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Wang W, Yu S, Huang S, Bi S, Han H, Zhang JR, Lu Y, Zhu JJ. Bioapplications of DNA nanotechnology at the solid-liquid interface. Chem Soc Rev 2019; 48:4892-4920. [PMID: 31402369 PMCID: PMC6746594 DOI: 10.1039/c8cs00402a] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.
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Affiliation(s)
- Wenjing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.
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2
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A quencher-free DNAzyme beacon for fluorescently sensing uranyl ions via embedding 2-aminopurine. Biosens Bioelectron 2019; 135:166-172. [PMID: 31009884 DOI: 10.1016/j.bios.2019.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/24/2019] [Accepted: 04/10/2019] [Indexed: 01/23/2023]
Abstract
DNAzyme-based fluorescent probes have provided valuable protocols for detecting uranium, one of the most common radioactive contaminants in the environment, with ultra-high selectivity and sensitivity. Designing novel DNAzyme beacons to update the mode of fluorescence reporting and/or quenching will continuously enhance "turn-on" sensing performance as well as promote actual application of the biological probes. In this work, we developed a novel quencher-free DNAzyme beacon by embedding fluorescent 2-aminopurine for rapid detection of uranyl ion. 2-aminopurine is able to substitute adenine and keep strong fluorescence in single-stranded DNA whereas being quenched in the hybridized double-stranded DNA by the base-stacking interaction. The combination of such trait of 2-aminopurine and cleavage reaction of DNAzyme in the presence of target co-factors possesses two main advantages for ion sensing: simplicity for avoidance of extra quencher groups and high performance because of superiority of DNAzyme essence. The experimental conditions including embedding site, pH and salt concentration of buffer solutions, and the amount ratio of enzyme strand to substrate strand used to form DNAzymes were systematically optimized to inspire the highest performance of the biological beacon. Thus, a detection limit of 9.6 nM, a wide linear range from 5 nM to 400 nM (R2 = 0.997), and selectivity of more than 400 000-fold over other metal ions were achieved by the novel DNAzyme probes. The highly sensitive, selective and quencher-free DNAzyme probes accommodated a simple and cost-efficient alternative to current fluorescent counterparts, holding a great potential for further application in practical ion assay.
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3
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Shomali Z, Kompany-Zareh M, Omidikia N. Fluorescence Based Investigation of Temperature-Dependent Pb 2+-Specific 8-17E DNAzyme Catalytic Sensor. J Fluoresc 2019; 29:335-342. [PMID: 30778897 DOI: 10.1007/s10895-019-02346-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/14/2019] [Indexed: 12/13/2022]
Abstract
The 8-17E DNAzyme is a temperature-dependent DNA metalloenzyme catalyzing RNA trans esterification in the presence of Pb2+ metal ions. Labeling the stems of the substrate and DNAzyme with the Cy3 and Cy5 respectively, the considered DNAzyme was studied by the fluorescence spectroscopy. The temperature-dependent variability of the Pb2+-specific 8-17E DNAzyme catalytic sensor was investigated trough a number of successive temperature fluctuations from 4 to 25 °C to obtain information. Investigating underlined biochemical system reveals that in this sensor, free single strands Enzyme (Cy5-E) and Substrate (Cy3-S) have higher fluorescence intensities than hybridized forms, suggesting that the fluorophores are in a contact quenched. Increasing the temperature has three effects: 1) Fluorescence intensities for the free fluorophores were reduced, 2) stability of the hybridized form was reduced and cleavage of substrate in presence of Pb2+was occurred, and 3) conformation of ES hybridized form was changed (before cleavage). As a result of conformation changes in ES, S was more affected than E in the ES. Pb2+ ion shows quenching effect on both fluorophores and in the absence of N2(g) purge the effect was more considerable. A main goal that we had in mind was to find if significantly lower concentrations of Pb2+ and ES, compared to previous reports, can generate any observable cleavage in substrate. Analysis of the cleavage reaction for 50 nM ES indicates that S is cleaved at 25 °C in presence of N2(g) and 0.5 μM Pb2+, while in same condition no apparent change occurs in the 4 or 10 °C. The rapid, sensitive and low cost strategy presented here can be applicable to study temperature-dependent behavior of other nucleic acid-based biosensors.
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Affiliation(s)
- Zohreh Shomali
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Mohsen Kompany-Zareh
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran. .,Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, NS, B3H 4R2, Canada.
| | - Nematollah Omidikia
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, 98135-674, Iran
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4
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Pali M, Suni II. Impedance Detection of 3‐Phenoxybenzoic Acid Comparing Wholes Antibodies and Antibody Fragments for Biomolecular Recognition. ELECTROANAL 2018. [DOI: 10.1002/elan.201800495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Madhavi Pali
- Department of Chemistry & BiochemistryMaterials Technology CenterSouthern Illinois University Carbondale, IL 62901 USA
| | - Ian I. Suni
- Department of Chemistry & BiochemistryMaterials Technology CenterSouthern Illinois University Carbondale, IL 62901 USA
- Department of Mechanical Engineering & Energy ProcessesSouthern Illinois University Carbondale, IL 62901 USA
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5
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Xing H, Li J, Xu W, Hwang K, Wu P, Yin Q, Li Z, Cheng J, Lu Y. The Effects of Spacer Length and Composition on Aptamer-Mediated Cell-Specific Targeting with Nanoscale PEGylated Liposomal Doxorubicin. Chembiochem 2016; 17:1111-7. [PMID: 27123758 DOI: 10.1002/cbic.201600092] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Indexed: 12/27/2022]
Abstract
Aptamer-based targeted drug delivery systems have shown significant promise for clinical applications. Although much progress has been made in this area, it remains unclear how PEG coating would affect the selective binding of DNA aptamers and thus influence the overall targeting efficiency. To answer this question, we herein report a systematic investigation of the interactions between PEG and DNA aptamers on the surface of liposomes by using a series of nanoscale liposomal doxorubicin formulations with different DNA aptamer and PEG modifications. We investigated how the spatial size and composition of the spacer molecules affected the targeting ability of the liposome delivery system. We showed that a spacer of appropriate length was critical to overcome the shielding from surrounding PEG molecules in order to achieve the best targeting effect, regardless of the spacer composition. Our findings provide important guidelines for the design of aptamer-based targeted drug delivery systems.
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Affiliation(s)
- Hang Xing
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL, 61801, USA
| | - Ji Li
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL, 61801, USA
| | - Weidong Xu
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Kevin Hwang
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL, 61801, USA
| | - Peiwen Wu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL, 61801, USA
| | - Qian Yin
- Material Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL, 61801, USA
| | - Zhensheng Li
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL, 61801, USA
| | - Jianjun Cheng
- Material Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL, 61801, USA.
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6
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Yun W, Jiang J, Cai D, Wang X, Sang G, Liao J, Lu T, Yan K. Ultrasensitive electrochemical detection of UO22+ based on DNAzyme and isothermal enzyme-free amplification. RSC Adv 2016. [DOI: 10.1039/c5ra22773a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel enzyme-free amplification biosensor for uranyl detection was developed based on UO22+-specific DNAzyme and a hybridization chain reaction.
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Affiliation(s)
- Wen Yun
- Science and Technology on Surface Physics and Chemistry Laboratory
- Jiangyou 621908
- China
| | - Jiaolai Jiang
- Science and Technology on Surface Physics and Chemistry Laboratory
- Jiangyou 621908
- China
| | - Dingzhou Cai
- Science and Technology on Surface Physics and Chemistry Laboratory
- Jiangyou 621908
- China
| | - Xiaofang Wang
- Science and Technology on Surface Physics and Chemistry Laboratory
- Jiangyou 621908
- China
| | - Ge Sang
- Science and Technology on Surface Physics and Chemistry Laboratory
- Jiangyou 621908
- China
| | - Junsheng Liao
- Science and Technology on Surface Physics and Chemistry Laboratory
- Jiangyou 621908
- China
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7
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Avidin–biotin capped mesoporous silica nanoparticles as an ion-responsive release system to determine lead(II). Anal Biochem 2015; 471:17-22. [DOI: 10.1016/j.ab.2014.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 11/18/2022]
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8
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Wang W, Ding X, He M, Wang J, Lou X. Kinetic adsorption profile and conformation evolution at the DNA-gold nanoparticle interface probed by dynamic light scattering. Anal Chem 2014; 86:10186-92. [PMID: 25222203 PMCID: PMC4204920 DOI: 10.1021/ac502440h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The
kinetic adsorption profile at the DNA–gold nanoparticle
(AuNP) interface is probed by following the binding and organization
of thiolated linear DNA and aptamers of varying chain lengths (15,
30, 44, and 51 mer) to the surface of AuNPs (13.0 ± 1.0 nm diameter).
A systematic investigation utilizing dynamic light scattering has
been performed to directly measure the changes in particle size during
the course of a typical aging-salting thiolated DNA/AuNP preparation
procedure. We discuss the effect of DNA chain length, composition,
salt concentration, and secondary structure on the kinetics and conformation
at the DNA–AuNP interface. The adsorption kinetics are chain-length
dependent, composition independent, and not diffusion rate limited
for the conditions we report here. The kinetic data support a mechanism
of stepwise adsorption of thiols to the surface of AuNPs and reorganization
of the thiols at the interface. Very interestingly, the kinetic increases
of the particle sizes are modeled accurately by the pseudo-second-order
rate model, suggesting that DNA could possess the statistically well-defined
conformational evolution. Together with other experimental evidence,
we propose a dynamic inner-layer and outer-tail (DILOT) model to describe
the evolution of the DNA conformation after the initial adsorption
of a single oligonucleotide layer. According to this model, the length
of the tails that extend from the surface of AuNPs, capable for hybridization
or molecular recognition, can be conveniently calculated. Considering
the wide applications of DNA/AuNPs, the results should have important
implications in sensing and DNA-directed nanoparticle assembly.
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Affiliation(s)
- Wenjie Wang
- Department of Chemistry, Capital Normal University , Xisanhuan North Road. 105, Beijing 100048, China
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9
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Agrahari SK, Kumar SD, Srivastava AK. Ion selective electrode for uranium based on composite multiwalled carbon nanotube-benzo-15-crown-5 in PVC matrix coated on graphite rod. JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1134/s106193481401002x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Cepeda-Plaza M, Null EL, Lu Y. Metal ion as both a cofactor and a probe of metal-binding sites in a uranyl-specific DNAzyme: a uranyl photocleavage study. Nucleic Acids Res 2013; 41:9361-70. [PMID: 23939617 PMCID: PMC3814387 DOI: 10.1093/nar/gkt694] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
DNAzymes are known to bind metal ions specifically to carry out catalytic functions. Despite many studies since DNAzymes were discovered nearly two decades ago, the metal-binding sites in DNAzymes are not fully understood. Herein, we adopt uranyl photocleavage to probe specific uranyl-binding sites in the 39E DNAzyme with catalytically relevant concentrations of uranyl. The results indicate that uranyl binds between T23 and C25 in the bulge loop, G11 and T12 in the stem loop of the enzyme strand, as well as between T2.4 and G3 close to the cleavage site in the substrate strand. Control experiments using two 39E DNAzyme mutants revealed a different cleavage pattern of the mutated region. Another DNAzyme, the 8–17 DNAzyme, which has a similar secondary structure but shows no activity in the presence of uranyl, indicated a different uranyl-dependent photocleavage as well. In addition, a close correlation between the concentration-dependent photocleavage and enzymatic activities is also demonstrated. Together, these experiments suggest that uranyl photocleavage has been successfully used to probe catalytically relevant uranyl-binding sites in the 39E DNAzyme. As uranyl is the cofactor of the 39E DNAzyme as well as the probe, specific uranyl binding has now been identified without disruption of the structure.
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Affiliation(s)
- Marjorie Cepeda-Plaza
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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11
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Ghosh S, Biswas S, Bauzá A, Barceló-Oliver M, Frontera A, Ghosh A. Use of Metalloligands [CuL] (H2L = Salen Type Di-Schiff Bases) in the Formation of Heterobimetallic Copper(II)-Uranyl Complexes: Photophysical Investigations, Structural Variations, and Theoretical Calculations. Inorg Chem 2013; 52:7508-23. [DOI: 10.1021/ic400422d] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soumavo Ghosh
- Department
of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata-700 009, India
| | - Saptarshi Biswas
- Department
of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata-700 009, India
| | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa
km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Miquel Barceló-Oliver
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa
km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa
km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Ashutosh Ghosh
- Department
of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata-700 009, India
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12
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Josephs EA, Ye T. Nanoscale spatial distribution of thiolated DNA on model nucleic acid sensor surfaces. ACS NANO 2013; 7:3653-3660. [PMID: 23540444 DOI: 10.1021/nn400659m] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The nanoscale arrangement of the DNA probe molecules on sensor surfaces has a profound impact on molecular recognition and signaling reactions on DNA biosensors and microarrays. Using electrochemical atomic force microscopy, we have directly determined the nanoscale spatial distribution of thiolated DNA that are attached to gold via different methods. We discovered significant heterogeneity in the probe density and limited stability for DNA monolayers prepared by the backfilling method, that is, first exposing the surface to thiolated DNA then "backfilling" with a passivating alkanethiol. On the other hand, the monolayers prepared by "inserting" thiolated DNA into a preformed alkanethiol monolayer lead to a more uniformly distributed layer of DNA. With high-resolution images of single DNA molecules on the surface, we have introduced spatial statistics to characterize the nanoscale arrangement of DNA probes. The randomness of the spatial distribution has been characterized. By determining the local densities surrounding individual molecules, we observed subpopulations of probes with dramatically different levels of "probe crowding". We anticipate that the novel application of spatial statistics to DNA monolayers can enable a framework to understand heterogeneity in probe spatial distributions, interprobe interactions, and ultimately probe activity on sensor surfaces.
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Affiliation(s)
- Eric A Josephs
- School of Engineering, University of California, Merced, California 95343, United States
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13
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Josephs EA, Ye T. Electric-field dependent conformations of single DNA molecules on a model biosensor surface. NANO LETTERS 2012; 12:5255-5261. [PMID: 22963660 DOI: 10.1021/nl3024356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Despite the variety of nucleic acid sensors developed, we still do not have definite answers to some questions that are important to the molecular binding and, ultimately, the sensitivity and reliability of the sensors. How do the DNA probes distribute on the surface at the nanoscale? As the functionalized surfaces are highly heterogeneous, how are the conformations affected when the probe molecules interact with defects? How do DNA molecules respond to electric fields on the surface, which are applied in a variety of detection methods? With in situ electrochemical atomic force microscopy and careful tailoring of nanoscale surface interactions, we are able to observe the nanoscale conformations of individual DNA molecules on a model biosensor surface: thiolated DNA on a gold surface passivated with a hydroxyl-terminated alkanethiol self-assembled monolayer. We find that under applied electric fields, the conformations are highly sensitive to the choice of the alkanethiol molecule. Depending on the monolayer and the nature of the defects, the DNA molecules may either adopt a highly linear or a highly curved conformation. These unusual structures are difficult to observe through existing "ensemble" characterizations of nucleic acid sensors. These findings provide a step toward correlating target-binding affinity, selectivity, and kinetics to the nanoscale chemical structure of and around the probe molecules in practical nucleic acid devices.
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Affiliation(s)
- Eric A Josephs
- School of Engineering, University of California, Merced, California 95343, USA
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14
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Fu XB, Qu F, Li NB, Luo HQ. A label-free thrombin binding aptamer as a probe for highly sensitive and selective detection of lead(II) ions by a resonance Rayleigh scattering method. Analyst 2012; 137:1097-9. [PMID: 22273760 DOI: 10.1039/c2an15980e] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The binding of lead(II) ions with unusually high affinity to a thrombin binding aptamer resulted in an enhancement of resonance Rayleigh scattering (RRS). A simple, sensitive, and selective assay for the direct determination of trace amounts of Pb(2+) on the basis of RRS has been proposed.
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Affiliation(s)
- Xiao Bei Fu
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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15
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Jacobi ZE, Li L, Liu J. Visual detection oflead(II) using a label-free DNA-based sensor and its immobilization within a monolithic hydrogel. Analyst 2012; 137:704-9. [DOI: 10.1039/c2an15754c] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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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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17
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Lin Z, Li X, Kraatz HB. Impedimetric Immobilized DNA-Based Sensor for Simultaneous Detection of Pb2+, Ag+, and Hg2+. Anal Chem 2011; 83:6896-901. [DOI: 10.1021/ac2014096] [Citation(s) in RCA: 246] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Zhenzhen Lin
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
| | - Xiaohong Li
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
| | - Heinz-Bernhard Kraatz
- Department of Chemistry, University of Western Ontario,1151 Richmond Street, London, N6A 5B7, Canada
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18
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Lin Z, Chen Y, Li X, Fang W. Pb2+ induced DNA conformational switch from hairpin to G-quadruplex: electrochemical detection of Pb2+. Analyst 2011; 136:2367-72. [DOI: 10.1039/c1an15080d] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Zhang XB, Kong RM, Lu Y. Metal ion sensors based on DNAzymes and related DNA molecules. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:105-28. [PMID: 21370984 PMCID: PMC3119750 DOI: 10.1146/annurev.anchem.111808.073617] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Metal ion sensors are an important yet challenging field in analytical chemistry. Despite much effort, only a limited number of metal ion sensors are available for practical use because sensor design is often a trial-and-error-dependent process. DNAzyme-based sensors, in contrast, can be developed through a systematic selection that is generalizable for a wide range of metal ions. Here, we summarize recent progress in the design of DNAzyme-based fluorescent, colorimetric, and electrochemical sensors for metal ions, such as Pb(2+), Cu(2+), Hg(2+), and UO(2)(2+). In addition, we also describe metal ion sensors based on related DNA molecules, including T-T or C-C mismatches and G-quadruplexes.
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Affiliation(s)
- Xiao-Bing Zhang
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Rong-Mei Kong
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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20
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Wang F, Wu Z, Lu Y, Wang J, Jiang JH, Yu RQ. A label-free DNAzyme sensor for lead(II) detection by quantitative polymerase chain reaction. Anal Biochem 2010; 405:168-73. [DOI: 10.1016/j.ab.2010.06.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/08/2010] [Accepted: 06/12/2010] [Indexed: 10/19/2022]
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21
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Chien MP, Thompson MP, Gianneschi NC. DNA-nanoparticle micelles as supramolecular fluorogenic substrates enabling catalytic signal amplification and detection by DNAzyme probes. Chem Commun (Camb) 2010; 47:167-9. [PMID: 20830351 DOI: 10.1039/c0cc02291h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic DNA molecules have tremendous potential in propagating detection events via nucleic acid sequence selective signal amplification. However, they suffer from product inhibition limiting their widespread utility. Herein, this limitation is overcome utilizing a novel fluorogenic substrate design consisting of cooperatively assembled DNA-nanoparticle micelles.
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Affiliation(s)
- Miao-Ping Chien
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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22
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Piruska A, Branagan SP, Minnis AB, Wang Z, Cropek DM, Sweedler JV, Bohn PW. Electrokinetic control of fluid transport in gold-coated nanocapillary array membranes in hybrid nanofluidic-microfluidic devices. LAB ON A CHIP 2010; 10:1237-1244. [PMID: 20445875 DOI: 10.1039/b924164g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The introduction of metallic elements into microfluidic devices that support electrokinetic transport creates several fundamental issues relative to the high conductivity of the metal, which can act as a current shunt, causing profound effects on the transport process. Here we examine the use of Au-coated nanocapillary array membranes (Au NCAMs) as electrically addressable fluid control elements in multi-layer microfluidic architectures. Three alternative methods for fluid injection across Au NCAMs are presented: electrokinetic injection across NCAMs with Au coated on one side (asymmetric NCAM), electrokinetic injection across NCAMs with an embedded Au layer (symmetric NCAM), and field-free electroosmotic flow (EOF) pumping across either type of Au NCAM. Injection efficiency across asymmetric NCAMs depends on the orientation of the asymmetric membrane relative to the driving potential. Efficient injections are enabled when the Au coating is on the receiving side of the membrane, however, some distortion of the injected volume element is observed, especially with large injection potentials. These results for asymmetric membranes agree qualitatively with two-dimensional numerical simulations of injections across a single slit pore, which suggest that the direction-selective transport behavior is related to electrophoretic transport of the anionic fluorescein probe. Reproducible, high quality injections are also achieved in symmetric Au NCAMs having an embedded gold nanoband region within the nanopores. Nanoband Au NCAMs are excellent candidates for a range of applications, including high efficiency electrochemical sensing, electrochemically catalyzed conversion or pretreatment and label free sensing utilizing extraordinary optical transmission. EOF pumping could be an alternative to electrokinetic injections in some applications, however, this approach is only useful for relatively large pore sizes (>400 nm) and presents considerably worse sample spreading via Taylor dispersion.
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Affiliation(s)
- Aigars Piruska
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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Molecular diagnostic and drug delivery agents based on aptamer-nanomaterial conjugates. Adv Drug Deliv Rev 2010; 62:592-605. [PMID: 20338204 DOI: 10.1016/j.addr.2010.03.003] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 02/03/2010] [Indexed: 12/16/2022]
Abstract
Recent progress in an emerging area of designing aptamer and nanomaterial conjugates as molecular diagnostic and drug delivery agents in biomedical applications is summarized. Aptamers specific for a wide range of targets are first introduced and compared to antibodies. Methods of integrating these aptamers with a variety of nanomaterials, such as gold nanoparticles, quantum dots, carbon nanotubes, and superparamagnetic iron oxide nanoparticles, each with unique optical, magnetic, and electrochemical properties, are reviewed. Applications of these systems as fluorescent, colorimetric, magnetic resonance imaging, and electrochemical sensors in medical diagnostics are given, along with new applications as smart drug delivery agents.
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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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25
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Xiang Y, Tong A, Lu Y. Abasic site-containing DNAzyme and aptamer for label-free fluorescent detection of Pb(2+) and adenosine with high sensitivity, selectivity, and tunable dynamic range. J Am Chem Soc 2009; 131:15352-7. [PMID: 19807110 PMCID: PMC2783749 DOI: 10.1021/ja905854a] [Citation(s) in RCA: 303] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An abasic site called dSpacer has been introduced into duplex regions of the 8-17 DNAzyme and adenosine aptamer for label-free fluorescent detection of Pb(2+) and adenosine, respectively. The dSpacer can bind an extrinsic fluorescent compound, 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), and quench its fluorescence. Addition of Pb(2+) enables the DNAzyme to cleave its substrate and release ATMND from DNA duplex, recovering the fluorescence of ATMND. Similarly, the presence of adenosine induces structural switching of the aptamer, resulting in the release of ATMND from the DNA duplex and a subsequent fluorescence enhancement. Under optimized conditions, this label-free method exhibits detection limits of 4 nM for Pb(2+) and 3.4 muM for adenosine, which are even lower than those of the corresponding labeled-DNAzyme and aptamer sensors. These low detection limits have been obtained without compromising any of the selectivity of the sensors. Finally, the dynamic range of the adenosine sensor has been tuned by varying the number of hybridized base-pairs in the aptamer duplex. The method demonstrated here can be applied for label-free detection and quantification of a broad range of analytes using other DNAzymes and aptamers.
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Affiliation(s)
- Yu Xiang
- Department of Chemistry, Tsinghua University, Beijing 100084, PR China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aijun Tong
- Department of Chemistry, Tsinghua University, Beijing 100084, PR China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Nagraj N, Liu J, Sterling S, Wu J, Lu Y. DNAzyme catalytic beacon sensors that resist temperature-dependent variations. Chem Commun (Camb) 2009:4103-5. [PMID: 19568647 DOI: 10.1039/b903059j] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The temperature-dependent variability of a Pb2+-specific 8-17E DNAzyme catalytic beacon sensor has been addressed through the introduction of mismatches in the DNAzyme, and the resulting sensors resist temperature-dependent variations from 4 to 30 degrees C.
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Affiliation(s)
- Nandini Nagraj
- Department of Chemistry, University of Illinois at Urbana, Champaign Urbana, IL 61801, USA
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27
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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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28
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Cho EJ, Lee JW, Ellington AD. Applications of aptamers as sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2009; 2:241-64. [PMID: 20636061 DOI: 10.1146/annurev.anchem.1.031207.112851] [Citation(s) in RCA: 572] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Aptamers are ligand-binding nucleic acids whose affinities and selectivities can rival those of antibodies. They have been adapted to analytical applications not only as alternatives to antibodies, but as unique reagents in their own right. In particular, aptamers can be readily site-specifically modified during chemical or enzymatic synthesis to incorporate particular reporters, linkers, or other moieties. Also, aptamer secondary structures can be engineered to undergo analyte-dependent conformational changes, which, in concert with the ability to specifically place chemical agents, opens up a wealth of possible signal transduction schemas, irrespective of whether the detection modality is optical, electrochemical, or mass based. Finally, because aptamers are nucleic acids, they are readily adapted to sequence- (and hence signal-) amplification methods. However, application of aptamers without a basic knowledge of their biochemistry or technical requirements can cause serious analytical difficulties.
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Affiliation(s)
- Eun Jeong Cho
- The Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, Texas 78712, USA.
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Lee JH, Wang Z, Liu J, Lu Y. Highly sensitive and selective colorimetric sensors for uranyl (UO2(2+)): development and comparison of labeled and label-free DNAzyme-gold nanoparticle systems. J Am Chem Soc 2008; 130:14217-26. [PMID: 18837498 PMCID: PMC2667950 DOI: 10.1021/ja803607z] [Citation(s) in RCA: 391] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Colorimetric uranium sensors based on uranyl (UO2(2+)) specific DNAzyme and gold nanoparticles (AuNP) have been developed and demonstrated using both labeled and label-free methods. In the labeled method, a uranyl-specific DNAzyme was attached to AuNP, forming purple aggregates. The presence of uranyl induced disassembly of the DNAzyme functionalized AuNP aggregates, resulting in red individual AuNPs. Once assembled, such a "turn-on" sensor is highly stable, works in a single step at room temperature, and has a detection limit of 50 nM after 30 min of reaction time. The label-free method, on the other hand, utilizes the different adsorption properties of single-stranded and double-stranded DNA on AuNPs, which affects the stability of AuNPs in the presence of NaCl. The presence of uranyl resulted in cleavage of substrate by DNAzyme, releasing a single stranded DNA that can be adsorbed on AuNPs and protect them from aggregation. Taking advantage of this phenomenon, a "turn-off" sensor was developed, which is easy to control through reaction quenching and has 1 nM detection limit after 6 min of reaction at room temperature. Both sensors have excellent selectivity over other metal ions and have detection limits below the maximum contamination level of 130 nM for UO2(2+) in drinking water defined by the U.S. Environmental Protection Agency (EPA). This study represents the first direct systematic comparison of these two types of sensor methods using the same DNAzyme and AuNPs, making it possible to reveal advantages, disadvantages, versatility, limitations, and potential applications of each method. The results obtained not only allow practical sensing application for uranyl but also serve as a guide for choosing different methods for designing colorimetric sensors for other targets.
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Affiliation(s)
- Jung Heon Lee
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana IL 61801
- Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign, Urbana IL 61801
| | - Zidong Wang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana IL 61801
- Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign, Urbana IL 61801
| | - Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana IL 61801
- Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign, Urbana IL 61801
| | - Yi Lu
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana IL 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana IL 61801
- Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign, Urbana IL 61801
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Piruska A, Branagan S, Cropek DM, Sweedler JV, Bohn PW. Electrokinetically driven fluidic transport in integrated three-dimensional microfluidic devices incorporating gold-coated nanocapillary array membranes. LAB ON A CHIP 2008; 8:1625-1631. [PMID: 18813383 DOI: 10.1039/b805768k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Electrokinetically driven fluid transport was evaluated within three-dimensional hybrid nanofluidic-microfluidic devices incorporating Au-coated nanocapillary array membranes (NCAMs). Gold NCAMs, prepared by electroless gold deposition on polymeric track-etched membranes, were susceptible to gas bubble formation if the interfacial potential difference exceeded approximately 2 V along the length of the gold region. Gold membranes were etched to yield 250 microm wide coated regions that overlap the intersection of two orthogonal microfluidic channels in order to minimize gas evolution. The kinetics of electrolysis of water at the opposing ends of the gold region was modeled and found to be in satisfactory agreement with experimental measurements of the onset of gas bubble formation. Conditions to achieve electrokinetic injection across Au-coated NCAMs were identified, with significant reproducible injections being possible for NCAMs modified with this relatively thin gold stripe. Continuous gold films led to suppressed injections and to a variety of ion enrichment/depletion effects in the microfluidic source channel. The suppression of injections was understood through finite element modeling which revealed the presence of a significant electrophoretic velocity component in opposition to electroosmotic flow at the edge of the Au-dielectric regions.
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Affiliation(s)
- Aigars Piruska
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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31
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Abstract
BACKGROUND Although catalytic RNA enzymes (CRzs) are naturally occurring in many organisms, their DNA counterparts (CDzs) were developed by in vitro selection/evolution from random sequence libraries. OBJECTIVE To provide a brief overview of how CDzs have been selected in vitro, and of their properties and functions, as well as their possible future utility. METHODS We concentrated on examples of 'direct' selection of CDzs. Many CDzs have been used in biological settings, for example downregulation of target mRNAs, while many more recent applications use CDzs in biosensor and nanotechnology settings. CONCLUSIONS Although much work has concentrated on using CDzs for regulating gene expression, their potential as nucleic acid medicines has diminished substantially, supplanted by simple antisense oligonucleotides and, more recently, by small interfering RNAs (siRNAs). It seems unlikely that CDzs will have clinical utility. In contrast, they are likely to have significant potential in the sensor/nanotechnology arena.
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Affiliation(s)
- Weihua Pan
- Department of Pathology, Pennsylvania State University, Gittlen Cancer Research Foundation, Hershey Medical Center, Hershey, PA 17033, USA
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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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Dalavoy TS, Wernette DP, Gong M, Sweedler JV, Lu Y, Flachsbart BR, Shannon MA, Bohn PW, Cropek DM. Immobilization of DNAzyme catalytic beacons on PMMA for Pb2+ detection. LAB ON A CHIP 2008; 8:786-793. [PMID: 18432350 DOI: 10.1039/b718624j] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Due to the numerous toxicological effects of lead, its presence in the environment needs to be effectively monitored. Incorporating a biosensing element within a microfluidic platform enables rapid and reliable determinations of lead at trace levels. A microchip-based lead sensor is described here that employs a lead-specific DNAzyme (also called catalytic DNA or deoxyribozyme) as a recognition element that cleaves its complementary substrate DNA strand only in the presence of cationic lead (Pb(2+)). Fluorescent tags on the DNAzyme translate the cleavage events to measurable, optical signals proportional to Pb(2+) concentration. The DNAzyme responds sensitively and selectively to Pb(2+), and immobilizing DNAzyme in the sensor permits both sensor regeneration and localization of the detection zone. Here, the DNAzyme has been immobilized on a PMMA surface using the highly specific biotin-streptavidin interaction. The strategy includes using streptavidin physisorbed on a PMMA surface to immobilize DNAzyme both on planar PMMA and on the walls of a PMMA microfluidic device. The immobilized DNAzyme retains its Pb(2+) detection activity in the microfluidic device and can be regenerated and reused. The DNAzyme shows no response to other common metal cations and the presence of these contaminants does not interfere with the lead-induced fluorescence signal. While prior work has shown lead-specific catalytic DNA can be used in its solubilized form and while attached to gold substrates to quantitate Pb(2+) in solution, this is the first use of the DNAzyme immobilized within a microfluidic platform for real time Pb(2+) detection.
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Affiliation(s)
- Tulika S Dalavoy
- U.S. Army Corps of Engineers, Construction Engineering Research Laboratory, 2902 Newmark Drive, Champaign, Illinois 61822, USA
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34
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Miller EW, He Q, Chang CJ. Preparation and use of Leadfluor-1, a synthetic fluorophore for live-cell lead imaging. Nat Protoc 2008; 3:777-83. [DOI: 10.1038/nprot.2008.43] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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