1
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Sun C, Li M, Wang F. Programming and monitoring surface-confined DNA computing. Bioorg Chem 2024; 143:107080. [PMID: 38183684 DOI: 10.1016/j.bioorg.2023.107080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.
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Affiliation(s)
- Chenyun Sun
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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2
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Walczak M, Brady RA, Leathers A, Kotar J, Di Michele L. Influence of hydrophobic moieties on the crystallization of amphiphilic DNA nanostructures. J Chem Phys 2023; 158:084501. [PMID: 36859089 DOI: 10.1063/5.0132484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Three-dimensional crystalline frameworks with nanoscale periodicity are valuable for many emerging technologies, from nanophotonics to nanomedicine. DNA nanotechnology has emerged as a prime route for constructing these materials, with most approaches taking advantage of the structural rigidity and bond directionality programmable for DNA building blocks. Recently, we have introduced an alternative strategy reliant on flexible, amphiphilic DNA junctions dubbed C-stars, whose ability to crystallize is modulated by design parameters, such as nanostructure topology, conformation, rigidity, and size. While C-stars have been shown to form ordered phases with controllable lattice parameter, response to stimuli, and embedded functionalities, much of their vast design space remains unexplored. Here, we investigate the effect of changing the chemical nature of the hydrophobic modifications and the structure of the DNA motifs in the vicinity of these moieties. While similar design variations should strongly alter key properties of the hydrophobic interactions between C-stars, such as strength and valency, only limited differences in self-assembly behavior are observed. This finding suggests that long-range order in C-star crystals is likely imposed by structural features of the building block itself rather than the specific characteristics of the hydrophobic tags. Nonetheless, we find that altering the hydrophobic regions influences the ability of C-star crystals to uptake hydrophobic molecular cargoes, which we exemplify by studying the encapsulation of antibiotic penicillin V. Besides advancing our understanding of the principles governing the self-assembly of amphiphilic DNA building blocks, our observations thus open up new routes to chemically program the materials without affecting their structure.
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Affiliation(s)
- Michal Walczak
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ryan A Brady
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Adrian Leathers
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jurij Kotar
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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3
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Zhu L, Luo J, Ren K. Nucleic acid-based artificial nanocarriers for gene therapy. J Mater Chem B 2023; 11:261-279. [PMID: 36524395 DOI: 10.1039/d2tb01179d] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid nanotechnology is a powerful tool in the fields of biosensing and nanomedicine owing to their high editability and easy synthesis and modification. Artificial nucleic acid nanostructures have become an emerging research hotspot as gene carriers with low cytotoxicity and immunogenicity for therapeutic approaches. In this review, recent progress in the design and functional mechanisms of nucleic acid-based artificial nano-vectors especially for exogenous siRNA and antisense oligonucleotide delivery is summarized. Different types of DNA nanocarriers, including DNA junctions, tetrahedrons, origami, hydrogels and scaffolds, are introduced. The enhanced targeting strategies to improve the delivery efficacy are demonstrated. Furthermore, RNA based gene nanocarrier systems by self-assembly of short strands, rolling circle transcription, chemical crosslinking and using RNA motifs and DNA-RNA hybrids are demonstrated. Finally, the outlook and potential challenges are highlighted. The nucleic acid-based artificial nanocarriers offer a promising and precise tool for gene delivery and therapy.
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Affiliation(s)
- Longyi Zhu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Jun Luo
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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4
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Hariri AA, Newman SS, Tan S, Mamerow D, Adams AM, Maganzini N, Zhong BL, Eisenstein M, Dunn AR, Soh HT. Improved immunoassay sensitivity and specificity using single-molecule colocalization. Nat Commun 2022; 13:5359. [PMID: 36097164 PMCID: PMC9468026 DOI: 10.1038/s41467-022-32796-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Enzyme-linked immunosorbent assays (ELISAs) are a cornerstone of modern molecular detection, but the technique still faces notable challenges. One of the biggest problems is discriminating true signal generated by target molecules versus non-specific background. Here, we developed a Single-Molecule Colocalization Assay (SiMCA) that overcomes this problem by employing total internal reflection fluorescence microscopy to quantify target proteins based on the colocalization of fluorescent signal from orthogonally labeled capture and detection antibodies. By specifically counting colocalized signals, we can eliminate the effects of background produced by non-specific binding of detection antibodies. Using TNF-α, we show that SiMCA achieves a three-fold lower limit of detection compared to conventional single-color assays and exhibits consistent performance for assays performed in complex specimens such as serum and blood. Our results help define the pernicious effects of non-specific background in immunoassays and demonstrate the diagnostic gains that can be achieved by eliminating those effects.
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Affiliation(s)
- Amani A Hariri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Sharon S Newman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Steven Tan
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Dan Mamerow
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Alexandra M Adams
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Nicolò Maganzini
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Brian L Zhong
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA.
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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5
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Chen YR, Sun S, Yin H, Wang W, Liu R, Xu H, Yang Y, Wu ZS. Tumor-targeting [2]catenane-based grid-patterned periodic DNA monolayer array for in vivo theranostic application. J Mater Chem B 2022; 10:1969-1979. [PMID: 35014661 DOI: 10.1039/d1tb01978c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology is often used to build various nano-structures for signaling and/or drug delivery, but it essentially suffers from several major limitations, such as a large number of DNA strands and limited targeting ligands. Moreover, there is no report on in vivo two-dimensional DNA arrays because of various technical challenges. By cross-catenating two palindromic DNA rings, herein, we demonstrate a catenane-based grid-patterned periodic DNA monolayer array ([2]GDA) capable of preferentially accumulating in tumor tissues without any targeting ligands, with a thickness equal to the double-helical DNA monolayer (nearly 2 nm). The structural flexibility of [2]GDA enabled it to fold into a spherical object in solution, favoring cellular uptake. Thus, its cellular internalization activity was comparable with that of the commercial lipofectamine 3000. Moreover, [2]GDA retained the structural integrity over 24 h incubation in biological solutions, achieving a 360-fold improvement in in vivo stability. Significantly, anticancer drug-loaded [2]GDA exhibits desirable therapeutic efficacy in tumor-bearing animals without detectable side effects.
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Affiliation(s)
- Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Shujuan Sun
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Hongwei Yin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Ran Liu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Huo Xu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Ya Yang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
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6
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Ultrasensitive electrochemical detection of hepatitis C virus core antigen using terminal deoxynucleotidyl transferase amplification coupled with DNA nanowires. Mikrochim Acta 2021; 188:285. [PMID: 34347172 DOI: 10.1007/s00604-021-04939-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/09/2021] [Indexed: 01/15/2023]
Abstract
Early diagnosis of hepatitis C virus (HCV) infection is essential to prevent disease from spreading and progression. Herein, a novel electrochemical biosensor was developed for ultrasensitive detection of HCV core antigen (HCVcAg) based on terminal deoxynucleotidyl transferase (TdT) amplification and DNA nanowires (DNW). After sandwich-type antibody-antigen recognition, the antibody-conjugated DNA was pulled to the electrode surface and further extended into a long DNA sequence by robust TdT reaction. Then, large numbers of methylene blue-loaded DNW (MB@DNW) as signal labels are linked to the extended DNA sequence. This results in an amplified electrochemical signal for HCVcAg determination, typically measured at around -0.25 V (Ag/AgCl). Under the optimum conditions, the proposed biosensor achieved a wide linear range for HCVcAg from 0.1 to 312.5 pg/mL with a low limit of detection of 32 fg/mL. The good practicality of the biosensor was demonstrated by recovery experiment (recoveries from 98 to 104% with RSD of 2.5-4.4%) and comparison with enzyme-linked immunosorbent assay (ELISA). Given the highlighted performance, the biosensor is expected to act as a reliable sensing tool for HCVcAg determination in clinics. Schematic representation of the ultrasensitive electrochemical biosensor based on terminal deoxynucleotidyl transferase (TdT) amplification linked with methylene blue-loaded DNA nanowires (MB@DNW), which can be applied to the determination of hepatitis C virus core antigen (HCVcAg) in clinical samples. dTTPs, 2'-deoxythymidine 5'-triphosphate.
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7
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Platnich CM, Rizzuto FJ, Cosa G, Sleiman HF. Single-molecule methods in structural DNA nanotechnology. Chem Soc Rev 2021; 49:4220-4233. [PMID: 32538403 DOI: 10.1039/c9cs00776h] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single molecules can now be visualised with unprecedented precision. As the resolution of single-molecule experiments improves, so too does the breadth, quantity and quality of information that can be extracted using these methodologies. In the field of DNA nanotechnology, we use programmable interactions between nucleic acids to generate complex, multidimensional structures. We can use single-molecule techniques - ranging from electron and fluorescence microscopies to electrical and force spectroscopies - to report on the structure, morphology, robustness, sample heterogeneity and other properties of these DNA nanoconstructs. In this Tutorial Review, we will detail how complementarity between static and dynamic single-molecule techniques can provide a unified image of DNA nanoarchitectures. The single-molecule methods that we discuss provide unprecedented insight into chemical and structural behaviour, yielding not just an average outcome but reporting on the distribution of values, ultimately showing how bulk properties arise from the collective behaviour of individual structures. As the fields of both DNA nanotechnology and single-molecule characterisation intertwine, a feedback loop is generated between disciplines, providing new opportunities for the development and operation of DNA-based materials as sensors, delivery vehicles, machinery and structural scaffolds.
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Affiliation(s)
- Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
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8
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Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H. A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail. Angew Chem Int Ed Engl 2020; 59:18619-18626. [PMID: 32533629 DOI: 10.1002/anie.202005505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 11/08/2022]
Abstract
DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.
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Affiliation(s)
- Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
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9
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Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H. A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chad R. Simmons
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
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10
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Xue C, Zhang S, Yu X, Hu S, Lu Y, Wu Z. Periodically Ordered, Nuclease‐Resistant DNA Nanowires Decorated with Cell‐Specific Aptamers as Selective Theranostic Agents. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
- College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
| | - Xin Yu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Shuyao Hu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Yi Lu
- Department of Chemistry Cancer Center at Illinois University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Zai‐Sheng Wu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
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11
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Xue C, Zhang S, Yu X, Hu S, Lu Y, Wu ZS. Periodically Ordered, Nuclease-Resistant DNA Nanowires Decorated with Cell-Specific Aptamers as Selective Theranostic Agents. Angew Chem Int Ed Engl 2020; 59:17540-17547. [PMID: 32613705 DOI: 10.1002/anie.202004805] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Indexed: 12/21/2022]
Abstract
DNA nanostructures have shown potential in cancer therapy. However, their clinical application is hampered by the difficulty to deliver them into cancer cells and susceptibility to nuclease degradation. To overcome these limitations, we report herein a periodically ordered nick-hidden DNA nanowire (NW) with high serum stability and active targeting functionality. The inner core is made of multiple connected DNA double helices, and the outer shell is composed of regularly arranged standing-up hairpin aptamers. All termini of the components are hidden from nuclease attack, whereas the target-binding sites are exposed to allow delivery to the cancer target. The DNA NW remained intact during incubation for 24 h in serum solution. Animal imaging and cell apoptosis showed that NWs loaded with an anticancer drug displayed long blood-circulation time and high specificity in inducing cancer-cell apoptosis, thus validating this approach for the targeted imaging and therapy of cancers.
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Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China.,College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde, 415000, China
| | - Xin Yu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Shuyao Hu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Yi Lu
- Department of Chemistry, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
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12
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Encoding quantized fluorescence states with fractal DNA frameworks. Nat Commun 2020; 11:2185. [PMID: 32366822 PMCID: PMC7198603 DOI: 10.1038/s41467-020-16112-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 04/14/2020] [Indexed: 02/02/2023] Open
Abstract
Signal amplification in biological systems is achieved by cooperatively recruiting multiple copies of regulatory biomolecules. Nevertheless, the multiplexing capability of artificial fluorescent amplifiers is limited due to the size limit and lack of modularity. Here, we develop Cayley tree-like fractal DNA frameworks to topologically encode the fluorescence states for multiplexed detection of low-abundance targets. Taking advantage of the self-similar topology of Cayley tree, we use only 16 DNA strands to construct n-node (n = 53) structures of up to 5 megadalton. The high level of degeneracy allows encoding 36 colours with 7 nodes by site-specifically anchoring of distinct fluorophores onto a structure. The fractal topology minimises fluorescence crosstalk and allows quantitative decoding of quantized fluorescence states. We demonstrate a spectrum of rigid-yet-flexible super-multiplex structures for encoded fluorescence detection of single-molecule recognition events and multiplexed discrimination of living cells. Thus, the topological engineering approach enriches the toolbox for high-throughput cell imaging. Though DNA framework-based scaffolds for biomolecular assembly are attractive for bioimaging applications, realizing super-multiplex fluorescent amplifiers remains a challenge. Here, the authors report a topological engineering approach to designing fractal DNA frameworks for multiplexed amplifiers.
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13
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Gao X, Cai Q, Li H, Jie G. Supersandwich Nanowire/Quantum Dots Sensitization Structure-Based Photoelectrochemical “Signal-On” Platform for Ultrasensitive Detection of Thrombin. Anal Chem 2020; 92:6734-6740. [DOI: 10.1021/acs.analchem.0c00849] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiaoshan Gao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Qianqian Cai
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Hongkun Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Guifen Jie
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
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14
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Gao X, Niu S, Ge J, Luan Q, Jie G. 3D DNA nanosphere-based photoelectrochemical biosensor combined with multiple enzyme-free amplification for ultrasensitive detection of cancer biomarkers. Biosens Bioelectron 2020; 147:111778. [DOI: 10.1016/j.bios.2019.111778] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/16/2022]
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15
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Platnich CM, Hariri AA, Sleiman HF, Cosa G. Advancing Wireframe DNA Nanostructures Using Single-Molecule Fluorescence Microscopy Techniques. Acc Chem Res 2019; 52:3199-3210. [PMID: 31675207 DOI: 10.1021/acs.accounts.9b00424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA nanotechnology relies on the molecular recognition properties of DNA to produce complex architectures through self-assembly. The resulting DNA nanostructures allow scientists to organize functional materials at the nanoscale and have therefore found applications in many domains of materials science over the past several years. These scaffolds have been used to position proteins, nanoparticles, carbon nanotubes, and other nanomaterials with high spatial resolution. In addition to their remarkable performance as frameworks for other species, DNA constructs also possess interesting dynamic properties, which have led to their use in logic circuits, drug delivery vehicles, and molecular walkers. Although DNA nanostructures have become increasingly complex, the development of tools to study them has lagged. Currently, gel electrophoresis, dynamic light scattering, and ensemble fluorescence measurements are widely used to characterize DNA-based assemblies. Unfortunately, ensemble averaging in these methods obscures malformed structures and may mask properties associated with structure, length, and shape in polydisperse samples. While atomic force microscopy allows for the determination of morphology at the single-molecule level, this technique cannot typically be used to assess the dynamic properties of these constructs. To analyze the function of DNA-based devices such as molecular motors and reconfigurable nanostructures in real time, new single-molecule techniques are required. This Account details the work from our laboratories toward developing single-molecule fluorescence (SMF) methodologies for the structural and dynamic characterization of wireframe DNA nanostructures, one at a time. The methods described herein provide us with two separate yet related sets of information: First, we can statically examine the nanostructures one by one to assess their robustness, structural fidelity, and morphology. This is primarily done using two-color stepwise photobleaching, wherein we can examine the subunit stoichiometry of our assemblies before and after various perturbations to the structures. For example, we can introduce length mismatches to cause the nanotube to bend or perform strand displacement reactions to generate single-stranded, flexible analogues of our materials. Second, due to the unmatched spatiotemporal resolution of SMF techniques, we can study the dynamic character of these assemblies by implementing structural changes to the nanotube and monitoring them in real time. With this structural and dynamic information in hand, our groups have additionally developed new tools for the improved construction of DNA nanotubes, inspired by solid-phase DNA synthesis. By assembling the nanotubes in a stepwise manner, highly monodisperse nanostructures of any desired length can be made without a template strand. In this way, unique building blocks can also be added sequence-specifically, allowing for the production of user-defined scaffolds to organize nanoscale materials in three dimensions. This method, in combination with our imaging and analysis protocols, may be extended to assemble and inspect other supramolecular constructs in a controlled manner. Overall, by combining synthesis, characterization, and analysis, these single-molecule techniques hold the potential to advance the study of DNA nanostructures and dynamic DNA-based devices.
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Affiliation(s)
- Casey M. Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Amani A. Hariri
- 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
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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16
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Yassine SR, Hassoun SA, Karam P. Fluorescent thermal sensing using conjugated polyelectrolytes in thin polymer films. Anal Chim Acta 2019; 1077:249-254. [PMID: 31307716 DOI: 10.1016/j.aca.2019.05.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 04/20/2019] [Accepted: 05/20/2019] [Indexed: 01/23/2023]
Abstract
Thermal sensing in thin films polymers has been a significant limitation towards optimizing the heat dissipation in micro- and nano-electronic devices as well as many other thin film-based technologies. In this work, we report on poly (phenylene ethynylene) fluorescent-based conjugated polyelectrolyte capable of detecting thermal fluctuations in polymer films prepared from polyvinylpyrrolidone-co-vinyl acetate. The sensor was first optimized in solution by testing two polyvinylpyrrolidone (PVP) copolymers (co-vinyl acetate (VA) and co-polystyrene (PS)) before it was spun cast onto quartz slides and imaged using a DSLR camera at different temperatures. The images were analyzed and showed a change in color with the increase in temperature. When not illuminated, the polymer thin film is clear and transparent.
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Affiliation(s)
- Sarah R Yassine
- Chemistry Department, American University of Beirut, P.O.Box 11-0236, Riad El-Solh, 1107 2020, Beirut, Lebanon
| | - Sarriah A Hassoun
- Chemistry Department, American University of Beirut, P.O.Box 11-0236, Riad El-Solh, 1107 2020, Beirut, Lebanon
| | - Pierre Karam
- Chemistry Department, American University of Beirut, P.O.Box 11-0236, Riad El-Solh, 1107 2020, Beirut, Lebanon.
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17
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetische DNA‐Nanoröhren: Gezielte Synthese und Anwendung nanoskopischer Kanäle. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
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18
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications. Angew Chem Int Ed Engl 2019; 58:8996-9011. [PMID: 30290046 DOI: 10.1002/anie.201807779] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/25/2018] [Indexed: 01/04/2023]
Abstract
Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter-cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom-up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel-aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site-specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.
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Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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19
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Programming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization. Nat Commun 2019; 10:1006. [PMID: 30824698 PMCID: PMC6397255 DOI: 10.1038/s41467-019-09004-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/21/2019] [Indexed: 12/12/2022] Open
Abstract
Formation of biological filaments via intracellular supramolecular polymerization of proteins or protein/nucleic acid complexes is under programmable and spatiotemporal control to maintain cellular and genomic integrity. Here we devise a bioinspired, catassembly-like isothermal chain-growth approach to copolymerize DNA hairpin tiles (DHTs) into nanofilaments with desirable composition, chain length and function. By designing metastable DNA hairpins with shape-defining intramolecular hydrogen bonds, we generate two types of DHT monomers for copolymerization with high cooperativity and low dispersity indexes. Quantitative single-molecule dissection methods reveal that catalytic opening of a DHT motif harbouring a toehold triggers successive branch migration, which autonomously propagates to form copolymers with alternate tile units. We find that these shape-defined supramolecular nanostructures become substrates for efficient endocytosis by living mammalian cells in a stiffness-dependent manner. Hence, this catassembly-like in-vitro reconstruction approach provides clues for understanding structure-function relationship of biological filaments under physiological and pathological conditions.
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20
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Brady RA, Kaufhold WT, Brooks NJ, Foderà V, Di Michele L. Flexibility defines structure in crystals of amphiphilic DNA nanostars. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:074003. [PMID: 30523829 DOI: 10.1088/1361-648x/aaf4a1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and bond directionality have been recognised as key design features for DNA motifs to sustain long-range order in 3D, but the practical challenges associated with prescribing building-block geometry with sufficient accuracy have limited the variety of available designs. We have recently introduced a novel platform for the one-pot preparation of crystalline DNA frameworks supported by a combination of Watson-Crick base pairing and hydrophobic forces (Brady et al 2017 Nano Lett. 17 3276-81). Here we use small angle x-ray scattering and coarse-grained molecular simulations to demonstrate that, as opposed to available all-DNA approaches, amphiphilic motifs do not rely on structural rigidity to support long-range order. Instead, the flexibility of amphiphilic DNA building-blocks is a crucial feature for successful crystallisation.
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Affiliation(s)
- Ryan A Brady
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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21
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Platnich CM, Hariri AA, Rahbani JF, Gordon JB, Sleiman HF, Cosa G. Kinetics of Strand Displacement and Hybridization on Wireframe DNA Nanostructures: Dissecting the Roles of Size, Morphology, and Rigidity. ACS NANO 2018; 12:12836-12846. [PMID: 30485067 DOI: 10.1021/acsnano.8b08016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Dynamic wireframe DNA structures have gained significant attention in recent years, with research aimed toward using these architectures for sensing and encapsulation applications. For these assemblies to reach their full potential, however, knowledge of the rates of strand displacement and hybridization on these constructs is required. Herein, we report the use of single-molecule fluorescence methodologies to observe the reversible switching between double- and single-stranded forms of triangular wireframe DNA nanotubes. Specifically, by using fluorescently labeled DNA strands, we were able to monitor changes in intensity over time as we introduced different sequences. This allowed us to extract detailed kinetic information on the strand displacement and hybridization processes. Due to the polymeric nanotube structure, the ability to individually address each of the three sides, and the inherent polydispersity of our samples as a result of the step polymerization by which they are formed, a library of compounds could be studied independently yet simultaneously. Kinetic models relying on mono-exponential decays, multi-exponential decays, or sigmoidal behavior were adjusted to the different constructs to retrieve erasing and refilling kinetics. Correlations were made between the kinetic behavior observed, the site accessibility, the nanotube length, and the structural robustness of wireframe DNA nanostructures, including fully single-stranded analogs. Overall, our results reveal how the length, morphology, and rigidity of the DNA framework modulate the kinetics of strand displacement and hybridization as well as the overall addressability and structural stability of the structures under study.
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Affiliation(s)
- Casey M Platnich
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Amani A Hariri
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Janane F Rahbani
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Jesse B Gordon
- 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
| | - Gonzalo Cosa
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
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22
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Gidi Y, Bayram S, Ablenas CJ, Blum AS, Cosa G. Efficient One-Step PEG-Silane Passivation of Glass Surfaces for Single-Molecule Fluorescence Studies. ACS APPLIED MATERIALS & INTERFACES 2018; 10:39505-39511. [PMID: 30346695 DOI: 10.1021/acsami.8b15796] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Surface passivation to inhibit nonspecific interactions is a key requirement for in vitro single-molecule fluorescent studies. Although the standard passivation methods involve the covalent attachment of poly(ethylene glycol) (PEG) in two steps preferably over quartz surfaces, this protocol and improvements thereon require extensive labor and chemicals. Herein, we report an efficient one-step surface grafting of PEG-silane that yields enhanced passivation, as evidenced by reduced nonspecific interactions, over the conventional method at a minimal time and reagent cost and on glass surfaces. Our method is rooted in a mechanistic understanding of the silane reaction with the silanol groups on the glass surface. Single-molecule fluorescence studies with fluorescently tagged proteins and DNA on PEG-silane-functionalized glass surfaces validate the enhanced performance of the method. Combined with atomic force microscopy surface characterization, our study further illustrates that few remaining pinhole defects, plausibly from defects on the glass, on PEG-silane glass-coated surfaces account for the minimal background, where typically no more than one molecule is nonspecifically attached in a given diffraction-limited spot on the surface.
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Affiliation(s)
- Yasser Gidi
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM) , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Serene Bayram
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM) , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | | | - Amy Szuchmacher Blum
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM) , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM) , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
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23
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Brady RA, Brooks NJ, Foderà V, Cicuta P, Di Michele L. Amphiphilic-DNA Platform for the Design of Crystalline Frameworks with Programmable Structure and Functionality. J Am Chem Soc 2018; 140:15384-15392. [PMID: 30351920 DOI: 10.1021/jacs.8b09143] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The reliable preparation of functional, ordered, nanostructured frameworks would be a game changer for many emerging technologies, from energy storage to nanomedicine. Underpinned by the excellent molecular recognition of nucleic acids, along with their facile synthesis and breadth of available functionalizations, DNA nanotechnology is widely acknowledged as a prime route for the rational design of nanostructured materials. Yet, the preparation of crystalline DNA frameworks with programmable structure and functionality remains a challenge. Here we demonstrate the potential of simple amphiphilic DNA motifs, dubbed "C-stars", as a versatile platform for the design of programmable DNA crystals. In contrast to all-DNA materials, in which structure depends on the precise molecular details of individual building blocks, the self-assembly of C-stars is controlled uniquely by their topology and symmetry. Exploiting this robust self-assembly principle, we design a range of topologically identical, but structurally and chemically distinct C-stars that following a one-pot reaction self-assemble into highly porous, functional, crystalline frameworks. Simple design variations allow us to fine-tune the lattice parameter and thus control the partitioning of macromolecules within the frameworks, embed responsive motifs that can induce isothermal disassembly, and include chemical moieties to capture target proteins specifically and reversibly.
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Affiliation(s)
- Ryan A Brady
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
| | - Nicholas J Brooks
- Department of Chemistry , Imperial College London , London SW7 2AZ , United Kingdom
| | - Vito Foderà
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
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24
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Chakrabarty A, Raffy G, Maity M, Gartzia-Rivero L, Marre S, Aymonier C, Maitra U, Del Guerzo A. Nanofiber-Directed Anisotropic Self-Assembly of CdSe-CdS Quantum Rods for Linearly Polarized Light Emission Evidenced by Quantum Rod Orientation Microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802311. [PMID: 30112796 DOI: 10.1002/smll.201802311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Indexed: 06/08/2023]
Abstract
Hybrid soft materials composed of CdSe-CdS nanorods or "quantum rods" (QRs) and the fluorescent 2,3-didecyloxyanthracene (DDOA) low molecular weight organogelator are obtained through self-assembly. Spectroscopy, microscopy, and rheology studies show that the QRs and DDOA coassemble, thereby stabilizing the organogels. Depending on the QR load and excitation wavelength, single nanofibers (NFs) of the hybrid gel display either sharp polarized red luminescence (under green excitation), or dual perpendicularly polarized blue and red emissions (under UV excitation). Transmission electron microscopy, microspectroscopy, and quantum rod orientation microscopy (QROM) reveal that QRs align along the organogel NFs with order parameters reaching 76% and 87%. This paves the way for obtaining surfaces of QR/NF assemblies yielding sharp red linearly polarized emission. In addition, this work demonstrates that QRs can be used more generally to probe nanostructured soft materials, even nonemissive ones. QROM allows to establish maps of the orientation of single QRs dispersed onto or within a gel network by measuring the polarization of the emission of the individual QRs. As occurs within this work in which QRs and NFs interact, the orientation of each QR reveals information on the underlying nanostructure (such as surface striation, bundle formation, and helicity).
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Affiliation(s)
- Arkajyoti Chakrabarty
- Institut des Sciences Moléculaires, UMR 5255, Université de Bordeaux, CNRS, 351 Cours de la Libération, 33400, Talence, France
- ICMCB, Bordeaux INP, UMR 5026, Université de Bordeaux, CNRS, 87 av. du Dr. Schweitzer, 33600, Pessac, France
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Guillaume Raffy
- Institut des Sciences Moléculaires, UMR 5255, Université de Bordeaux, CNRS, 351 Cours de la Libération, 33400, Talence, France
| | - Mitasree Maity
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Leire Gartzia-Rivero
- Institut des Sciences Moléculaires, UMR 5255, Université de Bordeaux, CNRS, 351 Cours de la Libération, 33400, Talence, France
- Department of Physical Chemistry, University of the Basque Country (UPV/EHU), Apartado 644, 48080, Bilbao, Spain
| | - Samuel Marre
- ICMCB, Bordeaux INP, UMR 5026, Université de Bordeaux, CNRS, 87 av. du Dr. Schweitzer, 33600, Pessac, France
| | - Cyril Aymonier
- ICMCB, Bordeaux INP, UMR 5026, Université de Bordeaux, CNRS, 87 av. du Dr. Schweitzer, 33600, Pessac, France
| | - Uday Maitra
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - André Del Guerzo
- Institut des Sciences Moléculaires, UMR 5255, Université de Bordeaux, CNRS, 351 Cours de la Libération, 33400, Talence, France
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25
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Delcanale P, Miret-Ontiveros B, Arista-Romero M, Pujals S, Albertazzi L. Nanoscale Mapping Functional Sites on Nanoparticles by Points Accumulation for Imaging in Nanoscale Topography (PAINT). ACS NANO 2018; 12:7629-7637. [PMID: 30048592 DOI: 10.1021/acsnano.7b09063] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The ability of nanoparticles to selectively recognize a molecular target constitutes the key toward nanomedicine applications such as drug delivery and diagnostics. The activity of such devices is mediated by the presence of multiple copies of functional molecules on the nanostructure surface. Therefore, understanding the number and the distribution of nanoparticle functional groups is of utmost importance for the rational design of effective materials. Analytical methods are available, but to obtain quantitative information at the level of single particles and single functional sites, i. e., going beyond the ensemble, remains highly challenging. Here we introduce the use of an optical nanoscopy technique, DNA points accumulation for imaging in nanoscale topography (DNA-PAINT), to address this issue. Combining subdiffraction spatial resolution with molecular selectivity and sensitivity, DNA-PAINT provides both geometrical and functional information at the level of a single nanostructure. We show how DNA-PAINT can be used to image and quantify relevant functional proteins such as antibodies and streptavidin on nanoparticles and microparticles with nanometric accuracy in 3D and multiple colors. The generality and the applicability of our method without the need for fluorescent labeling hold great promise for the robust quantitative nanocharacterization of functional nanomaterials.
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Affiliation(s)
- Pietro Delcanale
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology , Baldiri Reixac 15-21 , 08028 Barcelona , Spain
| | - Bernat Miret-Ontiveros
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology , Baldiri Reixac 15-21 , 08028 Barcelona , Spain
| | - Maria Arista-Romero
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology , Baldiri Reixac 15-21 , 08028 Barcelona , Spain
| | - Silvia Pujals
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology , Baldiri Reixac 15-21 , 08028 Barcelona , Spain
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology , Baldiri Reixac 15-21 , 08028 Barcelona , Spain
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , 5612AZ Eindhoven , The Netherlands
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26
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Li M, Xiong C, Zheng Y, Liang W, Yuan R, Chai Y. Ultrasensitive Photoelectrochemical Biosensor Based on DNA Tetrahedron as Nanocarrier for Efficient Immobilization of CdTe QDs-Methylene Blue as Signal Probe with Near-Zero Background Noise. Anal Chem 2018; 90:8211-8216. [DOI: 10.1021/acs.analchem.8b01641] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Mengjie Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Chuan Xiong
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yingning Zheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Wenbin Liang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
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27
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Deng R, Zhang K, Wang L, Ren X, Sun Y, Li J. DNA-Sequence-Encoded Rolling Circle Amplicon for Single-Cell RNA Imaging. Chem 2018. [DOI: 10.1016/j.chempr.2018.03.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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28
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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29
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Engel S, Spitzer D, Rodrigues LL, Fritz EC, Straßburger D, Schönhoff M, Ravoo BJ, Besenius P. Kinetic control in the temperature-dependent sequential growth of surface-confined supramolecular copolymers. Faraday Discuss 2017; 204:53-67. [PMID: 28766626 DOI: 10.1039/c7fd00100b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the sequential growth of supramolecular copolymers on gold surfaces, using oppositely charged dendritic peptide amphiphiles. By including water-solubilising thermoresponsive chains in the monomer design, we observed non-linear effects in the temperature-dependent sequential growth. The step-wise copolymerisation process is characterised using temperature dependent SPR and QCM-D measurements. At higher temperatures, dehydration of peripheral oligoethylene glycol chains supports copolymer growth due to more favourable comonomer interactions. Both monomers incorporate methionine amino acids but remarkably, desorption of the copolymers via competing sulphur gold interactions with the initial monomer layer is not observed. The surface-confined supramolecular copolymers remain kinetically trapped on the metal surface at near neutral pH and form viscoelastic films with a tuneable thickness.
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Affiliation(s)
- Sabrina Engel
- Organic Chemistry Institute, Westfälische Wilhelms-University Münster, Corrensstraße 40, 48149 Münster, Germany.
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30
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Zhang L, Jean SR, Ahmed S, Aldridge PM, Li X, Fan F, Sargent EH, Kelley SO. Multifunctional quantum dot DNA hydrogels. Nat Commun 2017; 8:381. [PMID: 28851869 PMCID: PMC5575008 DOI: 10.1038/s41467-017-00298-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/19/2017] [Indexed: 02/02/2023] Open
Abstract
Biotemplated nanomaterials offer versatile functionality for multimodal imaging, biosensing, and drug delivery. There remains an unmet need for traceable and biocompatible nanomaterials that can be synthesized in a precisely controllable manner. Here, we report self-assembled quantum dot DNA hydrogels that exhibit both size and spectral tunability. We successfully incorporate DNA-templated quantum dots with high quantum yield, long-term photostability, and low cytotoxicity into a hydrogel network in a single step. By leveraging DNA-guided interactions, we introduce multifunctionality for a variety of applications, including enzyme-responsive drug delivery and cell-specific targeting. We report that quantum dot DNA hydrogels can be used for delivery of doxorubicin, an anticancer drug, to increase potency 9-fold against cancer cells. This approach also demonstrated high biocompatibility, trackability, and in vivo therapeutic efficacy in mice bearing xenografted breast cancer tumors. This work paves the way for the development of new tunable biotemplated nanomaterials with multiple synergistic functionalities for biomedical applications. The development of nanomaterials for imaging and drug delivery has been of great interest to the field. Here, the authors synthesized multifunctional enzyme-responsive hydrogels with self-assembling quantum dots for nucleic acid and drug delivery as well as having imaging capability.
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Affiliation(s)
- Libing Zhang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada, M5S 3M2
| | - Sae Rin Jean
- Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, Ontario, Canada, M5S 3H6
| | - Sharif Ahmed
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada, M5S 3M2
| | - Peter M Aldridge
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G9
| | - Xiyan Li
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G4
| | - Fengjia Fan
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G4
| | - Edward H Sargent
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G4.
| | - Shana O Kelley
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada, M5S 3M2. .,Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, Ontario, Canada, M5S 3H6. .,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G9. .,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada, M5S 1A8.
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31
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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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32
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Maingi V, Burns JR, Uusitalo JJ, Howorka S, Marrink SJ, Sansom MSP. Stability and dynamics of membrane-spanning DNA nanopores. Nat Commun 2017; 8:14784. [PMID: 28317903 PMCID: PMC5364398 DOI: 10.1038/ncomms14784] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/31/2017] [Indexed: 01/05/2023] Open
Abstract
Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine. Although DNA nanopores are widely explored as synthetic membrane proteins, it is still unclear how the anionic DNA assemblies stably reside within the hydrophobic core of a lipid bilayer. Here, the authors use molecular dynamics simulations to reveal the key dynamic interactions and energetics stabilizing the nanopore-membrane interaction.
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Affiliation(s)
- Vishal Maingi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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33
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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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34
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Darwish GH, Fakih HH, Karam P. Temperature Mapping in Hydrogel Matrices Using Unmodified Digital Camera. J Phys Chem B 2017; 121:1033-1040. [DOI: 10.1021/acs.jpcb.6b11844] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ghinwa H. Darwish
- Department of Chemistry, American University of Beirut, P.O.
Box 11-0236, Beirut 1107 2020, Lebanon
| | - Hassan H. Fakih
- Department of Chemistry, American University of Beirut, P.O.
Box 11-0236, Beirut 1107 2020, Lebanon
| | - Pierre Karam
- Department of Chemistry, American University of Beirut, P.O.
Box 11-0236, Beirut 1107 2020, Lebanon
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35
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Wang J, Chao J, Liu H, Su S, Wang L, Huang W, Willner I, Fan C. Clamped Hybridization Chain Reactions for the Self-Assembly of Patterned DNA Hydrogels. Angew Chem Int Ed Engl 2017; 56:2171-2175. [DOI: 10.1002/anie.201610125] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Indexed: 02/01/2023]
Affiliation(s)
- Jianbang Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Shao Su
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Wei Huang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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36
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Wang J, Chao J, Liu H, Su S, Wang L, Huang W, Willner I, Fan C. Clamped Hybridization Chain Reactions for the Self-Assembly of Patterned DNA Hydrogels. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jianbang Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Shao Su
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Wei Huang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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37
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Glembockyte V, Lin J, Cosa G. Improving the Photostability of Red- and Green-Emissive Single-Molecule Fluorophores via Ni2+ Mediated Excited Triplet-State Quenching. J Phys Chem B 2016; 120:11923-11929. [DOI: 10.1021/acs.jpcb.6b10725] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Viktorija Glembockyte
- Department of Chemistry and
Center for Self-Assembled Chemical Structures (CSACS/CRMAA), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Junan Lin
- Department of Chemistry and
Center for Self-Assembled Chemical Structures (CSACS/CRMAA), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry and
Center for Self-Assembled Chemical Structures (CSACS/CRMAA), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
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38
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Frisch H, Fritz EC, Stricker F, Schmüser L, Spitzer D, Weidner T, Ravoo BJ, Besenius P. Kinetically Controlled Sequential Growth of Surface-Grafted Chiral Supramolecular Copolymers. Angew Chem Int Ed Engl 2016; 55:7242-6. [DOI: 10.1002/anie.201601048] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Hendrik Frisch
- Institute of Organic Chemistry; Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 55128 Mainz Germany
- Organic Chemistry Institute; Westfälische Wilhelms-Universität Münster; Correnstrasse 40 48149 Münster Germany
| | - Eva-Corinna Fritz
- Organic Chemistry Institute; Westfälische Wilhelms-Universität Münster; Correnstrasse 40 48149 Münster Germany
| | - Friedrich Stricker
- Institute of Organic Chemistry; Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 55128 Mainz Germany
| | - Lars Schmüser
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Daniel Spitzer
- Institute of Organic Chemistry; Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 55128 Mainz Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Bart Jan Ravoo
- Organic Chemistry Institute; Westfälische Wilhelms-Universität Münster; Correnstrasse 40 48149 Münster Germany
| | - Pol Besenius
- Institute of Organic Chemistry; Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 55128 Mainz Germany
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39
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Frisch H, Fritz EC, Stricker F, Schmüser L, Spitzer D, Weidner T, Ravoo BJ, Besenius P. Kinetisch kontrolliertes, sequenzielles Wachstum von chiralen supramolekularen Copolymeren auf Oberflächen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hendrik Frisch
- Institut für Organische Chemie; Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 55128 Mainz Deutschland
- Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Correnstraße 40 48149 Münster Deutschland
| | - Eva-Corinna Fritz
- Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Correnstraße 40 48149 Münster Deutschland
| | - Friedrich Stricker
- Institut für Organische Chemie; Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 55128 Mainz Deutschland
| | - Lars Schmüser
- Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Daniel Spitzer
- Institut für Organische Chemie; Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 55128 Mainz Deutschland
| | - Tobias Weidner
- Max-Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Bart Jan Ravoo
- Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Correnstraße 40 48149 Münster Deutschland
| | - Pol Besenius
- Institut für Organische Chemie; Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 55128 Mainz Deutschland
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40
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Krieg E, Bastings MMC, Besenius P, Rybtchinski B. Supramolecular Polymers in Aqueous Media. Chem Rev 2016; 116:2414-77. [DOI: 10.1021/acs.chemrev.5b00369] [Citation(s) in RCA: 527] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Pol Besenius
- Institute
of Organic Chemistry, Johannes Gutenberg-Universität Mainz, Mainz 55128, Germany
| | - Boris Rybtchinski
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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41
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Rahbani JF, Hariri AA, Cosa G, Sleiman HF. Dynamic DNA Nanotubes: Reversible Switching between Single and Double-Stranded Forms, and Effect of Base Deletions. ACS NANO 2015; 9:11898-11908. [PMID: 26556531 DOI: 10.1021/acsnano.5b04387] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.
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Affiliation(s)
- Janane F Rahbani
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Amani A Hariri
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
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42
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Maingi V, Lelimousin M, Howorka S, Sansom MSP. Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations. ACS NANO 2015; 9:11209-17. [PMID: 26506011 DOI: 10.1021/acsnano.5b06357] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Recently developed synthetic membrane pores composed of folded DNA enrich the current range of natural and engineered protein pores and of nonbiogenic channels. Here we report all-atom molecular dynamics simulations of a DNA nanotube (DNT) pore scaffold to gain fundamental insight into its atomic structure, dynamics, and interactions with ions and water. Our multiple simulations of models of DNTs that are composed of a six-duplex bundle lead to a coherent description. The central tube lumen adopts a cylindrical shape while the mouth regions at the two DNT openings undergo gating-like motions which provide a possible molecular explanation of a lower conductance state observed in our previous experimental study on a membrane-spanning version of the DNT (ACS Nano 2015, 9, 1117-26). Similarly, the central nanotube lumen is filled with water and ions characterized by bulk diffusion coefficients while the gating regions exhibit temporal fluctuations in their aqueous volume. We furthermore observe that the porous nature of the walls allows lateral leakage of ions and water. This study will benefit rational design of DNA nanopores of enhanced stability of relevance for sensing applications, of nanodevices with tunable gating properties that mimic gated ion channels, or of nanopores featuring defined permeation behavior.
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Affiliation(s)
- Vishal Maingi
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, Oxford, United Kingdom
| | - Mickaël Lelimousin
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, Oxford, United Kingdom
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London , London WC1H 0AJ, England, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, Oxford, United Kingdom
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