1
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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] [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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2
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Hou S, Hasnat M, Chen Z, Liu Y, Faran Ashraf Baig MM, Liu F, Chen Z. Application Perspectives of Nanomedicine in Cancer Treatment. Front Pharmacol 2022; 13:909526. [PMID: 35860027 PMCID: PMC9291274 DOI: 10.3389/fphar.2022.909526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer is a disease that seriously threatens human health. Based on the improvement of traditional treatment methods and the development of new treatment modes, the pattern of cancer treatment is constantly being optimized. Nanomedicine plays an important role in these evolving tumor treatment modalities. In this article, we outline the applications of nanomedicine in three important tumor-related fields: chemotherapy, gene therapy, and immunotherapy. According to the current common problems, such as poor targeting of first-line chemotherapy drugs, easy destruction of nucleic acid drugs, and common immune-related adverse events in immunotherapy, we discuss how nanomedicine can be combined with these treatment modalities, provide typical examples, and summarize the advantages brought by the application of nanomedicine.
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Affiliation(s)
- Shanshan Hou
- Department of Pharmacy, Zhejiang Pharmaceutical College, Ningbo, China
| | - Muhammad Hasnat
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ziwei Chen
- Department of Pharmacy, Zhejiang Pharmaceutical College, Ningbo, China
| | - Yinong Liu
- Hospital Laboratory of Nangjing Lishui People’s Hospital, Nangjing, China
| | - Mirza Muhammad Faran Ashraf Baig
- Laboratory of Biomedical Engineering for Novel Bio-functional, and Pharmaceutical Nanomaterials, Prince Philip Dental Hospital, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Fuhe Liu
- Department of Pharmacy, Zhejiang Pharmaceutical College, Ningbo, China
- *Correspondence: Zelong Chen, ; Fuhe Liu,
| | - Zelong Chen
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Province Engineering Research Center of Artificial Intelligence and Internet of Things Wise Medical, Zhengzhou, China
- *Correspondence: Zelong Chen, ; Fuhe Liu,
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3
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Saliba D, Trinh T, Lachance-Brais C, Prinzen AL, Rizzuto FJ, de Rochambeau D, Sleiman HF. Asymmetric patterning drives the folding of a tripodal DNA nanotweezer. Chem Sci 2021; 13:74-80. [PMID: 35059153 PMCID: PMC8694393 DOI: 10.1039/d1sc04793k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 11/21/2022] Open
Abstract
DNA tweezers have emerged as powerful devices for a wide range of biochemical and sensing applications; however, most DNA tweezers consist of single units activated by DNA recognition, limiting their range of motion and ability to respond to complex stimuli. Herein, we present an extended, tripodal DNA nanotweezer with a small molecule junction. Simultaneous, asymmetric elongation of our molecular core is achieved using polymerase chain reaction (PCR) to produce length- and sequence-specific DNA arms with repeating DNA regions. When rigidified, our DNA tweezer can be addressed with streptavidin-binding ligands. Full control over the number, separation, and location of these ligands enables site-specific streptavidin recognition; all three arms of the DNA nanotweezer wrap around multiple streptavidin units simultaneously. Our approach combines the simplicity of DNA tile arrays with the size regime normally provided by DNA origami, offering an integrated platform for the use of branched DNA scaffolds as structural building blocks, protein sensors, and dynamic, stimuli-responsive materials.
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Affiliation(s)
- Daniel Saliba
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | | | - Alexander L Prinzen
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Felix J Rizzuto
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Donatien de Rochambeau
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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4
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Dobscha JR, Castillo HD, Li Y, Fadler RE, Taylor RD, Brown AA, Trainor CQ, Tait SL, Flood AH. Sequence-Defined Macrocycles for Understanding and Controlling the Build-up of Hierarchical Order in Self-Assembled 2D Arrays. J Am Chem Soc 2019; 141:17588-17600. [PMID: 31503483 PMCID: PMC7461245 DOI: 10.1021/jacs.9b06410] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Anfinsen's dogma that sequence dictates structure is fundamental to understanding the activity and assembly of proteins. This idea has been applied to all manner of oligomers but not to the behavior of cyclic oligomers, aka macrocycles. We do this here by providing the first proofs that sequence controls the hierarchical assembly of nonbiological macrocycles, in this case, at graphite surfaces. To design macrocycles with one (AAA), two (AAB), or three (ABC) different carbazole units, we needed to subvert the synthetic preferences for one-pot macrocyclizations. We developed a new stepwise synthesis with sequence-defined targets made in 11, 17, and 22 steps with 25, 10, and 5% yields, respectively. The linear build up of primary sequence (1°) also enabled a thermal Huisgen cycloaddition to proceed regioselectively for the first time using geometric control. The resulting macrocycles are planar (2° structure) and form H-bonded dimers (3°) at surfaces. Primary sequences encoded into the suite of tricarb macrocycles were shown by scanning-tunneling microscopy (STM) to impact the next levels of supramolecular ordering (4°) and 2D crystalline polymorphs (5°) at solution-graphite interfaces. STM imaging of an AAB macrocycle revealed the formation of a new gap phase that was inaccessible using only C3-symmetric macrocycles. STM imaging of two additional sequence-controlled macrocycles (AAD, ABE) allowed us to identify the factors driving the formation of this new polymorph. This demonstration of how sequence controls the hierarchical patterning of macrocycles raises the importance of stepwise syntheses relative to one-pot macrocyclizations to offer new approaches for greater understanding and control of hierarchical assembly.
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Affiliation(s)
- James R. Dobscha
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Henry D. Castillo
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Yan Li
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Rachel E. Fadler
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Rose D. Taylor
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Andrew A. Brown
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Colleen Q. Trainor
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Steven L. Tait
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Amar H. Flood
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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5
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Xing C, Dai J, Huang Y, Lin Y, Zhang KL, Lu C, Yang H. Active Self-Assembly of Train-Shaped DNA Nanostructures via Catalytic Hairpin Assembly Reactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901795. [PMID: 31120190 DOI: 10.1002/smll.201901795] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Biomolecular self-assembly is a powerful approach for fabricating supramolecular architectures. Over the past decade, a myriad of biomolecular assemblies, such as self-assembly proteins, lipids, and DNA nanostructures, have been used in a wide range of applications, from nano-optics to nanoelectronics and drug delivery. The method of controlling when and where the self-assembly starts is essential for assembly dynamics and functionalization. Here, train-shaped DNA nanostructures are actively self-assembled using DNA tiles as artificial "carriages," hairpin structures as "couplers," and initiators of catalytic hairpin assembly (CHA) reactions as "wrenches." The initiator wrench can selectively open the hairpin couplers to couple the DNA tile carriages with high product yield. As such, DNA nanotrains are actively prepared with two, three, four, or more carriages. Furthermore, by flexibly modifying the carriages with "biotin seats" (biotin-modified DNA tiles), streptavidin "passengers" are precisely arranged in corresponding seats. The applications of the CHA-triggered self-assembly mechanism are also extended for assembling the large DNA origami dimer. With the creation of 1D architectures established, it is thought that this CHA-triggered self-assembly mechanism may provide a new element of control for complex autonomous assemblies from a variety of starting materials with specific sites and times.
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Affiliation(s)
- Chao Xing
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Junduan Dai
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Yuqing Huang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Yuhong Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Kai-Long Zhang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350116, P. R. China
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6
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Zeng J, Fu W, Qi Z, Zhu Q, He H, Huang C, Zuo H, Mao C. Self-Assembly of Microparticles by Supramolecular Homopolymerization of One Component DNA Molecule. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805552. [PMID: 30734479 DOI: 10.1002/smll.201805552] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/18/2019] [Indexed: 06/09/2023]
Abstract
DNA is a superb molecule for self-assembly of nanostructures. Often many DNA strands are required for the assembly of one DNA nanostructure. For lowering the cost of synthesizing DNA strands and facilitating the assembly process, it is highly desirable to use a minimal number of unique strands for potential technological applications. Herein, a strategy is reported to assemble a series of DNA microparticles (DNAµPs) from one component DNA strand. As a demonstration of the application of the resulting DNAµPs, the design and assembled DNAµPs are modified to carry additional single-stranded tails on their surfaces. The modified DNAµPs can either capture other nucleic acids or display CpG motifs to stimulate immune responses.
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Affiliation(s)
- Jie Zeng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Wenhao Fu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Zhenping Qi
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Qiushuang Zhu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Huawei He
- Biological Science Research Center, Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400716, China
| | - Chengzhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Hua Zuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Chengde Mao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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7
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Trinh T, Saliba D, Liao C, de Rochambeau D, Prinzen AL, Li J, Sleiman HF. “Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence. Angew Chem Int Ed Engl 2019; 58:3042-3047. [PMID: 30290048 DOI: 10.1002/anie.201809251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Tuan Trinh
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Chenyi Liao
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Donatien de Rochambeau
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Alexander Lee Prinzen
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Jianing Li
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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8
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Trinh T, Saliba D, Liao C, de Rochambeau D, Prinzen AL, Li J, Sleiman HF. “Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tuan Trinh
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Chenyi Liao
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Donatien de Rochambeau
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Alexander Lee Prinzen
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Jianing Li
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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9
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Rahbani JF, Hsu JCC, Chidchob P, Sleiman HF. Single-stranded templates as railroad tracks for hierarchical assembly of DNA origami. NANOSCALE 2018; 10:13994-13999. [PMID: 29995052 DOI: 10.1039/c8nr03185a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA origami is one of the most effective tools for bottom-up construction of novel objects and devices at the nanometer-scale. However, many applications require larger structures than can be obtained with the conventional single-stranded scaffold, typically 7249 nucleotides. Here, we address this limitation by developing custom-made single-stranded scaffolds that bind pre-assembled origami tiles and induce their one-dimensional organization in high yields. Our synthetic method allows the conversion of multiple repetitive and unique sequences into correctly assembled, large backbones, and to finely tune the position and frequency of each building block. Granted with these regions, three and five origami tiles were successfully arranged in 1-D with the aid of one or two scaffolds, forming a nano-"railroad track". This new method increases length scale in DNA origami without increasing cost and complexity, and is anticipated to increase the yield of other approaches aiming to assemble large origami structures.
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Affiliation(s)
- Janane F Rahbani
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - John C C Hsu
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
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10
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Karadeema RJ, Stancescu M, Steidl TP, Bertot SC, Kolpashchikov DM. The owl sensor: a 'fragile' DNA nanostructure for the analysis of single nucleotide variations. NANOSCALE 2018; 10:10116-10122. [PMID: 29781024 DOI: 10.1039/c8nr01107a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes. Using two DNA and two RNA analytes we demonstrated that owl sensors differentiate SNVs in a wide temperature range of 5 °C-32 °C, a performance unachievable by conventional hybridization probes including the molecular beacon probe. The owl sensor reliably detects cognate analytes even in the presence of 100 times excess of single base mismatched sequences. The approach, therefore, promises to add to the toolbox for the diagnosis of SNVs at ambient temperatures.
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Affiliation(s)
- Rebekah J Karadeema
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA.
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11
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Chidchob P, Sleiman HF. Recent advances in DNA nanotechnology. Curr Opin Chem Biol 2018; 46:63-70. [PMID: 29751162 DOI: 10.1016/j.cbpa.2018.04.012] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/14/2018] [Accepted: 04/20/2018] [Indexed: 12/28/2022]
Abstract
DNA is a powerful guiding molecule to achieve the precise construction of arbitrary structures and high-resolution organization of functional materials. The combination of sequence programmability, rigidity and highly specific molecular recognition in this molecule has resulted in a wide range of exquisitely designed DNA frameworks. To date, the impressive potential of DNA nanomaterials has been demonstrated from fundamental research to technological advancements in materials science and biomedicine. This review presents a summary of some of the most recent developments in structural DNA nanotechnology regarding new assembly approaches and efforts in translating DNA nanomaterials into practical use. Recent work on incorporating blunt-end stacking and hydrophobic interactions as orthogonal instruction rules in DNA assembly, and several emerging applications of DNA nanomaterials will also be highlighted.
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Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada.
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12
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Luo X, Chidchob P, Rahbani JF, Sleiman HF. Encapsulation of Gold Nanoparticles into DNA Minimal Cages for 3D-Anisotropic Functionalization and Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:1702660. [PMID: 29205958 DOI: 10.1002/smll.201702660] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/06/2017] [Indexed: 06/07/2023]
Abstract
Gold nanoparticles (AuNPs) endowed with anisotropic DNA valency are an important class of materials, as they can assemble into complex structures with a minimal number of DNA strands. However, methods to encode 3D DNA strand patterns on AuNPs with a controlled number of unique DNA strands in a predesigned spatial arrangement remain elusive. In this work, a simple one-step method to yield such DNA-decorated AuNPs is demonstrated, through encapsulating AuNPs into DNA minimal nanocages. The AuNP@DNA cage encapsulation complex inherits the 3D anisotropic molecular information from the DNA nanocage with enhanced structural stability. The DNA nanocage can be further functionalized and used as a building block for the self-assembly of complex architectures, such as dimers and trimers, programmed assemblies with sequential growth DNA backbones and DNA origami.
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Affiliation(s)
- Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
| | - Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
| | - Janane F Rahbani
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
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13
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Hariri AA, Hamblin GD, Hardwick JS, Godin R, Desjardins JF, Wiseman PW, Sleiman HF, Cosa G. Stoichiometry and Dispersity of DNA Nanostructures Using Photobleaching Pair-Correlation Analysis. Bioconjug Chem 2017; 28:2340-2349. [DOI: 10.1021/acs.bioconjchem.7b00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | | | - Jean-Francois Desjardins
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 0B8, Canada
| | - Paul W. Wiseman
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 0B8, Canada
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14
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Li M, Zuo H, Yu J, Zhao X, Mao C. One DNA strand homo-polymerizes into defined nanostructures. NANOSCALE 2017; 9:10601-10605. [PMID: 28726950 DOI: 10.1039/c7nr03640j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report a strategy for programmed DNA self-assembly that is favorable in terms of both thermodynamics and kinetics. In a previous study, it has been demonstrated that DNA self-assembly is primarily driven by thermodynamics and the assembly kinetics is not considered. To reach such stable states at equilibria, prolonged annealing duration is needed. In addition, there are cases where the desired structures could not compete with alternative structures. For example, a single-stranded DNA with a palindromic sequence quickly folds into a one-stranded hairpin instead of forming a two-stranded DNA duplex. Given that most of the DNA tiles are multi-stranded complexes, the kinetic trap represents a challenge to DNA self-assembly. To overcome this problem, we have developed a one-stranded motif that can intramolecularly and quickly fold from a single DNA strand and can be programmed to assemble into a range of nanostructures, including a one-dimensional (1D) ladder, a 1D chain, a two-dimensional (2D) array, and a three-dimensional (3D) triangular prism. All structures have been characterized by polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) imaging.
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Affiliation(s)
- Mo Li
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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Idili A, Ricci F, Vallée-Bélisle A. Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves. Nucleic Acids Res 2017; 45:7571-7580. [PMID: 28605461 PMCID: PMC5737623 DOI: 10.1093/nar/gkx498] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/13/2022] Open
Abstract
DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson-Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers.
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Affiliation(s)
- Andrea Idili
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors and Nanomachines, Département de Chimie, Université de Montréal, Montreal, Québec H3T-1J4, Canada
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16
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Jorgenson TD, Mohammed AM, Agrawal DK, Schulman R. Self-Assembly of Hierarchical DNA Nanotube Architectures with Well-Defined Geometries. ACS NANO 2017; 11:1927-1936. [PMID: 28085250 DOI: 10.1021/acsnano.6b08008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
An essential motif for the assembly of biological materials such as actin at the scale of hundreds of nanometers and beyond is a network of one-dimensional fibers with well-defined geometry. Here, we demonstrate the programmed organization of DNA filaments into micron-scale architectures where component filaments are oriented at preprogrammed angles. We assemble L-, T-, and Y-shaped DNA origami junctions that nucleate two or three micron length DNA nanotubes at high yields. The angles between the nanotubes mirror the angles between the templates on the junctions, demonstrating that nanoscale structures can control precisely how micron-scale architectures form. The ability to precisely program filament orientation could allow the assembly of complex filament architectures in two and three dimensions, including circuit structures, bundles, and extended materials.
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Affiliation(s)
- Tyler D Jorgenson
- Chemical and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Abdul M Mohammed
- Chemical and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Deepak K Agrawal
- Chemical and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, United States
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17
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Mathur D, Medintz IL. Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community. Anal Chem 2017; 89:2646-2663. [DOI: 10.1021/acs.analchem.6b04033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
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