1
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Yang S, Wang Y, Wang Q, Li F, Ling D. DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:340-355. [PMID: 37501793 PMCID: PMC10369495 DOI: 10.1021/cbmi.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/07/2023] [Indexed: 07/29/2023]
Abstract
DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.
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Affiliation(s)
- Shengfei Yang
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuqi Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Qiyue Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Fangyuan Li
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
| | - Daishun Ling
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
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2
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Simonoff E, Van Muñoz LX, Lewis NS. Increased spatial randomness and disorder of nucleates in dark-phase electrodeposition lead to increased spatial order and pattern fidelity in phototropically grown Se-Te electrodeposits. NANOSCALE 2020; 12:22478-22486. [PMID: 33169777 DOI: 10.1039/d0nr07617a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The role of nucleation was investigated during phototropic growth of Se-Te. Under low levels of mass deposition (mass equivalent of -3.75 mC cm-2 of charge passed) that produced small nucleate spacings, patterns in photoelectrochemically deposited Se-Te films converged at relatively earlier levels of mass deposition and ultimately exhibited higher pattern fidelity throughout pattern development as compared to pattern formation from larger initial nucleate spacings. Consistently, use of an applied striking potential during very early levels of mass deposition produced more spatially random dark-phase electrodeposited nucleates and led to phototropic Se-Te photoelectrodeposited films that exhibited improved pattern fidelity relative to depositions performed with no striking step. Collectively, the data indicate that increases in randomness and spatial disorder of the dispersion of the initial nucleates produces increases in the fidelity and spatial order in the resulting phototropically grown electrodeposits.
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Affiliation(s)
- Ethan Simonoff
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 127-72, 210 Noyes Laboratory, Pasadena, CA 91125, USA.
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3
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Tian B, Han Y, Wetterskog E, Donolato M, Hansen MF, Svedlindh P, Strömberg M. MicroRNA Detection through DNAzyme-Mediated Disintegration of Magnetic Nanoparticle Assemblies. ACS Sens 2018; 3:1884-1891. [PMID: 30188122 DOI: 10.1021/acssensors.8b00850] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-assembled nanoparticle superstructures offer numerous bioresponsive properties that can be utilized for point-of-care diagnostics. Functional DNA sequences such as deoxyribozymes (DNAzymes) provide novel bioresponsive strategies and further extend the application of DNA-assembled nanoparticle superstructures. In this work, we describe a microRNA detection biosensor that combines magnetic nanoparticle (MNP) assemblies with DNAzyme-assisted target recycling. The DNA scaffolds of the MNP assemblies contain substrate sequences for DNAzyme and can form cleavage catalytic structures in the presence of target DNA or RNA sequences, leading to rupture of the scaffolds and disintegration of the MNP assemblies. The target sequences are preserved during the cleavage reaction and release into the suspension to trigger the digestion of multiple DNA scaffolds. The high local concentration of substrate sequences in the MNP assemblies reduces the diffusion time for target recycling. The concentration of released MNPs, which is proportional to the concentration of the target, can be quantified by a 405 nm laser-based optomagnetic sensor. For the detection of let-7b in 10% serum, after 1 h of isothermal reaction at 50 °C, we found a linear detection range between 10 pM and 100 nM with a limit of detection of 6 pM. For the quantification of DNA target in buffer solution, a limit of detection of 1.5 pM was achieved. Compared to protein enzyme-based microRNA detection methods, the proposed DNAzyme-based biosensor has an increased stability, a reduced cost and a possibility to be used in living cells, all of which are valuable features for biosensing applications.
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Affiliation(s)
- Bo Tian
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech,
Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Yuanyuan Han
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
| | - Erik Wetterskog
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
| | - Marco Donolato
- BluSense Diagnostics, Fruebjergvej 3, DK-2100 Copenhagen, Denmark
| | - Mikkel Fougt Hansen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech,
Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Peter Svedlindh
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
| | - Mattias Strömberg
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
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4
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Eppel S, Portnoy M. Reversible Multistep Synthesis with Equilibrium Properties Based on a Selection-Oriented Process with a Repetitive Sequence of Steps. J Phys Chem B 2014; 118:9733-44. [DOI: 10.1021/jp5051645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sagi Eppel
- School of Chemistry, Raymond
and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moshe Portnoy
- School of Chemistry, Raymond
and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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5
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Tan LH, Xing H, Lu Y. DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles. Acc Chem Res 2014; 47:1881-90. [PMID: 24871359 PMCID: PMC4066914 DOI: 10.1021/ar500081k] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Several properties of nanomaterials, such as
morphologies (e.g.,
shapes and surface structures) and distance dependent properties (e.g.,
plasmonic and quantum confinement effects), make nanomaterials uniquely
qualified as potential choices for future applications from catalysis
to biomedicine. To realize the full potential of these nanomaterials,
it is important to demonstrate fine control of the morphology of individual
nanoparticles, as well as precise spatial control of the position,
orientation, and distances between multiple nanoparticles. In addition,
dynamic control of nanomaterial assembly in response to multiple stimuli,
with minimal or no error, and the reversibility of the assemblies
are also required. In this Account, we summarize recent progress of
using DNA as a powerful programmable tool to realize the above goals.
First, inspired by the discovery of genetic codes in biology, we have
discovered DNA sequence combinations to control different morphologies
of nanoparticles during their growth process and have shown that these
effects are synergistic or competitive, depending on the sequence
combination. The DNA, which guides the growth of the nanomaterial,
is stable and retains its biorecognition ability. Second, by taking
advantage of different reactivities of phosphorothioate and phosphodiester
backbone, we have placed phosphorothioate at selective positions on
different DNA nanostructures including DNA tetrahedrons. Bifunctional
linkers have been used to conjugate phosphorothioate on one end and
bind nanoparticles or proteins on the other end. In doing so, precise
control of distances between two or more nanoparticles or proteins
with nanometer resolution can be achieved. Furthermore, by developing
facile methods to functionalize two hemispheres of Janus nanoparticles
with two different DNA sequences regioselectively, we have demonstrated
directional control of nanomaterial assembly, where DNA strands with
specific hybridization serve as orthogonal linkers. Third, by using
functional DNA that includes DNAzyme, aptamer, and aptazyme, dynamic
control of assemblies of gold nanoparticles, quantum dots, carbon
nanotubes, and iron oxide nanoparticles in response to one or more
stimuli cooperatively have been achieved, resulting in colorimetric,
fluorescent, electrochemical, and magnetic resonance signals for a
wide range of targets, such as metal ions, small molecules, proteins,
and intact cells. Fourth, by mimicking biology, we have employed DNAzymes
as proofreading units to remove errors in nanoparticle assembly and
further used DNAzyme cascade reactions to modify or repair DNA sequences
involved in the assembly. Finally, by taking advantage of different
affinities of biotin and desthiobiotin toward streptavidin, we have
demonstrated reversible assembly of proteins on DNA origami.
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Affiliation(s)
- Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Hang Xing
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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6
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Wong NY, Xing H, Tan LH, Lu Y. Nano-encrypted Morse code: a versatile approach to programmable and reversible nanoscale assembly and disassembly. J Am Chem Soc 2013; 135:2931-4. [PMID: 23373425 PMCID: PMC3612397 DOI: 10.1021/ja3122284] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code "NANO" and reversible exchange of uppercase letter "I" with lowercase "i". The yields of the conjugations are high (>90%), and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates.
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Affiliation(s)
- Ngo Yin Wong
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Hang Xing
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Yi Lu
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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7
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Shao C, Lu N, Sun D. A G‐Quadruplex/Hemin Complex with Switchable Peroxidase Activity by DNA Hybridization. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201200360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Congying Shao
- School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Na Lu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dengming Sun
- School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, China
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8
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Lan T, Lu Y. Metal Ion-Dependent DNAzymes and Their Applications as Biosensors. Met Ions Life Sci 2012; 10:217-48. [DOI: 10.1007/978-94-007-2172-2_8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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9
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Sun Y, Cai S, Cao Z, Lau C, Lu J. Aptameric system for the highly selective and ultrasensitive detection of protein in human serum based on non-stripping gold nanoparticles. Analyst 2011; 136:4144-51. [PMID: 21881666 DOI: 10.1039/c1an15520b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A novel approach is proposed in this study for the development of an aptameric assay system for protein based on non-stripping gold nanoparticles (NPs)-triggered chemiluminescence (CL) upon target binding. The strategy chiefly depends on the formation of a sandwich-type immunocomplex among the capture antibody immobilized on the polystyrene microwells, target protein and aptamer-functionalized gold NPs. Introduction of target protein into the assay system leads to the attachment of gold NPs onto the surface of the microwells and thus the assembled gold NPs could trigger the reaction between luminol and AgNO(3) with a CL emission. Further signal amplification was achieved by a simple gold metal catalytic deposition onto the gold NPs. Such an amplified CL transduction allowed for the detection of model target IgE down to the 50 fM, which is better than most existing aptameric methods for IgE detection. This new protocol also provided a good capability in discriminating IgE from nontarget proteins such as IgG, IgA, IgM and interferon. The practical application of the proposed gold NPs-based immunoassay was successfully carried out for the determination of IgE in 35 human serum samples. Overall, the proposed assay system exhibits excellent analytical characteristics (e.g., a detection limit on the attomolar scale and a linear dynamic range of 4 orders of magnitude), and it is also straightforward to adapt this strategy to detect a spectrum of other proteins by using different aptamers. This new CL strategy might create a novel technology for developing simple biosensors in the sensitive and selective detection of target protein in a variety of clinical, environmental and biodefense applications.
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Affiliation(s)
- Yanhua Sun
- School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education & PLA, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
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10
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Schlosser K, Li Y. A Versatile Endoribonuclease Mimic Made of DNA: Characteristics and Applications of the 8-17 RNA-Cleaving DNAzyme. Chembiochem 2010; 11:866-79. [DOI: 10.1002/cbic.200900786] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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11
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Abstract
Nature uses deoxyribonucleic acid (DNA) as the main material for the storage and transmission of life’s blueprint. Today, DNA is being used as a “smart” material to help solve a number of long-standing issues facing researchers in materials science and nanotechnology. In DNA nanotechnology, DNA’s powerful base-pair molecular recognition criteria are utilized to control the final structure and function of the material being generated. A sub-area of research that our group has recently termed “supramolecular DNA nanotechnology” is emerging and is extending the limits of this molecule in nanotechnology by further fine-tuning DNA’s structural and functional potential. This review will discuss the fruition and fundamentals of supramolecular DNA nanotechnology, as well as its future as a viable science in a material world.
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Affiliation(s)
- Faisal A. Aldaye
- 1Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA
| | - Hanadi F. Sleiman
- 2Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A2K6, Canada
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12
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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13
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Abstract
DNA's remarkable molecular recognition properties and structural features make it one of the most promising templates to pattern materials with nanoscale precision. The emerging field of DNA nanotechnology strips this molecule from any preconceived biological role and exploits its simple code to generate addressable nanostructures in one, two, and three dimensions. These structures have been used to precisely position proteins, nanoparticles, transition metals, and other functional components into deliberately designed patterns. They can also act as templates for the growth of nanowires, aid in the structural determination of proteins, and provide new platforms for genomics applications. The field of DNA nanotechnology is growing in a number of directions, carrying with it the promise to substantially affect materials science and biology.
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Affiliation(s)
- Faisal A Aldaye
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 2K6, Canada
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14
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Shyr MHS, Wernette DP, Wiltzius P, Lu Y, Braun PV. DNA and DNAzyme-Mediated 2D Colloidal Assembly. J Am Chem Soc 2008; 130:8234-40. [DOI: 10.1021/ja711026r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Margaret H. S. Shyr
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Daryl P. Wernette
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Pierre Wiltzius
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Yi Lu
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Paul V. Braun
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
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15
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Willner I, Shlyahovsky B, Zayats M, Willner B. DNAzymes for sensing, nanobiotechnology and logic gate applications. Chem Soc Rev 2008; 37:1153-65. [DOI: 10.1039/b718428j] [Citation(s) in RCA: 669] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Kim HK, Liu J, Li J, Nagraj N, Li M, Pavot CMB, Lu Y. Metal-Dependent Global Folding and Activity of the 8-17 DNAzyme Studied by Fluorescence Resonance Energy Transfer. J Am Chem Soc 2007; 129:6896-902. [PMID: 17488081 DOI: 10.1021/ja0712625] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 8-17 DNAzyme is a DNA metalloenzyme catalyzing RNA transesterification in the presence of divalent metal ions, with activity following the order Pb2+ >> Zn2+ >>Mg2+. Since the DNAzyme has been used as a metal ion sensor, its metal-induced global folding was studied by fluorescence resonance energy transfer (FRET) by labeling the three stems of the DNAzyme with the Cy3/Cy5 FRET pair two stems at a time in order to gain deeper insight into the role of different metal ions in its structure and function. FRET results indicated that, in the presence of Zn2+ and Mg2+, the DNAzyme folds into a compact structure, stem III approaching a configuration defined by stems I and II without changing the angle between stems I and II. Correlations between metal-induced folding and activity were also studied. For Zn2+ and Mg2+, the metal ion with higher affinity for the DNAzyme in global folding (Kd(Zn) = 52.6 microM and Kd(Mg) = 1.36 mM) also displays higher affinity in activity (Kd(Zn) = 1.15 mM and Kd(Mg) = 53 mM) under the same conditions. Global folding was saturated at much lower concentrations of Zn2+ and Mg2+ than the cleavage activities, indicating the global folding of the DNAzyme occurs before the cleavage activity for those metal ions. Surprisingly, no Pb2+-dependent global folding was observed. These results suggest that for Pb2+ global folding of the DNAzyme may not be a necessary step in its function, which may contribute to the DNAzyme having the highest activity in the presence of Pb2+.
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Affiliation(s)
- Hee-Kyung Kim
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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17
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Lu Y, Liu J. Smart nanomaterials inspired by biology: dynamic assembly of error-free nanomaterials in response to multiple chemical and biological stimuli. Acc Chem Res 2007; 40:315-23. [PMID: 17474707 DOI: 10.1021/ar600053g] [Citation(s) in RCA: 209] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three-dimensional functional nanoscale assembly requires not only self-assembly of individual nanomaterials responsive to external stimuli, such as temperature, light, and concentrations, but also directed assembly of many different nanomaterials in one-pot responsive to multiple internal stimuli signaling the needs for such materials at a specific location and a particular time. The use of functional DNA (DNAzymes, aptamers, and aptazymes) to meet these challenges is reviewed. In addition, a biology-inspired proof-reading and error correction method is introduced to cope with errors in nanomaterials assembly.
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Affiliation(s)
- Yi Lu
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana--Champaign, Urbana, Illinois 61801, USA.
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18
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Affiliation(s)
- Ye Tian
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, IN 47907, USA
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19
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Beissenhirtz MK, Elnathan R, Weizmann Y, Willner I. The aggregation of Au nanoparticles by an autonomous DNA machine detects viruses. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2007; 3:375-9. [PMID: 17262868 DOI: 10.1002/smll.200600450] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Moritz K Beissenhirtz
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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20
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Baron R, Willner B, Willner I. Biomolecule–nanoparticle hybrids as functional units for nanobiotechnology. Chem Commun (Camb) 2007:323-32. [PMID: 17220964 DOI: 10.1039/b610721b] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biomolecule-metal or semiconductor nanoparticle (NP) hybrid systems combine the recognition and catalytic properties of biomolecules with the unique electronic and optical properties of NPs. This enables the application of the hybrid systems in developing new electronic and optical biosensors, to synthesize nanowires and nanocircuits, and to fabricate new devices. Metal NPs are employed as nano-connectors that activate redox enzymes, and they act as electrical or optical labels for biorecognition events. Similarly, semiconductor NPs act as optical probes for biorecognition processes. Double-stranded DNA or protein chains that are modified with metallic nanoclusters act as templates for the synthesis of metallic nanowires. The nanowires are used as building blocks to assemble nano-devices such as a transistor or a nanotransporter.
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Affiliation(s)
- Ronan Baron
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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21
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Lu Y, Liu J. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Curr Opin Biotechnol 2006; 17:580-8. [PMID: 17056247 DOI: 10.1016/j.copbio.2006.10.004] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 08/23/2006] [Accepted: 10/11/2006] [Indexed: 11/20/2022]
Abstract
In the past 25 years, DNA molecules have been utilized both as powerful synthetic building blocks to create nanoscale architectures and as versatile programmable templates for assembly of nanomaterials. In parallel, the functions of DNA molecules have been expanded from pure genetic information storage to catalytic functions like those of protein enzymes (DNAzymes) and specific binding functions like antibodies (aptamers). In the past few years, a new interdisciplinary field has emerged that aims to combine functional DNA biology with nanotechnology to generate more dynamic and controllable DNA-based nanostructures or DNA-templated nanomaterials that are responsive to chemical stimuli.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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22
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Liu J, Lu Y. Design of asymmetric DNAzymes for dynamic control of nanoparticle aggregation states in response to chemical stimuli. Org Biomol Chem 2006; 4:3435-41. [PMID: 17036137 DOI: 10.1039/b605799c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic control of nanomaterial assembly states in response to chemical stimuli is critical in making multi-component materials with interesting properties. Previous work has shown that a Pb2+-specific DNAzyme allowed dynamic control of gold nanoparticle aggregation states in response to Pb2+, and the resulting color change from blue aggregates to red dispersed particles can be used as a convenient way of sensing Pb2+. However, a small piece of DNA (called invasive DNA) and low ionic strength (approximately 30 mM) were required for the process, limiting the scope of application in assembly and sensing. To overcome this limitation, a series of asymmetric DNAzymes, in which one of the two substrate binding regions is longer than the other, has been developed. With such a system, we demonstrated Pb2+-induced disassembly of gold nanoparticle aggregates and corresponding color change at room temperature without the need for invasive DNA, while also making the system more tolerant to ionic strength (33-100 mM). The optimal lengths of the long and short arms were determined to be 14 and 5 base pairs, respectively. In nanoparticle aggregates, the activity of the DNAzyme increased with decreasing ionic strength of the reaction buffer. This simpler and more versatile system allows even better dynamic control of nanoparticle aggregation states in response to chemical stimuli such as Pb2+, and can be used in a wider range of applications for colorimetric sensing of metal ions.
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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