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - Q Wang
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - R Sha
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - A T Xie
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - G B Liang
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
| | - Y Q Tao
- Department of Neurosurgery, the General Hospital of Northern Theater Command, Shenyang 110016, China
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3
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Zhou F, Ni H, Zhu G, Bershadsky L, Sha R, Seeman NC, Chaikin PM. Toward three-dimensional DNA industrial nanorobots. Sci Robot 2023; 8:eadf1274. [PMID: 38055806 DOI: 10.1126/scirobotics.adf1274] [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: 09/30/2022] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Nanoscale industrial robots have potential as manufacturing platforms and are capable of automatically performing repetitive tasks to handle and produce nanomaterials with consistent precision and accuracy. We demonstrate a DNA industrial nanorobot that fabricates a three-dimensional (3D), optically active chiral structure from optically inactive parts. By making use of externally controlled temperature and ultraviolet (UV) light, our programmable robot, ~100 nanometers in size, grabs different parts, positions and aligns them so that they can be welded, releases the construct, and returns to its original configuration ready for its next operation. Our robot can also self-replicate its 3D structure and functions, surpassing single-step templating (restricted to two dimensions) by using folding to access the third dimension and more degrees of freedom. Our introduction of multiple-axis precise folding and positioning as a tool/technology for nanomanufacturing will open the door to more complex and useful nano- and microdevices.
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Affiliation(s)
- Feng Zhou
- Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
- Department of Physics, New York University, New York, NY, USA
- Department of Chemistry, New York University, New York, NY, USA
| | - Heng Ni
- Department of Physics, New York University, New York, NY, USA
| | - Guolong Zhu
- Department of Physics, New York University, New York, NY, USA
- Department of Chemistry, Biochemistry, and Physics, Fairleigh Dickinson University, Madison, NJ, USA
| | - Lev Bershadsky
- Department of Physics, New York University, New York, NY, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, USA
| | | | - Paul M Chaikin
- Department of Physics, New York University, New York, NY, USA
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4
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Huang Q, Kim J, Wang K, Vecchioni S, Ohayon YP, Seeman NC, Jonoska N, Sha R. Environmentally Controlled Oscillator with Triplex Guided Displacement of DNA Duplexes. Nano Lett 2023; 23:7593-7598. [PMID: 37561947 PMCID: PMC10450806 DOI: 10.1021/acs.nanolett.3c02176] [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] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/07/2023] [Indexed: 08/12/2023]
Abstract
The use of DNA triplex association is advantageous for the reconfiguration of dynamic DNA nanostructures through pH alteration and can provide environmental control for both structural changes and molecular signaling. The combination of pH-induced triplex-forming oligonucleotide (TFOs) binding with toehold-mediated strand displacement has recently garnered significant attention in the field of structural DNA nanotechnology. While most previous studies use single-stranded DNA to displace or replace TFOs within the triplex, here we demonstrate that pH alteration allows a DNA duplex, with a toehold assistance, to displace TFOs from the components of another DNA duplex. We examined the dependence of this process on toehold length and show that the pH changes allow for cyclic oscillations between two molecular formations. We implemented the duplex/triplex design onto the surface of 2D DNA origami in the form outlining binary digits 0 or 1 and verified the oscillatory conformational changes between the two formations with atomic force microscopy.
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Affiliation(s)
- Qiuyan Huang
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Jiyeon Kim
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Kun Wang
- Department
of Physics, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P. Ohayon
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Nadrian C. Seeman
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Nataša Jonoska
- Department
of Mathematics and Statistics, University
of South Florida, Tampa, Florida 33620, United States
| | - Ruojie Sha
- Department
of Chemistry, New York University, New York, New York 10003, United States
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5
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Lu B, Ohayon YP, Woloszyn K, Yang CF, Yoder JB, Rothschild LJ, Wind SJ, Hendrickson WA, Mao C, Seeman NC, Canary JW, Sha R, Vecchioni S. Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals. J Am Chem Soc 2023; 145:17945-17953. [PMID: 37530628 DOI: 10.1021/jacs.3c05478] [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] [Indexed: 08/03/2023]
Abstract
Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces drive the programmable chelation of metals between pyrimidine base pairs. Here, we developed a crystallographic method using the three-dimensional (3D) DNA tensegrity triangle motif to capture single- and multi-metal binding modes across granular changes to environmental pH using anomalous scattering. Leveraging this programmable crystal, we determined 28 biomolecular structures to capture mmDNA reactions. We found that silver(I) binds with increasing occupancy in T-T and U-U pairs at elevated pH levels, and we exploited this to capture silver(I) and mercury(II) within the same base pair and to isolate the titration points for homo- and heterometal base pair modes. We additionally determined the structure of a C-C pair with both silver(I) and mercury(II). Finally, we extend our paradigm to capture cadmium(II) in T-T pairs together with mercury(II) at high pH. The precision self-assembly of heterobimetallic DNA chemistry at the sub-nanometer scale will enable atomistic design frameworks for more elaborate mmDNA-based nanodevices and nanotechnologies.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, Illinois 60439, United States
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, California 94035, United States
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - James W Canary
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
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6
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Zhang C, Paluzzi VE, Sha R, Jonoska N, Mao C. Implementing Logic Gates by DNA Crystal Engineering. Adv Mater 2023; 35:e2302345. [PMID: 37220213 DOI: 10.1002/adma.202302345] [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] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/03/2023] [Indexed: 05/25/2023]
Abstract
DNA self-assembly computation is attractive for its potential to perform massively parallel information processing at the molecular level while at the same time maintaining its natural biocompatibility. It has been extensively studied at the individual molecule level, but not as much as ensembles in 3D. Here, the feasibility of implementing logic gates, the basic computation operations, in large ensembles: macroscopic, engineered 3D DNA crystals is demonstrated. The building blocks are the recently developed DNA double crossover-like (DXL) motifs. They can associate with each other via sticky-end cohesion. Common logic gates are realized by encoding the inputs within the sticky ends of the motifs. The outputs are demonstrated through the formation of macroscopic crystals that can be easily observed. This study points to a new direction of construction of complex 3D crystal architectures and DNA-based biosensors with easy readouts.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Natasha Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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7
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Vecchioni S, Lu B, Livernois W, Ohayon YP, Yoder JB, Yang CF, Woloszyn K, Bernfeld W, Anantram MP, Canary JW, Hendrickson WA, Rothschild LJ, Mao C, Wind SJ, Seeman NC, Sha R. Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. Adv Mater 2023; 35:e2210938. [PMID: 37268326 DOI: 10.1002/adma.202210938] [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] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/06/2023] [Indexed: 06/04/2023]
Abstract
DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.
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Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Livernois
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, IL, 60439, USA
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Bernfeld
- Department of Chemistry, New York University, New York, NY, 10003, USA
- ASPIRE Program, King School, Stamford, CT, 06905, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, CA, 94035, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Math, Columbia University, New York, NY, 10027, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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8
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Zhao J, Zhang C, Lu B, Sha R, Noinaj N, Mao C. Divergence and Convergence: Complexity Emerges in Crystal Engineering from an 8-mer DNA. J Am Chem Soc 2023; 145:10475-10479. [PMID: 37134185 DOI: 10.1021/jacs.3c01941] [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] [Indexed: 05/05/2023]
Abstract
Biology provides plenty of examples on achieving complicated structures out of minimal numbers of building blocks. In contrast, structural complexity of designed molecular systems is achieved by increasing the numbers of component molecules. In this study, the component DNA strand assembles into a highly complex crystal structure via an unusual path of divergence and convergence. This assembly path suggests a route to minimalists for increasing structural complexity. The original purpose of this study is to engineer DNA crystals with high resolution, which is the primary motivation and a key objective for structural DNA nanotechnology. Despite great efforts in the last 40 years, engineered DNA crystals have not yet consistently reached resolution better than 2.5 Å, limiting their potential uses. Our research has shown that small, symmetrical building blocks generally lead to high resolution crystals. Herein, by following this principle, we report an engineered DNA crystal with unprecedented high resolution (2.17 Å) assembled from one single DNA component: an 8-base-long DNA strand. This system has three unique characteristics: (1) It has a very complex architecture, (2) the same DNA strand forms two different structural motifs, both of which are incorporated into the final crystal, and (3) the component DNA molecule is only an 8-base-long DNA strand, which is, arguably, the smallest DNA motif for DNA nanostructures to date. This high resolution opens the possibility of using these DNA crystals to precisely organize guest molecules at the Å level, which could stimulate a range of new investigations.
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Affiliation(s)
- Jiemin Zhao
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei 230032, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brandon Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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9
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Vecchioni S, Lu B, Livernois W, Ohayon YP, Yoder JB, Yang CF, Woloszyn K, Bernfeld W, Anantram MP, Canary JW, Hendrickson WA, Rothschild LJ, Mao C, Wind SJ, Seeman NC, Sha R. Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. Adv Mater 2023:e2201938. [PMID: 36939292 DOI: 10.1002/adma.202201938] [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] [Received: 11/03/2022] [Revised: 03/06/2023] [Indexed: 06/18/2023]
Abstract
DNA double helices containing metal-mediated DNA (mmDNA) base pairs have been constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials has been impractical without a complete lexical and structural description. Here, we explore the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination. We employed the tensegrity triangle to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and elucidated generalized design rules for mmDNA construction. We uncovered two binding modes: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations showed additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Livernois
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, IL, 60439, USA
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Bernfeld
- Department of Chemistry, New York University, New York, NY, 10003, USA
- ASPIRE Program, King School, Stamford, CT, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, CA, 94035, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Math, Columbia University, New York, NY, 10027, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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10
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Vecchioni S, Lu B, Janowski J, Woloszyn K, Jonoska N, Seeman NC, Mao C, Ohayon YP, Sha R. The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles. Small 2023; 19:e2206511. [PMID: 36585389 DOI: 10.1002/smll.202206511] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The successful self-assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally-designed, nanoscale components. This 3D DNA tile owes its "tensegrity" nature to its three rotationally stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter-junction regions, corresponding to two-thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed ( Z + 2 / 3 ) \[\left( {Z{\bm{ + }}2{\bf /}3} \right)\] turn inter-junction segments, yielding right-handed, antiparallel, "J1" junctions. Here a minimal DNA triangle motif consisting of 3-bp inter-junction segments, or one-third of a helical turn is reported. It is found that the minimal motif exhibits a reversed morphology with a left-handed tertiary structure mediated by a locally-parallel Holliday junction-the "L1" junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. A Rule of Thirds by which supramolecular chirality can be programmed through inter-junction DNA segment length is identified. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under-explored class of self-assembling, chiral nanomaterials for topological processes in biological systems.
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Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jordan Janowski
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Nataša Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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11
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Zhang C, Zhao J, Lu B, Seeman NC, Sha R, Noinaj N, Mao C. Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions. J Am Chem Soc 2023; 145:4853-4859. [PMID: 36791277 DOI: 10.1021/jacs.3c00081] [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] [Indexed: 02/17/2023]
Abstract
Sequence-selective recognition of DNA duplexes is important for a wide range of applications including regulating gene expression, drug development, and genome editing. Many small molecules can bind DNA duplexes with sequence selectivity. It remains as a challenge how to reliably and conveniently obtain the detailed structural information on DNA-molecule interactions because such information is critically needed for understanding the underlying rules of DNA-molecule interactions. If those rules were understood, we could design molecules to recognize DNA duplexes with a sequence preference and intervene in related biological processes, such as disease treatment. Here, we have demonstrated that DNA crystal engineering is a potential solution. A molecule-binding DNA sequence is engineered to self-assemble into highly ordered DNA crystals. An X-ray crystallographic study of molecule-DNA cocrystals reveals the structural details on how the molecule interacts with the DNA duplex. In this approach, the DNA will serve two functions: (1) being part of the molecule to be studied and (2) forming the crystal lattice. It is conceivable that this method will be a general method for studying drug/peptide-DNA interactions. The resulting DNA crystals may also find use as separation matrices, as hosts for catalysts, and as media for material storage.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jiemin Zhao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei 230032, China
| | - Brandon Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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12
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Zhao Y, Chandrasekaran AR, Rusling DA, Woloszyn K, Hao Y, Hernandez C, Vecchioni S, Ohayon YP, Mao C, Seeman NC, Sha R. The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals. J Am Chem Soc 2023; 145:3599-3605. [PMID: 36731121 PMCID: PMC10032566 DOI: 10.1021/jacs.2c12667] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnology. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addition of the Watson-Crick complement to a TFO containing a short toehold, and (c) the addition of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.
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Affiliation(s)
- Yue Zhao
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University of Albany, State University of New York, Albany, New York 12222, United States
| | - David A Rusling
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yudong Hao
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Carina Hernandez
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
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13
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Lu B, Woloszyn K, Ohayon YP, Yang B, Zhang C, Mao C, Seeman NC, Vecchioni S, Sha R. Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles. Angew Chem Int Ed Engl 2023; 62:e202213451. [PMID: 36520622 DOI: 10.1002/anie.202213451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson-Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Bena Yang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
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14
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Wang T, Bai T, Tan Z, Ohayon YP, Sha R, Vecchioni S, Seeman NC, Wei B. Mesojunction-Based Design Paradigm of Structural DNA Nanotechnology. J Am Chem Soc 2023; 145:2455-2460. [PMID: 36657115 DOI: 10.1021/jacs.2c11731] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mesojunctions were introduced as a basic type of crossover configuration in the early development of structural DNA nanotechnology. However, the investigations of self-assembly from multiple mesojunction complexes have been overlooked in comparison to their counterparts based on regular junctions. In this work, we designed standardized component strands for the construction of complex mesojunction lattices. Three typical mesojunction configurations with three and four arms were showcased in the self-assembly of 1-, 2-, and 3-dimensional lattices constructed from both a scaffold-free tiling approach and a scaffolded origami approach.
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Affiliation(s)
- Tianqi Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tanxi Bai
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhenyu Tan
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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15
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Lu B, Vecchioni S, Ohayon YP, Woloszyn K, Markus T, Mao C, Seeman NC, Canary JW, Sha R. Highly Symmetric, Self-Assembling 3D DNA Crystals with Cubic and Trigonal Lattices. Small 2023; 19:e2205830. [PMID: 36408817 DOI: 10.1002/smll.202205830] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/03/2022] [Indexed: 06/16/2023]
Abstract
The rational design of nanoscopic DNA tiles has yielded highly ordered crystalline matter in 2D and 3D. The most well-studied 3D tile is the DNA tensegrity triangle, which is known to self-assemble into macroscopic crystals. However, contemporary rational design parameters for 3D DNA crystals nearly universally invoke integer numbers of DNA helical turns and Watson-Crick (WC) base pairs. In this study, 24-bp edges are substituted into a previously 21-bp (two helical turns of DNA) tensegrity triangle motif to explore whether such unconventional motif can self-assemble into 3D crystals. The use of noncanonical base pairs in the sticky ends results in a cubic arrangement of tensegrity triangles with exceedingly high symmetry, assembling a lattice from winding helical axes and diamond-like tessellation patterns. Reverting this motif to sticky ends with Watson-Crick pairs results in a trigonal hexagonal arrangement, replicating this diamond arrangement in a hexagonal context. These results showcase that the authors can generate unexpected, highly complex, pathways for materials design by testing modifications to 3D tiles without prior knowledge of the ensuing symmetry. This study expands the rational design toolbox for DNA nanotechnology; and it further illustrates the existence of yet-unexplored arrangements of crystalline soft matter.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Tiffany Markus
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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16
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Lu B, Vecchioni S, Ohayon YP, Canary JW, Sha R. The wending rhombus: Self-assembling 3D DNA crystals. Biophys J 2022; 121:4759-4765. [PMID: 36004779 PMCID: PMC9808540 DOI: 10.1016/j.bpj.2022.08.019] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
In this perspective, we provide a summary of recent developments in self-assembling three-dimensional (3D) DNA crystals. Starting from the inception of this subfield, we describe the various advancements in structure that have led to an increase in the diversity of macromolecular crystal motifs formed through self-assembly, and we further comment on the future directions of the field, which exploit noncanonical base pairing interactions beyond Watson-Crick. We then survey the current applications of self-assembling 3D DNA crystals in reversibly active nanodevices and materials engineering and provide an outlook on the direction researchers are taking these structures. Finally, we compare 3D DNA crystals with DNA origami and suggest how these distinct subfields might work together to enhance biomolecule structure solution, nanotechnological motifs, and their applications.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York
| | - James W Canary
- Department of Chemistry, New York University, New York, New York.
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York.
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17
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Lu B, Woloszyn K, Ohayon YP, Yang B, Zhang C, Mao C, Seeman NC, Vecchioni S, Sha R. Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202213451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Brandon Lu
- New York University Chemistry UNITED STATES
| | | | | | - Bena Yang
- New York University Chemistry UNITED STATES
| | | | | | | | | | - Ruojie Sha
- New York University Chemistry 100 Washington Square East 10003 NEW YORK UNITED STATES
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18
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Woloszyn K, Vecchioni S, Ohayon YP, Lu B, Ma Y, Huang Q, Zhu E, Chernovolenko D, Markus T, Jonoska N, Mao C, Seeman NC, Sha R. Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants. Adv Mater 2022; 34:e2206876. [PMID: 36100349 DOI: 10.1002/adma.202206876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/09/2022] [Indexed: 06/15/2023]
Abstract
The DNA tensegrity triangle is known to reliably self-assemble into a 3D rhombohedral crystalline lattice via sticky-end cohesion. Here, the library of accessible motifs is expanded through covalent extensions of intertriangle regions and sticky-end-coordinated linkages of adjacent triangles with double helical segments using both geometrically symmetric and asymmetric configurations. The molecular structures of 18 self-assembled architectures at resolutions of 3.32-9.32 Å are reported; the observed cell dimensions, cavity sizes, and cross-sectional areas agree with theoretical expectations. These data demonstrate that fine control over triclinic and rhombohedral crystal parameters and the customizability of more complex 3D DNA lattices are attainable via rational design. It is anticipated that augmented DNA architectures may be fine-tuned for the self-assembly of designer nanocages, guest-host complexes, and proscriptive 3D nanomaterials, as originally envisioned. Finally, designer asymmetric crystalline building blocks can be seen as a first step toward controlling and encoding information in three dimensions.
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Affiliation(s)
- Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Yinglun Ma
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Qiuyan Huang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Eric Zhu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | | | - Tiffany Markus
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Nataša Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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19
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Abstract
This manuscript introduces geometry as a means to program the tile-based DNA self-assembly in two and three dimensions. This strategy complements the sequence-focused programmable assembly. DNA crystal assembly critically relies on intermotif, sticky-end cohesion, which requires complementarity not only in sequence but also in geometry. For DNA motifs to assemble into crystals, they must be associated with each other in the proper geometry and orientation to ensure that geometric hindrance does not prevent sticky ends from associating. For DNA motifs with exactly the same pair of sticky-end sequences, by adjusting the length (thus, helical twisting phase) of the motif branches, it is possible to program the assembly of these distinct motifs to either mix with one another, to self-sort and consequently separate from one another, or to be alternatingly arranged. We demonstrate the ability to program homogeneous crystals, DNA "alloy" crystals, and definable grain boundaries through self-assembly. We believe that the integration of this strategy and conventional sequence-focused assembly strategy could further expand the programming versatility of DNA self-assembly.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Natasha Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, Florida 33620, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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20
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Wang X, Deshmukh R, Sha R, Birktoft JJ, Menon V, Seeman NC, Canary JW. Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiao Wang
- Department of Chemistry New York University New York NY 10003 USA
| | - Rahul Deshmukh
- Department of Physics City College of New York New York NY 10031 USA
| | - Ruojie Sha
- Department of Chemistry New York University New York NY 10003 USA
| | - Jens J. Birktoft
- Department of Chemistry New York University New York NY 10003 USA
| | - Vinod Menon
- Department of Physics City College of New York New York NY 10031 USA
| | | | - James W. Canary
- Department of Chemistry New York University New York NY 10003 USA
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21
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Wang X, Sha R, Knowlton WB, Seeman NC, Canary JW, Yurke B. Exciton Delocalization in a DNA-Templated Organic Semiconductor Dimer Assembly. ACS Nano 2022; 16:1301-1307. [PMID: 34979076 PMCID: PMC8793135 DOI: 10.1021/acsnano.1c09143] [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] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/29/2021] [Indexed: 06/01/2023]
Abstract
A chiral dimer of an organic semiconductor was assembled from octaniline (octamer of polyaniline) conjugated to DNA. Facile reconfiguration between the monomer and dimer of octaniline-DNA was achieved. The geometry of the dimer and the exciton coupling between octaniline molecules in the assembly was studied both experimentally and theoretically. The octaniline dimer was readily switched between different electronic states by protonic doping and exhibited a Davydov splitting comparable to those previously reported for DNA-dye systems employing dyes with strong transition dipoles. This approach provides a possible platform for studying the fundamental properties of organic semiconductors with DNA-templated assemblies, which serve as candidates for artificial light-harvesting systems and excitonic devices.
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Affiliation(s)
- Xiao Wang
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - William B. Knowlton
- Micron
School for Materials Science and Engineering and Department of Electrical
& Computer Engineering, Boise State
University, Boise, Idaho 83725, United States
| | - Nadrian C. Seeman
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - James W. Canary
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Bernard Yurke
- Micron
School for Materials Science and Engineering and Department of Electrical
& Computer Engineering, Boise State
University, Boise, Idaho 83725, United States
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22
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Wang W, Chen C, Vecchioni S, Zhang T, Wu C, Ohayon YP, Sha R, Seeman NC, Wei B. Reconfigurable Two‐Dimensional DNA Lattices: Static and Dynamic Angle Control. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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)
- Wen Wang
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Chunyu Chen
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Simon Vecchioni
- Department of Chemistry New York University New York New York 10003 USA
| | - Tianqing Zhang
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Chengxian Wu
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Yoel P. Ohayon
- Department of Chemistry New York University New York New York 10003 USA
| | - Ruojie Sha
- Department of Chemistry New York University New York New York 10003 USA
| | - Nadrian C. Seeman
- Department of Chemistry New York University New York New York 10003 USA
| | - Bryan Wei
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
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23
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Wang W, Chen C, Vecchioni S, Zhang T, Wu C, Ohayon YP, Sha R, Seeman NC, Wei B. Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control. Angew Chem Int Ed Engl 2021; 60:25781-25786. [PMID: 34596325 DOI: 10.1002/anie.202112487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/11/2022]
Abstract
Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle-enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson-Crick base pairing or non-canonical nucleobase interactions (e.g., i-motif and G-quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely-ordered three-dimensional architectures.
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Affiliation(s)
- Wen Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chunyu Chen
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Tianqing Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chengxian Wu
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
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24
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Wang X, Deshmukh R, Sha R, Birktoft JJ, Menon V, Seeman NC, Canary JW. Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds. Angew Chem Int Ed Engl 2021; 61:e202115155. [PMID: 34847266 DOI: 10.1002/anie.202115155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Indexed: 11/07/2022]
Abstract
A quasi-one-dimensional organic semiconductor, hepta(p-phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self-assembled from an HPV-DNA pseudo-rhombohedron edge by rational design and characterized by X-ray diffraction. Templated by the DNA motif, HPV molecules exist as single-molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV-DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.
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Affiliation(s)
- Xiao Wang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Rahul Deshmukh
- Department of Physics, City College of New York, New York, NY 10031, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Jens J Birktoft
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Vinod Menon
- Department of Physics, City College of New York, New York, NY 10031, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY 10003, USA
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25
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Abstract
The tensegrity triangle motif utilizes Watson-Crick sticky end cohesion to self-assemble into a rhombohedral crystal lattice using complementary 5'-GA and 5'-TC sticky ends. Here, we report that using noncanonical 5'-AG and 5'-TC sticky ends in otherwise isomorphic tensegrity triangles results in crystal self-assembly in the P63 hexagonal space group as revealed by X-ray crystallography. In this structure, the DNA double helices bend at the crossover positions, a feature that was not observed in the original design. Instead of propagating linearly, the tilt between base pairs of each right-handed helix results in a left-handed superstructure along the screw axis, forming a microtubule-like structure composed of three double helices with an unbroken channel at the center. This hexagonal lattice has a cavity diameter of 11 nm and a unit cell volume of 886 000 Å3-far larger than the rhombohedral counterpart (5 nm, 330 000 Å3).
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Bena Yang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
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26
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Xavier PL, Ayyer K, Yefanov O, Gelisio L, Bielecki J, Samanta AK, Bajt S, Sha R, Bushnell DA, Kornberg RD, Ovcharenko Y, Kuepper J, Meyer M, Seeman NC, Chapman HN. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1697] [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: 12/01/2022] Open
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27
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Ben Zion MY, Caba Y, Sha R, Seeman NC, Chaikin PM. Mix and match-a versatile equilibrium approach for hybrid colloidal synthesis. Soft Matter 2020; 16:4358-4365. [PMID: 32364206 DOI: 10.1039/d0sm00202j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Colloidal synthesis is a powerful bottom-up approach for programmed self-assembly which holds promise for both research and industry. While diverse, each synthetic process is typically restricted to a specific chemistry. Many applications however require composite materials, whereas a chemical equilibrium can typically only match one material but not the other. Here, a scalable general approach is presented, alleviating the dependency on a specific chemical reaction, by resorting to a mechanical equilibrium; an isopycnic density-gradient-step is tailored to form clusters with prescribed composition. Valence control is demonstrated, making dimers, trimers, and tetramers with purity as high as 96%. The measured kinetics shows a scaleable throughput. The density gradient step plays a dual role of both filtering out undesired products and concentrating the target structures. The "Mix-and-Match" approach is general, and applies to a broad range of colloidal matter: diverse material compositions (plastics, glasses, and emulsions); a range of colloidal interactions (van der Waals, Coulomb, and DNA hybridization); and a spectrum of sizes (nanoscale to multiple micrometers). Finally, the strength of the method is displayed by producing a monodisperse suspension from a highly polydisperse emulsion. The ability to combine colloids into architectures of hybrid materials has applications in pharmaceuticals, cosmetics, and photonics.
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Affiliation(s)
- Matan Yah Ben Zion
- Center for Soft Matter Research, Department of Physics, New York University, 726 Broadway, New York, NY 10003, USA.
| | - Yaelin Caba
- Center for Soft Matter Research, Department of Physics, New York University, 726 Broadway, New York, NY 10003, USA.
| | - Ruojie Sha
- Chemistry Department, New York University, 24 Waverly Pl., New York, NY 10003, USA
| | - Nadrian C Seeman
- Chemistry Department, New York University, 24 Waverly Pl., New York, NY 10003, USA
| | - Paul M Chaikin
- Center for Soft Matter Research, Department of Physics, New York University, 726 Broadway, New York, NY 10003, USA.
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28
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Xavier PL, Yefanov O, Ayyer K, Sha R, Knoška J, Seuring C, Boutet S, Liang M, Bushnell DA, Kornberg R, Barty A, Bajt S, Millane RP, Seeman NC, Chapman HN. DNA-Origami-Assisted Flow-Aligned Single-Particle Diffractive Imaging using XFEL Pulses. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.877] [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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29
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Ohayon Y, Hernandez C, Chandrasekaran AR, Wang X, Abdallah H, Jong MA, Mohsen M, Sha R, Birktoft JJ, Lukeman PS, Chaikin PM, Ginell SL, Mao C, Seeman NC. Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications. ACS Nano 2019; 13:7957-7965. [PMID: 31264845 PMCID: PMC6660133 DOI: 10.1021/acsnano.9b02430] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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] [Indexed: 05/27/2023]
Abstract
DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 Å at beamline NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences as well as the impact of 5'- and 3'-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2-, 3-, and 4-nt sticky ends all form crystals. X-ray diffraction data from the same beamline reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 and 4.2 Å, respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5'-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 Å for 1-2P-3P) and 2-turn dimer sticky ended (4.1 Å for 1-2-3P) systems. We have also examined the impact of the identity of the base flanking the sticky ends as well as the use of 3'-phosphate. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.
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Affiliation(s)
- Yoel Ohayon
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Carina Hernandez
- Department of Chemistry, New York University, New York, NY 10003, USA
| | | | - Xinyu Wang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Hatem Abdallah
- Department of Chemistry, New York University, New York, NY 10003, USA
| | | | - Michael Mohsen
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Jens J. Birktoft
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Philip S. Lukeman
- Department of Chemistry, St. John’s University, New York, NY 11439, USA
| | - Paul M. Chaikin
- Department of Physics, New York University, New York, NY 10003, USA
| | - Stephen L. Ginell
- Structural Biology Center, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
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30
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Abstract
Single-wall carbon nanotubes (SWCNTs) are known to embody many desirable features for nanoelectronic and photonic applications, including excellent electronic and optical properties and mechanical robustness. To utilize these species in a bottom-up nanotechnological approach, it is necessary to be able to place them in precise absolute positions within a larger framework, without disturbing the conduction surface. Although it is well-known how to orient one or two nanotubes on a DNA origami, precise placement has eluded investigators previously. Here, we report a method of attaching a strand of DNA on the reactive end of a SWCNT, and then of using that DNA strand to place the nanotube at a specific site on a 2D DNA origami raft. We demonstrate that it is possible to place one or two nanotubes on such a DNA origami raft.
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Affiliation(s)
- Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecule Engineering , East China Normal University , Shanghai 200241 , P.R. China
| | - Ruojie Sha
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
| | - Xiwei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecule Engineering , East China Normal University , Shanghai 200241 , P.R. China
| | - Ming Zheng
- Materials Science and Engineering Division , National Institute of Standards and Technology , 100 Bureau Drive , Gaithersburg , Maryland 20899 , United States
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - James W Canary
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
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31
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Gao X, Gethers M, Han SP, Goddard WA, Sha R, Cunningham RP, Seeman NC. The PX Motif of DNA Binds Specifically to Escherichia coli DNA Polymerase I. Biochemistry 2018; 58:575-581. [PMID: 30557012 DOI: 10.1021/acs.biochem.8b01148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The PX motif of DNA is a four-stranded structure in which two parallel juxtaposed double-helical domains are fused by crossovers at every point where the strands approach each other. Consequently, its twist and writhe are approximately half of those of conventional DNA. This property has been shown to relax supercoiled plasmid DNA under circumstances in which head-to-head homology exists within the plasmid; the homology can be either complete homology or every-other-half-turn homology, known as PX homology. It is clearly of interest to establish whether the cell contains proteins that interact with this unusual and possibly functional motif. We have examined Escherichia coli extracts to seek such a protein. We find by gel mobility studies that the PX motif is apparently bound by a cellular component. Fractionation of this binding activity reveals that the component is DNA polymerase I (Pol I). Although the PX motif binds to Pol I, we find that PX-DNA is not able to serve as a substrate for the extension of a shortened strand. We cannot say at this time whether the binding is a coincidence or whether it represents an activity of Pol I that is currently unknown. We have modeled the interaction of Pol I and PX-DNA using symmetry considerations and molecular dynamics.
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Affiliation(s)
- Xiang Gao
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Matthew Gethers
- Materials and Process Simulation Center , MC139-74 California Institute of Technology , Pasadena , California 91125 , United States
| | - Si-Ping Han
- Materials and Process Simulation Center , MC139-74 California Institute of Technology , Pasadena , California 91125 , United States
| | - William A Goddard
- Materials and Process Simulation Center , MC139-74 California Institute of Technology , Pasadena , California 91125 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Richard P Cunningham
- Department of Biological Sciences , State University of New York at Albany , Albany , New York 12222 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10003 , United States
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32
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Affiliation(s)
- Jiemin Zhao
- Department of Chemistry; Purdue University; West Lafayette IN 47907 USA
| | - Yue Zhao
- Department of Chemistry; New York University; New York NY 10003 USA
| | - Zhe Li
- Department of Chemistry; Purdue University; West Lafayette IN 47907 USA
| | - Yong Wang
- Department of Chemistry; Purdue University; West Lafayette IN 47907 USA
- College of Chemistry; Nanchang University; Nanchang Jiangxi 330031 China
| | - Ruojie Sha
- Department of Chemistry; New York University; New York NY 10003 USA
| | | | - Chengde Mao
- Department of Chemistry; Purdue University; West Lafayette IN 47907 USA
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33
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Zhao J, Zhao Y, Li Z, Wang Y, Sha R, Seeman NC, Mao C. Modulating Self-Assembly of DNA Crystals with Rationally Designed Agents. Angew Chem Int Ed Engl 2018; 57:16529-16532. [PMID: 30240115 DOI: 10.1002/anie.201809757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Indexed: 11/08/2022]
Abstract
This manuscript reports a strategy for controlling the crystallization kinetics and improving the quality of engineered self-assembled 3D DNA crystals. Growing large, high-quality biomacromolecule crystals is critically important for determining the 3D structures of biomacromolecules. It often presents a great challenge to structural biologists. Herein, we introduce a rationally designed agent to modulate the crystallization process. Under such conditions, fewer, but larger, crystals that yield diffraction patterns of modestly higher resolution are produced compared with the crystals from conditions without the modulating agent. We attribute the improvement to a smaller number of nuclei and slow growth rate of crystallization. This strategy is expected to be generally applicable for crystallization of other biomacromolecules.
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Affiliation(s)
- Jiemin Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yue Zhao
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Zhe Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yong Wang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.,College of Chemistry, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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34
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Zhao Y, Sha R, Hao Y, Hernandez C, Zhao X, Rusling D, Birktoft JJ, Nemeth R, Ackerson CJ, Mao C, Seeman NC. Self-assembled three-dimensional deoxyribonucleic acid (DNA) crystals. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318097465] [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: 11/10/2022] Open
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35
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Wang X, Chandrasekaran AR, Shen Z, Ohayon YP, Wang T, Kizer ME, Sha R, Mao C, Yan H, Zhang X, Liao S, Ding B, Chakraborty B, Jonoska N, Niu D, Gu H, Chao J, Gao X, Li Y, Ciengshin T, Seeman NC. Paranemic Crossover DNA: There and Back Again. Chem Rev 2018; 119:6273-6289. [PMID: 29911864 DOI: 10.1021/acs.chemrev.8b00207] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.
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Affiliation(s)
- Xing Wang
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | | | - Zhiyong Shen
- College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241000 , China
| | - Yoel P Ohayon
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tong Wang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Megan E Kizer
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Chengde Mao
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Hao Yan
- Department of Chemistry and Biochemistry and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaoping Zhang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Shiping Liao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Baoquan Ding
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Banani Chakraborty
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Natasha Jonoska
- Department of Mathematics and Statistics , University of South Florida , Tampa , Florida 33620 , United States
| | - Dong Niu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Hongzhou Gu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Jie Chao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Xiang Gao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Yuhang Li
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tanashaya Ciengshin
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10012 , United States
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36
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Sha R, Xiang L, Liu C, Balaeff A, Zhang Y, Zhang P, Li Y, Beratan DN, Tao N, Seeman NC. Charge splitters and charge transport junctions based on guanine quadruplexes. Nat Nanotechnol 2018; 13:316-321. [PMID: 29483600 DOI: 10.1038/s41565-018-0070-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Self-assembling circuit elements, such as current splitters or combiners at the molecular scale, require the design of building blocks with three or more terminals. A promising material for such building blocks is DNA, wherein multiple strands can self-assemble into multi-ended junctions, and nucleobase stacks can transport charge over long distances. However, nucleobase stacking is often disrupted at junction points, hindering electric charge transport between the two terminals of the junction. Here, we show that a guanine-quadruplex (G4) motif can be used as a connector element for a multi-ended DNA junction. By attaching specific terminal groups to the motif, we demonstrate that charges can enter the structure from one terminal at one end of a three-way G4 motif, and can exit from one of two terminals at the other end with minimal carrier transport attenuation. Moreover, we study four-way G4 junction structures by performing theoretical calculations to assist in the design and optimization of these connectors.
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Affiliation(s)
- Ruojie Sha
- Department of Chemistry, New York University, New York, NY, USA
| | - Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Chaoren Liu
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Alexander Balaeff
- Departments of Chemistry, Duke University, Durham, NC, USA
- Nanoscience Technology Center & Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Yuqi Zhang
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Peng Zhang
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - David N Beratan
- Departments of Chemistry, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University, Durham, NC, USA.
- Department of Physics, Duke University, Durham, NC, USA.
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, USA.
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37
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Ben Zion MY, He X, Maass CC, Sha R, Seeman NC, Chaikin PM. Self-assembled three-dimensional chiral colloidal architecture. Science 2018; 358:633-636. [PMID: 29097546 DOI: 10.1126/science.aan5404] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 09/28/2017] [Indexed: 01/01/2023]
Abstract
Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.
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Affiliation(s)
| | - Xiaojin He
- Department of Physics, New York University, New York, NY 10003, USA
| | - Corinna C Maass
- Department of Physics, New York University, New York, NY 10003, USA.,Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Goettingen, Germany
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paul M Chaikin
- Department of Physics, New York University, New York, NY 10003, USA.
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38
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Abstract
An electro-optical modulator was constructed using a DNA nanostructure scaffold with oligomers of poly(phenylenevinylene) and polyaniline. A molecular device containing one each of the functional molecules was assembled in a DNA origami. The constructs formed an "X" shape and were visualized by atomic force microscopy. In response to redox reconfiguration, the device reversibly altered fluorescence signal output. This molecular self-assembly strategy provides opportunities to make unique material composites that are difficult to achieve by blending. The strategy offers a "plug and play" format that may lead to many new functions.
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Affiliation(s)
- Xiao Wang
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Chen Li
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Dong Niu
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - James W Canary
- Department of Chemistry , New York University , New York , New York 10003 , United States
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39
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He X, Sha R, Zhuo R, Mi Y, Chaikin PM, Seeman NC. Exponential growth and selection in self-replicating materials from DNA origami rafts. Nat Mater 2017; 16:993-997. [PMID: 28920942 DOI: 10.1038/nmat4986] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is ∼1.3-1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8; similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.
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Affiliation(s)
- Xiaojin He
- Department of Chemistry, New York University, New York, New York 10003, USA
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
- Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemistry, Tongji University, Shanghai, 100024, China
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Rebecca Zhuo
- Department of Chemistry, New York University, New York, New York 10003, USA
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
| | - Yongli Mi
- Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemistry, Tongji University, Shanghai, 100024, China
| | - Paul M Chaikin
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, USA
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40
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Abstract
Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Although biology relies on such schemes, they have not been available in materials science. Here, we demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activates the next droplet in the sequence, akin to living polymerization. Our strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.Natural complex systems are often constructed by sequential assembly but this is not readily available for synthetic systems. Here, the authors program the sequential self-assembly of DNA functionalized emulsions by altering the DNA grafted strands.
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Affiliation(s)
- Yin Zhang
- Physics Department, Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York, 10003, USA
| | - Angus McMullen
- Physics Department, Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York, 10003, USA
| | - Lea-Laetitia Pontani
- Physics Department, Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York, 10003, USA.,Institut des NanoSciences de Paris, UMR 7588, Centre National de la Recherche Scientifique-University Pierre et Marie Curie, 4 Place Jussieu, Paris, France
| | - Xiaojin He
- Physics Department, Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York, 10003, USA
| | - Ruojie Sha
- Chemistry Department, New York University, 100 Washington Square East, New York, New York, 10003, USA
| | - Nadrian C Seeman
- Chemistry Department, New York University, 100 Washington Square East, New York, New York, 10003, USA.
| | - Jasna Brujic
- Physics Department, Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York, 10003, USA.
| | - Paul M Chaikin
- Physics Department, Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York, 10003, USA.
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41
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Wang X, Sha R, Kristiansen M, Hernandez C, Hao Y, Mao C, Canary JW, Seeman NC. An Organic Semiconductor Organized into 3D DNA Arrays by “Bottom‐up” Rational Design. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Xiao Wang
- Department of Chemistry New York University New York NY 10003 USA
| | - Ruojie Sha
- Department of Chemistry New York University New York NY 10003 USA
| | | | - Carina Hernandez
- Department of Chemistry New York University New York NY 10003 USA
| | - Yudong Hao
- Department of Chemistry New York University New York NY 10003 USA
| | - Chengde Mao
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
| | - James W. Canary
- Department of Chemistry New York University New York NY 10003 USA
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42
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Wang X, Sha R, Kristiansen M, Hernandez C, Hao Y, Mao C, Canary JW, Seeman NC. An Organic Semiconductor Organized into 3D DNA Arrays by “Bottom‐up” Rational Design. Angew Chem Int Ed Engl 2017; 56:6445-6448. [DOI: 10.1002/anie.201700462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Xiao Wang
- Department of Chemistry New York University New York NY 10003 USA
| | - Ruojie Sha
- Department of Chemistry New York University New York NY 10003 USA
| | | | - Carina Hernandez
- Department of Chemistry New York University New York NY 10003 USA
| | - Yudong Hao
- Department of Chemistry New York University New York NY 10003 USA
| | - Chengde Mao
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
| | - James W. Canary
- Department of Chemistry New York University New York NY 10003 USA
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43
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Hao Y, Kristiansen M, Sha R, Birktoft JJ, Hernandez C, Mao C, Seeman NC. A device that operates within a self-assembled 3D DNA crystal. Nat Chem 2017; 9:824-827. [PMID: 28754940 DOI: 10.1038/nchem.2745] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 02/01/2017] [Indexed: 11/09/2022]
Abstract
Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.
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Affiliation(s)
- Yudong Hao
- Department of Chemistry, New York University, New York 10003, USA
| | | | - Ruojie Sha
- Department of Chemistry, New York University, New York 10003, USA
| | - Jens J Birktoft
- Department of Chemistry, New York University, New York 10003, USA
| | - Carina Hernandez
- Department of Chemistry, New York University, New York 10003, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York 10003, USA
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44
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Affiliation(s)
- Joseph S. Melinger
- Electronics
Science and Technology Division, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ruojie Sha
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Chengde Mao
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C. Seeman
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Mario G. Ancona
- Electronics
Science and Technology Division, Naval Research Laboratory, Washington, D.C. 20375, United States
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45
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Simmons CR, Zhang F, Birktoft JJ, Qi X, Han D, Liu Y, Sha R, Abdallah H, Hernandez C, Ohayon Y, Seeman NC, Yan H. Correction to "Construction and Structure Determination of a Three-dimensional DNA Crystal". J Am Chem Soc 2016; 138:12690. [PMID: 27643407 DOI: 10.1021/jacs.6b09106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Simmons CR, Zhang F, Birktoft JJ, Qi X, Han D, Liu Y, Sha R, Abdallah HO, Hernandez C, Ohayon YP, Seeman NC, Yan H. Construction and Structure Determination of a Three-Dimensional DNA Crystal. J Am Chem Soc 2016; 138:10047-54. [PMID: 27447429 DOI: 10.1021/jacs.6b06508] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Here we present a new DNA motif and a strategy that has led to the assembly of a 3D lattice. We have determined the X-ray crystal structures of two related constructs to 3.1 Å resolution using bromine-derivatized crystals. The motif we used employs a five-nucleotide repeating sequence that weaves through a series of two-turn DNA duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of four-arm junctions; these in turn assemble into continuous arrays facilitated by sequence-specific sticky-ended cohesion. The 3D X-ray structure of these DNA crystals holds promise for the design of new structural motifs to create programmable 3D DNA lattices with atomic spatial resolution. The two arrays differ by the use of four or six repeats of the five-nucleotide units in the repeating but statistically disordered central strand. In addition, we report a 2D rhombuslike array formed from similar components.
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Affiliation(s)
| | | | - Jens J Birktoft
- Department of Chemistry, New York University , New York, New York 10003, United States
| | | | | | | | - Ruojie Sha
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Hatem O Abdallah
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Carina Hernandez
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
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47
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Abdallah HO, Ohayon YP, Chandrasekaran AR, Sha R, Fox KR, Brown T, Rusling DA, Mao C, Seeman NC. Stabilisation of self-assembled DNA crystals by triplex-directed photo-cross-linking. Chem Commun (Camb) 2016; 52:8014-7. [DOI: 10.1039/c6cc03695c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cross-linked crystals: triplex-forming oligonucleotides can direct cross-linking reactions within or between tiles of a DNA crystal, improving their thermal stability.
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Affiliation(s)
| | | | | | - Ruojie Sha
- Department of Chemistry
- New York University
- New York
- USA
| | - Keith R. Fox
- Centre for Biological Sciences
- University of Southampton
- Southampton
- UK
| | - Tom Brown
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - David A. Rusling
- Centre for Biological Sciences
- University of Southampton
- Southampton
- UK
| | - Chengde Mao
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
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48
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Ohayon YP, Sha R, Flint O, Chandrasekaran AR, Abdallah HO, Wang T, Wang X, Zhang X, Seeman NC. Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion. ACS Nano 2015; 9:10296-10303. [PMID: 26364680 DOI: 10.1021/acsnano.5b04333] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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] [Indexed: 06/05/2023]
Abstract
Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.
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Affiliation(s)
- Yoel P Ohayon
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ortho Flint
- Department of Mathematics, University of Western Ontario , London, ON N6A 3K7, Canada
| | | | - Hatem O Abdallah
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Tong Wang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xing Wang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xiaoping Zhang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
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49
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Ohayon YP, Sha R, Flint O, Liu W, Chakraborty B, Subramanian HKK, Zheng J, Chandrasekaran AR, Abdallah HO, Wang X, Zhang X, Seeman NC. Covalent Linkage of One-Dimensional DNA Arrays Bonded by Paranemic Cohesion. ACS Nano 2015; 9:10304-10312. [PMID: 26343906 DOI: 10.1021/acsnano.5b04335] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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] [Indexed: 06/05/2023]
Abstract
The construction of DNA nanostructures from branched DNA motifs, or tiles, typically relies on the use of sticky-ended cohesion, owing to the specificity and programmability of DNA sequences. The stability of such constructs when unligated is restricted to a specific range of temperatures, owing to the disruption of base pairing at elevated temperatures. Paranemic (PX) cohesion was developed as an alternative to sticky ends for the cohesion of large topologically closed species that could be purified reliably on denaturing gels. However, PX cohesion is also of limited stability. In this work, we added sticky-ended interactions to PX-cohesive complexes to create interlocked complexes by functionalizing the sticky ends with psoralen, which can form cross-links between the two strands of a double helix. We were able to reinforce the stability of the constructs by creating covalent linkages between the 3'-ends and 5'-ends of the sticky ends; the sticky ends were added to double crossover domains via 3'-3' and 5'-5' linkages. Catenated arrays were obtained either by enzymatic ligation or by UV cross-linking. We have constructed finite-length one-dimensional arrays linked by interlocking loops and have positioned streptavidin-gold particles on these constructs.
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Affiliation(s)
- Yoel P Ohayon
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ortho Flint
- Department of Mathematics, University of Western Ontario , London, ON N6A 5B7, Canada
| | - Wenyan Liu
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Banani Chakraborty
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Hari K K Subramanian
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Jianping Zheng
- Department of Chemistry, New York University , New York, New York 10003, United States
| | | | - Hatem O Abdallah
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xing Wang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xiaoping Zhang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
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50
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Abstract
PX-DNA is a four-stranded DNA structure that has been implicated in the recognition of homology, either continuously, or in an every-other-half-turn fashion. Some of the structural features of the molecule have been noted previously, but the structure requires further characterization. Here, we report atomic force microscopic characterization of PX molecules that contain periodically placed biotin groups, enabling the molecule to be labeled by streptavidin molecules at these sites. In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure. Furthermore, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure. Circular dichroism spectroscopy indicates unusual features in the PX molecule that are absent in both the molecules to which it is compared.
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Affiliation(s)
- Dong Niu
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Hualin Jiang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
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