1
|
Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
Collapse
Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| |
Collapse
|
2
|
Tatarko M, Spagnolo S, Csiba M, Šubjaková V, Hianik T. Analysis of the Interaction between DNA Aptamers and Cytochrome C on the Surface of Lipid Films and on the MUA Monolayer: A QCM-D Study. BIOSENSORS 2023; 13:251. [PMID: 36832017 PMCID: PMC9953847 DOI: 10.3390/bios13020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
We analyzed the possibility of the detection of cytochrome c (cyt c) being physically adsorbed on lipid films or covalently bounded to 11-mercapto-1-undecanoic acid (MUA) chemisorbed on the gold layer using quartz crystal microbalance with dissipation monitoring (QCM-D). The negatively charged lipid film composed of a mixture of zwitterionic DMPC and negatively charged DMPG phospholipids at a molar ratio of 1:1 allowed the formation of a stable cyt c layer. Addition of DNA aptamers specific to cyt c, however, resulted in removal of cyt c from the surface. The interaction of cyt c with the lipid film and its removal by DNA aptamers were accompanied by changes in viscoelastic properties evaluated using the Kelvin-Voigt model. Cyt c covalently bound to MUA also provided a stable protein layer already at its relatively low concentrations (0.5 μM). A decrease in the resonant frequency following the addition of gold nanowires (AuNWs) modified by DNA aptamers was observed. The interaction of aptamers with cyt c on the surface can be a combination of specific and non-specific interactions due to electrostatic forces between negatively charged DNA aptamers and positively charged cyt c.
Collapse
|
3
|
ZIF-8 base-aptamer "gate-lock" probes enable the visualization of a cascade response between deoxynivalenol and cytochrome c inside living cells. Mikrochim Acta 2022; 190:39. [PMID: 36585487 DOI: 10.1007/s00604-022-05619-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/11/2022] [Indexed: 12/31/2022]
Abstract
Zeolitic imidazolate framework (ZIF-8) base-aptamer "gate-lock" biomaterial probes have been synthesized for monitoring intracellular deoxynivalenol (DON) and cytochrome c (cyt c) levels. The aptamer and organic fluorescent dye were regarded as a recognition element and a sensing element, respectively. In the presence of DON, the aptamers of DON and cyt c were specifically bound with the DON and induced cyt c, leading to the dissociation of aptamers from the porous surface of the probes. The gate was subsequently opened to release methylene blue (MB) and Rhodamine 6G (Rh6G), and their fluorescence (emission of MB at 700 nm and Rh6G at 550 nm) significantly recovered within 6 h. Cell imaging successfully monitored the exposure of DON and the biological process of cyt c discharge triggered by the activation of the DON-induced apoptosis pathway. In addition, the response between DON and cyt c was observed during the apoptosis process, which is of high significance for the comprehensive and systematic development of mycotoxins cytotoxicity.
Collapse
|
4
|
Wang J, Wang Z, Huang PJJ, Bai F, Liu J. Adsorption of DNA Oligonucleotides by Self-Assembled Metalloporphyrin Nanomaterials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3553-3560. [PMID: 35258306 DOI: 10.1021/acs.langmuir.2c00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Porphyrin assemblies have controllable morphology, high biocompatibility, and good optical properties and were widely used in biomedical diagnosis and treatment. With the development of DNA biotechnology, combining DNA with porphyrin assemblies can broaden the biological applications of porphyrins. Porphyrin assemblies can serve as nanocarriers for DNA, although the fundamental interactions between them are not well understood. In this work, zinc meso-tetra(4-pyridyl)porphyrin (ZnTPyP) assemblies were prepared in the presence of various surfactants and at different pH values, yielding a variety of aggregation forms. Among them, the hexagonal stacking form exposes more pyridine substituents, and the hydrogen bonding force between the substituents and the DNA bases allows the DNA to be quickly adsorbed on the surface of the assemblies. The effects of DNA sequence and length were systematically tested. In particular, the adsorption of duplex DNA was less efficient compared to the adsorption of single-stranded DNA. This fundamental study is useful for the further combination of DNA and porphyrin assemblies to prepare new functional hybrid nanomaterials.
Collapse
Affiliation(s)
- Jinghan Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
- Key Laboratory for Special Functional Materials of Ministry of Education, National & Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, School of Materials Science and Engineering, and Collaborative Innovation Center of Nano Functional Materials and Applications, Henan University, Kaifeng 475004, China
| | - Zhen Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Feng Bai
- Key Laboratory for Special Functional Materials of Ministry of Education, National & Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, School of Materials Science and Engineering, and Collaborative Innovation Center of Nano Functional Materials and Applications, Henan University, Kaifeng 475004, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
5
|
Raoof JB, Bagheryan Z, Hashkavayi AB. Development of a DNA biosensor based on MCM41 modified screen-printed graphite electrode for the study of the short sequence of the p53 tumor suppressor gene in hybridization and its interaction with the flutamide drug using hemin as the electrochemical label. NEW J CHEM 2020. [DOI: 10.1039/c9nj04569d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical DNA biosensors are particularly attractive because of their high sensitivity, suitability and compatibility with miniaturization in nucleic acid technology.
Collapse
Affiliation(s)
- Jahan Bakhsh Raoof
- Electroanalytical Chemistry Research Laboratory
- Department of Analytical Chemistry
- Faculty of Chemistry
- University of Mazandaran
- Babolsar
| | - Zahra Bagheryan
- Electroanalytical Chemistry Research Laboratory
- Department of Analytical Chemistry
- Faculty of Chemistry
- University of Mazandaran
- Babolsar
| | - Ayemeh Bagheri Hashkavayi
- Electroanalytical Chemistry Research Laboratory
- Department of Analytical Chemistry
- Faculty of Chemistry
- University of Mazandaran
- Babolsar
| |
Collapse
|
6
|
Cai S, Yan J, Xiong H, Liu Y, Peng D, Liu Z. Investigations on the interface of nucleic acid aptamers and binding targets. Analyst 2019; 143:5317-5338. [PMID: 30357118 DOI: 10.1039/c8an01467a] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA of 20-100 nucleotides in length that have attracted substantial scientific interest due to their ability to specifically bind to target molecules via the formation of three-dimensional structures. Compared to traditional protein antibodies, aptamers have several advantages, such as their small size, high binding affinity, specificity, flexible structure, being chemical synthesizable and modifiable, good biocompatibility, high stability and low immunogenicity, which all contribute to their widely applications in the biomedical field. To date, much progress has been made in the study and applications of aptamers, however, detailed information on how aptamers bind to their targets is still scarce. Over the past few decades, many methods have been introduced to investigate the aptamer-target binding process, such as measuring the main kinetic or thermodynamic parameters, detecting the structural changes of the binding complexes, etc. Apart from traditional physicochemical methods, various types of molecular docking programs have been applied to simulate the aptamer-target interactions, while these simulations also have limitations. To facilitate the further research on the interactions, herein, we provide a brief review to illustrate the recent advances in the study of aptamer-target interactions. We summarize the binding targets of aptamers, such as small molecules, macromolecules, and even cells. Their binding constants (KD) are also summarized. Methods to probe the aptamer-target binding process, such as surface plasmon resonance (SPR), circular dichroism spectroscopy (CD), isothermal titration calorimetry (ITC), footprinting assay, truncation and mutation assay, nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography and molecular docking simulation are indicated. The binding forces mediating the aptamer-target interactions, such as hydrogen bonding, electrostatic interaction, the hydrophobic effect, π-π stacking and van der Waals forces are summarized. The challenges and future perspectives are also discussed.
Collapse
Affiliation(s)
- Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, PR China.
| | | | | | | | | | | |
Collapse
|
7
|
Akki SU, Werth CJ. Critical Review: DNA Aptasensors, Are They Ready for Monitoring Organic Pollutants in Natural and Treated Water Sources? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8989-9007. [PMID: 30016080 DOI: 10.1021/acs.est.8b00558] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
There is a growing need to monitor anthropogenic organic contaminants detected in water sources. DNA aptamers are synthetic single-stranded oligonucleotides, selected to bind to target contaminants with favorable selectivity and sensitivity. These aptamers can be functionalized and are used with a variety of sensing platforms to develop sensors, or aptasensors. In this critical review, we (1) identify the state-of-the-art in DNA aptamer selection, (2) evaluate target and aptamer properties that make for sensitive and selective binding and sensing, (3) determine strengths and weaknesses of alternative sensing platforms, and (4) assess the potential for aptasensors to quantify environmentally relevant concentrations of organic contaminants in water. Among a suite of target and aptamer properties, binding affinity is either directly (e.g., organic carbon partition coefficient) or inversely (e.g., polar surface area) correlated to properties that indicate greater target hydrophobicity results in the strongest binding aptamers, and binding affinity is correlated to aptasensor limits of detection. Electrochemical-based aptasensors show the greatest sensitivity, which is similar to ELISA-based methods. Only a handful of aptasensors can detect organic pollutants at environmentally relevant concentrations, and interference from structurally similar analogs commonly present in natural waters is a yet-to-be overcome challenge. These findings lead to recommendations to improve aptasensor performance.
Collapse
Affiliation(s)
- Spurti U Akki
- Department of Civil and Environmental Engineering , University of Illinois at Urbana-Champaign , 205 North Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Charles J Werth
- Department of Civil, Architecture, and Environmental Engineering , University of Texas at Austin , 301 East Dean Keeton Street , Austin , Texas 78712 , United States
| |
Collapse
|
8
|
Russo Krauss I, Napolitano V, Petraccone L, Troisi R, Spiridonova V, Mattia CA, Sica F. Duplex/quadruplex oligonucleotides: Role of the duplex domain in the stabilization of a new generation of highly effective anti-thrombin aptamers. Int J Biol Macromol 2017; 107:1697-1705. [PMID: 29024684 DOI: 10.1016/j.ijbiomac.2017.10.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 12/19/2022]
Abstract
Recently, mixed duplex/quadruplex oligonucleotides have attracted great interest for use as biomedical aptamers. In the case of anti-thrombin aptamers, the addition of duplex-forming sequences to a G-quadruplex module identical or very similar to the best-known G-quadruplex of the Thrombin Binding Aptamer (HD1) results in new or improved biological properties, such as higher activity or different recognition properties with respect to HD1. Remarkably, this bimodular fold was hypothesized, based on its sequence, for the only anti-thrombin aptamer in advanced clinical trial, NU172. Whereas cation modulation of G-quadruplex conformation and stability is well characterized, only few data from similar analysis on duplex/quadruplex oligonucleotides exist. Here we have performed a characterization of structure and stability of four different duplex/quadruplex anti-thrombin aptamers, including NU172, in the presence of different cations and in physiological-mimicking conditions in comparison to HD1, by means of spectroscopic techniques (UV and circular dichroism) and differential scanning calorimetry. Our data show a strong reciprocal influence of each domain on the stability of the other and in particular suggest a stabilizing effect of the duplex region in the presence of solutions mimicking the physiological conditions, strengthening the idea that bimodular aptamers present better therapeutic potentialities than those containing a single G-quadruplex domain.
Collapse
Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy
| | - Valeria Napolitano
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Vera Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Carlo Andrea Mattia
- Department of Pharmacy, University of Salerno, Via Ponte Don Melillo, I-84084, Fisciano, SA, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy.
| |
Collapse
|
9
|
Hashkavayi AB, Raoof JB, Ojani R. Construction of a highly sensitive signal-on aptasensor based on gold nanoparticles/functionalized silica nanoparticles for selective detection of tryptophan. Anal Bioanal Chem 2017; 409:6429-6438. [PMID: 28852807 DOI: 10.1007/s00216-017-0588-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023]
Abstract
In this work, a highly sensitive, low-cost, and label-free aptasensor based on signal-on mechanisms of response was developed by immobilizing the aptamer on gold nanoparticles (AuNPs)/amine-functionalized silica nanoparticle (FSN)/screen-printed electrode (SPE) surface for highly selective electrochemical detection of tryptophan (Trp). The hemin (Hem), which interacted with the guanine bases of the aptamer, worked as a redox indicator to generate a readable electrochemical signal. The changes in the charge transfer resistance have been monitored using the voltammetry and electrochemical impedance spectroscopic (EIS) techniques. The peak current of Hem linearly increased with increasing concentration of Trp, in differential pulse voltammetry, from 0.06 to 250 nM with a detection limit of 0.026 nM. Also, the results obtained from EIS studies showed that the Trp was detected sensitively with the fabricated aptasensor in the range of 0.06-250 nM. The detection limit is 0.01 nM, much lower than that obtained by most of the reported electrochemical methods. The usage of aptamer as a recognition layer led to a sensor with high affinity for Trp, compared with control amino acids of tyrosine, histidine, arginine, lysine, valine, and methionine. The usability of the aptasensor was successfully evaluated by the determination of Trp in a human blood serum sample. Thus, the sensor could provide a promising plan for the construction of aptasensors. Graphical abstract Schematic outline the principle for tryptophan aptasensing.
Collapse
Affiliation(s)
- Ayemeh Bagheri Hashkavayi
- Electroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-1467, Iran
| | - Jahan Bakhsh Raoof
- Electroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-1467, Iran.
| | - Reza Ojani
- Electroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-1467, Iran
| |
Collapse
|
10
|
Li Y, Xu S, Wu X, Xu Q, Zhao Y, Lou X, Yang X. Thioflavin T as a fluorescence light-up probe for both parallel and antiparallel G-quadruplexes of 29-mer thrombin binding aptamer. Anal Bioanal Chem 2016; 408:8025-8036. [PMID: 27590320 DOI: 10.1007/s00216-016-9901-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/08/2016] [Accepted: 08/23/2016] [Indexed: 12/31/2022]
Abstract
A wide range of pathologies have been targeted with bimodular aptamers that contain both G-quadruplex (G4) and duplex motifs, while the structures and functions are poorly understood. G4-selective fluorescent dyes have served as facile tools to probe G4s, but not for bimodular aptamers, yet. Here, taking the 29-mer thrombin binding aptamer (TBA29) as an example, we demonstrated that 3,6-dimethyl-2-(4-dimethylaminophenyl)-benzothiazolium (ThT) was the most effective dye compared to NMM and PPIX in recognizing TBA29. Binding studies indicate that ThT recognized TBA29 via distinct buffer-dependent mechanisms. Specifically, ThT induced the formation of a bimolecular parallel G4 in cation-deficient buffer, showing 341-fold fluorescent enhancement. The competitive binding of thrombin disrupted the complex, leading to the monotonic fluorescence decrease. A similar mechanism was previously reported for the interaction between ThT and the 15-mer thrombin binding aptamer (TBA15). However, TBA29 bound with ThT in a more favorable state than TBA15, showing hyperchromic effects and two times stronger fluorescence enhancement. Differently, ThT bound with antiparallel TBA29/TBA15 in an intercalating/groove binding mode in 100 mM KCl, generating 181/28-fold fluorescence enhancement, respectively. These results revealed that ThT recognized both parallel and antiparallel G4s of TBA29 more efficiently than it recognized TBA15. The duplex structure of TBA29 may play an important role in its interaction with ThT. Our study broadens the application of ThT in screening G4 to bimodular aptamers and provides some insights into the structures of TBA29, along with the interaction between ThT and TBA29. Our study also is useful for the development of structure-switching-based biosensors using bimodular aptamers. Graphical abstract The buffer-dependent binding mechanisms of ThT with TBA29, and the competitive (top)/noncompetitive (bottom) binding of thrombin with TBA29-ThT complex.
Collapse
Affiliation(s)
- Ye Li
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Shi Xu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiao Wu
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Qing Xu
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Yinhua Zhao
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, 100048, China.
| | - Xianbin Yang
- AM Biotechnologies, 12521 Gulf Freeway, Houston, TX, 77034, USA.
| |
Collapse
|
11
|
Label-free and sensitive aptasensor based on dendritic gold nanostructures on functionalized SBA-15 for determination of chloramphenicol. Anal Bioanal Chem 2016; 408:2557-65. [PMID: 26879648 DOI: 10.1007/s00216-016-9358-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/16/2016] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
Abstract
A highly sensitive and low-cost electrochemical aptasensor was developed for the determination of chloramphenicol (CAP). The system was based on a CAP-binding aptamer, a molecular recognition element, and 1,4-diazabicyclo[2.2.2]octane (DABCO)-supported mesoporous silica SBA-15 on the surface of a screen-printed graphite electrode for formation of dendritic gold nanostructures and improving the performance and conductivity of the biosensor. Hemin has been applied as an electrochemical indicator which interacted with the guanine bases of the aptamer. In the absence of CAP, hemin binds to the aptamer and produces a weak differential pulse voltammetric (DPV) signal. The presence of CAP led to stabilization of the folded aptamer, which generated an amplified DPV signal. The peak current of hemin increased linearly with the concentration of CAP. Under optimal conditions, two linear ranges were obtained from 0.03 to 0.15 μM and 0.15 to 7.0 μM, respectively, and the detection limit was 4.0 nM. The prepared biosensor has good selectivity against other non-target drugs. Thus, the sensor could provide a promising platform for the fabrication of aptasensors. The feasibility of using this aptasensor was demonstrated by determination of CAP in a human blood serum sample.
Collapse
|
12
|
Cai N, Li Y, Chen S, Su X. A fluorometric assay platform for caffeic acid detection based on the G-quadruplex/hemin DNAzyme. Analyst 2016; 141:4456-62. [DOI: 10.1039/c6an00543h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fluorometric assay platform based on GQDs is designed for biochemical detection of caffeic acid.
Collapse
Affiliation(s)
- Nan Cai
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P.R. China
| | - Yan Li
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P.R. China
| | - Shufan Chen
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P.R. China
| | - Xingguang Su
- Department of Analytical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P.R. China
| |
Collapse
|
13
|
Lin F, Zhao X, Wang J, Yu S, Deng Y, Geng L, Li H. A novel microfluidic chip electrophoresis strategy for simultaneous, label-free, multi-protein detection based on a graphene energy transfer biosensor. Analyst 2015; 139:2890-5. [PMID: 24755615 DOI: 10.1039/c3an02279j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new type of high-throughput and parallel optical sensing platform with a single-color probe based on microfluidic chip electrophoresis combined with aptamer-carboxyfluorescein/graphene oxide energy transfer is reported here. Label-free protein multi-targets were detected, even in challenging complex samples without any pre-treatment.
Collapse
Affiliation(s)
- Fengming Lin
- School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P.R. China.
| | | | | | | | | | | | | |
Collapse
|
14
|
Ding C, Zhang W, Wang W, Chen Y, Li X. Amplification strategies using electrochemiluminescence biosensors for the detection of DNA, bioactive molecules and cancer biomarkers. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.10.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
15
|
Zhang FT, Nie J, Zhang DW, Chen JT, Zhou YL, Zhang XX. Methylene blue as a G-quadruplex binding probe for label-free homogeneous electrochemical biosensing. Anal Chem 2014; 86:9489-95. [PMID: 25211349 DOI: 10.1021/ac502540m] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein, G-quadruplex sequence was found to significantly decrease the diffusion current of methylene blue (MB) in homogeneous solution for the first time. Electrochemical methods combined with circular dichroism spectroscopy and UV-vis spectroscopy were utilized to systematically explore the interaction between MB and an artificial G-quadruplex sequence, EAD2. The interaction of MB and EAD2 (the binding constant, K ≈ 1.3 × 10(6) M(-1)) was stronger than that of MB and double-stranded DNA (dsDNA) (K ≈ 2.2 × 10(5) M(-1)), and the binding stoichiometry (n) of EAD2/MB complex was calculated to be 1.0 according to the electrochemical titration curve combined with Scatchard analysis. MB was proved to stabilize the G-quadruplex structure of EAD2 and showed a competitive binding to G-quadruplex in the presence of hemin. EAD2 might mainly interact with MB, a positive ligand of G-quadruplex, through the end-stacking with π-system of the guanine quartet, which was quite different from the binding mechanism of dsDNA with MB by intercalation. A novel signal read-out mode based on the strong affinity between G-quadruplex and MB coupling with aptamer/G-quadruplex hairpin structure was successfully implemented in cocaine detection with high specificity. G-quadruplex/MB complex will function as a promising electrochemical indicator for constructing homogeneous label-free electrochemical biosensors, especially in the field of simple, rapid, and noninvasive biochemical assays.
Collapse
Affiliation(s)
- Fang-Ting Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University , Beijing 100871, China
| | | | | | | | | | | |
Collapse
|
16
|
Seok Y, Byun JY, Mun H, Kim MG. Colorimetric detection of PCR products of DNA from pathogenic bacterial targets based on a simultaneously amplified DNAzyme. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1297-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
17
|
Sun A, Qi Q, Wang X, Bie P. Porous platinum nanotubes labeled with hemin/G-quadruplex based electrochemical aptasensor for sensitive thrombin analysis via the cascade signal amplification. Biosens Bioelectron 2014; 57:16-21. [PMID: 24534575 DOI: 10.1016/j.bios.2014.01.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/09/2014] [Accepted: 01/22/2014] [Indexed: 12/28/2022]
Abstract
For the first time, a sensitive electrochemical aptasensor for thrombin (TB) was developed by using porous platinum nanotubes (PtNTs) labeled with hemin/G-quadruplex and glucose dehydrogenase (GDH) as labels. Porous PtNTs with large surface area exhibited the peroxidase-like activity. Coupling with GDH and hemin/G-quadruplex as NADH oxidase and HRP-mimicking DNAzyme, the cascade signal amplification was achieved by the following ways: in the presence of glucose and NAD(+) in the working buffer, GDH electrocatalyzed the oxidation of glucose with the production of NADH. Then, hemin/G-quadruplex as NADH oxidase catalyzed the oxidation of NADH to in situ generate H2O2. Based on the corporate electrocatalysis of PtNTs and hemin/G-quadruplex toward H2O2, the electrochemical signal was significantly amplified, allowing the detection limit of TB down to 0.15 pM level. Moreover, the proposed strategy was simple because the intercalated hemin offered the readout signal, avoiding the adding of additional redox mediator as signal donator. Such an electrochemical aptasensor is highly promising for sensitive detection of other proteins in clinical diagnostics.
Collapse
Affiliation(s)
- Aili Sun
- Department of Chemistry and Chemical Engineering, Xinxiang University, Xinxiang 453000, PR China.
| | - Qingan Qi
- Southwest Hospital & Institute of Hepatobilitary Surgery, the Third Military Medical University, Chongqing 400038, PR China; Department of General Surgery, the 371th Hospital of PLA, Xinxiang 453000, PR China
| | - Xuannian Wang
- Department of Chemistry and Chemical Engineering, Xinxiang University, Xinxiang 453000, PR China
| | - Ping Bie
- Southwest Hospital & Institute of Hepatobilitary Surgery, the Third Military Medical University, Chongqing 400038, PR China
| |
Collapse
|
18
|
A novel fluorescence assay for the detection of hemoglobin based on the G-quadruplex/hemin complex. Talanta 2014; 118:118-22. [DOI: 10.1016/j.talanta.2013.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 11/19/2022]
|
19
|
Xiao L, Chai Y, Yuan R, Wang H, Bai L. Highly enhanced electrochemiluminescence based on pseudo triple-enzyme cascade catalysis and in situ generation of co-reactant for thrombin detection. Analyst 2014; 139:1030-6. [DOI: 10.1039/c3an02134c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a novel pseudo triple-enzyme cascade catalysis amplification strategy was employed to fabricate a highly sensitive electrochemiluminescence (ECL) aptasensor for thrombin (TB) detection.
Collapse
Affiliation(s)
- Lijuan Xiao
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715, People's Republic of China
| | - Yaqin Chai
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715, People's Republic of China
| | - Ruo Yuan
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715, People's Republic of China
| | - Haijun Wang
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715, People's Republic of China
| | - Lijuan Bai
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715, People's Republic of China
| |
Collapse
|
20
|
Zhou W, Gong X, Xiang Y, Yuan R, Chai Y. Target-triggered quadratic amplification for label-free and sensitive visual detection of cytokines based on hairpin aptamer DNAzyme probes. Anal Chem 2013; 86:953-8. [PMID: 24328253 DOI: 10.1021/ac403682c] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The employment of DNAzyme probes for visual biodetections has received increasing interest recently due to the simple nature of this type of assay. However, achieving high sensitivity and detecting targets beyond nucleic acids remain two major challenges in DNAzyme-based visual detections. In this work, based on a new quadratic amplification strategy, we developed a sensitive and visual detection method for cytokines by using hairpin aptamer DNAzyme probes. The target cytokine, interferon γ (IFN-γ), associates with the aptamer sequences and unfolds the hairpin structure of the probes, leading to simultaneous recycling of the target IFN-γ (assisted by Bst-polymerase) and the DNA sequences (aided by λ exonuclease) to achieve quadratic amplification. This quadratic amplification results in the generation of numerous peroxidase-mimicking DNAzymes, which cause significantly intensified color change of the probe solution for highly sensitive detection of IFN-γ by the naked eye down to 50 pM. The proposed visual sensing method shows also high selectivity toward the target IFN-γ and can be performed in homogeneous solutions with using completely unmodified, synthetic aptamer DNAzyme probes. These distinct advantages of our developed assay protocol make it a potential platform for detecting various types of biomolecules with careful probe designs.
Collapse
Affiliation(s)
- Wenjiao Zhou
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, People's Republic of China
| | | | | | | | | |
Collapse
|
21
|
Xia Y, Gao P, Qiu X, Xu Q, Gan S, Yang H, Huang S. Aptasensor based on triplex switch for SERS detection of cytochrome c. Analyst 2013; 137:5705-9. [PMID: 23099775 DOI: 10.1039/c2an36173f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report a sensitive approach for SERS detection of cytochrome c using target binding-induced conformational changes of signal transduction probe (STP). STP labeled with a SERS-active molecule, carboxy-X-rhodamine (ROX), is immobilized on the substrate where the formation of a rigid triplex switching structure with aptamers does not allow SERS amplification to take place. The target binding event leads to an enhancement in SERS intensity of ROX adsorbed on the gold surface. Meanwhile, we found that an appropriate STP surface density could shield the SERS signal produced by protein adsorption which would foul the sensing surface. In addition, cytochrome c aptamers used were not the original sequence but reorganized in the nonspecific binding site to adapt to our design. This method provides a low detection limit of 2 nM (10 fmol within 5 μL sample solution), and shows good selectivity toward cytochrome c compared to interfering proteins such as hemoglobin and immunoglobulin G. The general strategy of the method can also be extended to aptamer or DNA based sensors.
Collapse
Affiliation(s)
- Yunfeng Xia
- Life and Environmental Science College, Shanghai Normal University, Shanghai, 200234, P R China
| | | | | | | | | | | | | |
Collapse
|
22
|
Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica F. Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2403-11. [PMID: 24311581 DOI: 10.1107/s0907444913022269] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/08/2013] [Indexed: 11/10/2022]
Abstract
Potent second-generation thrombin aptamers adopt a duplex-quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and control their recruitment in thrombin binding.
Collapse
Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, I-80126 Naples, Italy
| | | | | | | | | |
Collapse
|
23
|
Pan J, Zhang H, Cha TG, Chen H, Choi JH. Multiplexed optical detection of plasma porphyrins using DNA aptamer-functionalized carbon nanotubes. Anal Chem 2013; 85:8391-6. [PMID: 23899095 DOI: 10.1021/ac401794n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A novel optical platform based on DNA aptamer-functionalized SWCNTs (a-SWCNTs) is developed for multiplexed detection of plasma porphyrins. We have investigated the interactions of a-SWCNTs with heme (FePP), protoporphyrin (PP), coproporphyrin (CP), and uroporphyrin (UP). Two interaction mechanisms, specific binding, and nonspecific adsorption between porphyrins and a-SWCNTs are proposed based on observed optical signal modulations. The optical transduction signals are used to formulate a multiplexed detection strategy for the four porphyrin species without a laborious separation process. The detection scheme is sensitive, selective, and can readily be used for porphyrin detection in plasma samples when combined with a solvent extraction method. Our optical platform offers novel analytical tools for probing the surface chemistry at the porphyrin/a-SWCNTs interface, showing great promise for both research and clinical applications.
Collapse
Affiliation(s)
- Jing Pan
- School of Mechanical Engineering, Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | | | |
Collapse
|
24
|
Pelossof G, Tel-Vered R, Shimron S, Willner I. Controlling interfacial electron transfer and electrocatalysis by pH- or ion-switchable DNA monolayer-modified electrodes. Chem Sci 2013. [DOI: 10.1039/c2sc22193d] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
|
25
|
Renaud de la Faverie A, Hamon F, Di Primo C, Largy E, Dausse E, Delaurière L, Landras-Guetta C, Toulmé JJ, Teulade-Fichou MP, Mergny JL. Nucleic acids targeted to drugs: SELEX against a quadruplex ligand. Biochimie 2011; 93:1357-67. [DOI: 10.1016/j.biochi.2011.05.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 05/24/2011] [Indexed: 01/01/2023]
|
26
|
Goda T, Miyahara Y. Thermo-responsive molecular switches for ATP using hairpin DNA aptamers. Biosens Bioelectron 2011; 26:3949-52. [PMID: 21419618 DOI: 10.1016/j.bios.2011.02.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/10/2011] [Accepted: 02/24/2011] [Indexed: 01/16/2023]
Abstract
Increasingly detailed structural designs are highlighting the utility of oligonucleotide aptamers for diagnostic systems. The primary and secondary structures of DNA aptamers are responsible for structural displacement upon target binding. We revealed that a hairpin aptamer enabled to capture target ATP only when the aptamer transformed into the open-loop conformation by temperature-induced self-dissociation. The recognition event with conformational transition of the hairpin aptamer on gold was identified by electrochemical impedance spectroscopy. The results presented label-free detections above 37°C with high sensitivity and specificity. The hairpin aptamer as a thermo-responsive ligand has much generality for its use as "smart" nano-switches.
Collapse
Affiliation(s)
- Tatsuro Goda
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan
| | | |
Collapse
|
27
|
Takashima H, Kitano M, Hirai C, Murakami H, Tsukahara K. Photophysical and DNA-binding properties of cytochrome c modified with a platinum(II) complex. J Phys Chem B 2011; 114:13889-96. [PMID: 20936831 DOI: 10.1021/jp106121n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c (cyt c) derivatives modified with a platinum(II) complex at the lysine residue, cyt c(III)-[Pt(bpy)(dapap)](1) {bpy = 2,2'-bipyridine, and dapap = 3-(2,3-diaminopropionylamino)propionic acid}, have been prepared. The modified residues are Lys8, Lys13, Lys55, Lys60, Lys73, and Lys88. In the case of the cyt c(III)-[Pt(bpy)(dapap)](1) dyad, the photoexcited singlet state of (1)([Pt(bpy)(dapap)](1))* was quenched by the heme Fe(III) moiety through the intramolecular photoinduced energy-transfer reaction via a through-space mechanism. Next, in the presence of calf thymus (CT)-DNA, the DNA-responsive fluorescence properties of cyt c(III)-[Pt(bpy)(dapap)](1) isomers were investigated. The order of the obtained binding constants between the cyt c(III)-[Pt(bpy)(dapap)](1) isomer and CT-DNA in an aqueous solution suggested that the electrostatic interaction is one of the important factors to stabilize the cyt c-DNA complex. Finally, we discussed the rotational motion of the [Pt(bpy)(dapap)](2+) moiety at the surface of cyt c by fluorescence anisotropy measurement. The increase in the anisotropy parameter, r, for each cyt c isomer clearly revealed that the noncovalent recognition of the [Pt(bpy)(dapap)](2+) moiety by CT-DNA is an essential event in the formation of the cyt c-DNA complex and generation of DNA-sensitive fluorescence signals.
Collapse
Affiliation(s)
- Hiroshi Takashima
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara, 630-8506 Japan.
| | | | | | | | | |
Collapse
|
28
|
Sharon E, Freeman R, Willner I. CdSe/ZnS quantum dots-G-quadruplex/hemin hybrids as optical DNA sensors and aptasensors. Anal Chem 2011; 82:7073-7. [PMID: 20695436 DOI: 10.1021/ac101456x] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The luminescence of CdSe/ZnS QDs is quenched via electron transfer by hemin/G-quadruplex associated with the particles. This phenomenon is implemented to develop DNA sensors or aptasensors by tailoring hairpin-functionalized QDs that generate the hemin/G-quadruplex quenchers upon sensing of the respective analytes.
Collapse
Affiliation(s)
- Etery Sharon
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | | |
Collapse
|
29
|
Yeung MCL, Wong KMC, Tsang YKT, Yam VWW. Aptamer-induced self-assembly of a NIR-emissive platinum(II) terpyridyl complex for label- and immobilization-free detection of lysozyme and thrombin. Chem Commun (Camb) 2010; 46:7709-11. [PMID: 20871876 DOI: 10.1039/c0cc02631j] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With the aptamer-induced self-assembly feature of NIR-emissive platinum(ii) terpyridyl complex, a "proof-of-principle" concept in label- and immobilization-free probing strategies of lysozyme and thrombin has been demonstrated with good selectivity and specificity.
Collapse
Affiliation(s)
- Margaret Ching-Lam Yeung
- Institute of Molecular Functional Materials (Areas of Excellence Scheme, University Grants Committee, Hong Kong) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, PR China
| | | | | | | |
Collapse
|
30
|
Li T, Dong S, Wang E. G-quadruplex aptamers with peroxidase-like DNAzyme functions: which is the best and how does it work? Chem Asian J 2009; 4:918-922. [PMID: 19422006 DOI: 10.1002/asia.200900019] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Some G-quadruplex DNA aptamers have been found to strongly bind hemin to form DNAzymes with peroxidase-like activity. To help determine the most suitable DNAzymes and to understand how they work, five previously reported G-quadruplex aptamers were compared for their binding affinity and then the potential catalytic mechanism of their corresponding hemin-G-quadruplex DNAzymes was explored. Among these aptamers, a G-quadruplex named AGRO100 was shown to possess the highest hemin-binding affinity and the best DNAzyme function. This means that AGRO100 is the most ideal candidate for DNAzyme-based analysis. Furthermore, we found the peroxidase-like activity of DNAzyme to be primarily dependent on the concentration of H(2)O(2) and independent of that of the peroxidase substrate (that is, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)diammonium salt). Accordingly, a reaction mechanism for DNAzyme-catalyzed peroxidation is proposed. This study provides new insights into the G-quadruplex-based DNAzymes and will help us to further extend their applications in the analytical field.
Collapse
Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | | | | |
Collapse
|
31
|
Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | | | | |
Collapse
|
32
|
Li T, Wang E, Dong S. A grafting strategy for the design of improved G-quadruplex aptamers and high-activity DNAzymes. PLoS One 2009; 4:e5126. [PMID: 19357767 PMCID: PMC2663033 DOI: 10.1371/journal.pone.0005126] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 03/13/2009] [Indexed: 11/19/2022] Open
Abstract
Nucleic acid aptamers are generally obtained by in vitro selection. Some have G-rich consensus sequences with ability to fold into the four-stranded structures known as G-quadruplexes. A few G-quadruplex aptamers have proven to bind hemin to form a new class of DNAzyme with the peroxidase-like activity, which can be significantly promoted by appending an appropriate base-pairing duplex onto the G-quadruplex structures of aptamers. Knowing the structural role of base pairing, here we introduce a novel grafting strategy for the design of improved G-quadruplex aptamers and high-activity DNAzymes. To demonstrate this strategy, three existing G-quadruplex aptamers are chosen as the first generation. A base-pairing DNA duplex is grafted onto the G-quadruplex motif of the first generation aptamers. Consequently, three new aptamers with the quadruplex/duplex DNA structures are produced as the second generation. The hemin-binding affinities and DNAzyme functions of the second generation aptamers are characterized and compared with the first generation. The results indicate three G-quadruplex aptamers obtained by the grafting strategy have more excellent properties than the corresponding original aptamers. Our findings suggest that, if the structures and functions of existing aptamers are thoroughly known, the grafting strategy can be facilely utilized to improve the aptamer properties and thereby producing better next-generation aptamers. This provides a simple but effective approach to the design of nucleic acid aptamers and DNAzymes.
Collapse
Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | | | | |
Collapse
|
33
|
Li T, Wang E, Dong S. Base-pairing directed folding of a bimolecular G-quadruplex: new insights into G-quadruplex-based DNAzymes. Chemistry 2009; 15:2059-63. [PMID: 19137559 DOI: 10.1002/chem.200801825] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Base pairs, magic hands: An additional base-pairing duplex is utilized to control the folding topologies of a bimolecular G-quadruplex formed by two G-rich single-stranded DNAs (see picture), which is dependent on the position of base pairs. This study clearly reveals an important intrinsic role of additional base pairs in the G-quadruplex structure, and also provides a clue to the formation mechanism of the G-quadruplex-based DNAzyme.
Collapse
Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | | | | |
Collapse
|
34
|
Li T, Dong S, Wang E. Label-Free Colorimetric Detection of Aqueous Mercury Ion (Hg2+) Using Hg2+-Modulated G-Quadruplex-Based DNAzymes. Anal Chem 2009; 81:2144-9. [DOI: 10.1021/ac900188y] [Citation(s) in RCA: 422] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China, and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China, and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China, and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China
| |
Collapse
|
35
|
Li T, Shi L, Wang E, Dong S. Multifunctional G-quadruplex aptamers and their application to protein detection. Chemistry 2009; 15:1036-42. [PMID: 19053089 DOI: 10.1002/chem.200801282] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Two significant G-quadruplex aptamers named AGRO100 and T30695 are identified as multifunctional aptamers that can bind the protein ligands nucleolin or HIV-1 integrase and hemin. Besides their strong binding to target proteins, both AGRO100 and T30695 exhibit high hemin-binding affinities comparable to that of the known aptamer (termed PS2M) selected by the in vitro evolution process. Most importantly, their corresponding hemin-DNA complexes reveal excellent peroxidase-like activities, higher than that of the reported hemin-PS2M DNAzyme. This enables these multifunctional aptamers to be applied to the sensitive detection of proteins, which is demonstrated by applying AGRO100 to the chemiluminescence detection of nucleolin expressed at the surface of HeLa cells. Based on the specific AGRO100-nucleolin interaction, the surface-expressed nucleolin of HeLa cells is labeled in situ with the hemin-AGRO100 DNAzyme, and then determined in the luminol-H(2)O(2) system. Through this approach, the sensitive detection of total nucleolin expressed at the surface of about 6000 HeLa cells is accomplished. Our results suggest that exploiting new functions of existing aptamers will help to extend their potential applications in the biochemical field.
Collapse
Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | | | | | | |
Collapse
|
36
|
Li T, Li B, Wang E, Dong S. G-quadruplex-based DNAzyme for sensitive mercury detection with the naked eye. Chem Commun (Camb) 2009:3551-3. [DOI: 10.1039/b903993g] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
37
|
Zhu X, Zhang W, Xiao H, Huang J, Li G. Electrochemical study of a hemin–DNA complex and its activity as a ligand binder. Electrochim Acta 2008. [DOI: 10.1016/j.electacta.2008.01.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
38
|
Zhao Q, Li XF, Le XC. Aptamer-modified monolithic capillary chromatography for protein separation and detection. Anal Chem 2008; 80:3915-20. [PMID: 18363332 DOI: 10.1021/ac702567x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A capillary chromatography technique was developed for the separation and detection of proteins, taking advantage of the specific affinity of aptamers and the porous property of the monolith. A biotinylated DNA aptamer targeting cytochrome c was successfully immobilized on a streptavidin-modified polymer monolithic capillary column. The aptamer, having a G-quartet structure, could bind to both cytochrome c and thrombin, enabling the separation of these proteins from each other and from the unretained proteins. Elution of strongly bound proteins was achieved by increasing the ionic strength of the mobile phase. The following proteins were tested using the aptamer affinity monolithic columns: human immunoglobulin G (IgG), hemoglobin, transferrin, human serum albumin, cytochrome c, and thrombin. Determination of cytochrome c and thrombin spiked into dilute serum samples showed no interference from the serum matrix. The benefit of porous properties of the affinity monolithic column was demonstrated by selective capture and preconcentration of thrombin at low ionic strength and subsequent rapid elution at high ionic strength. The combination of the polymer monolithic column and the aptamer affinities makes the aptamer-modified monolithic columns useful for protein detection and separation.
Collapse
Affiliation(s)
- Qiang Zhao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada T6G 2G3
| | | | | |
Collapse
|
39
|
Borbone N, Oliviero G, Amato J, Piccialli G, Mayol L, Miccio L, Pescen G, Sasso A. Optical tweezers as a probe for oligodeoxyribonucleotide structuration. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1295-9. [PMID: 18066771 DOI: 10.1080/15257770701530541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The aim of this work is to investigate if the optical tweezers (OT) are suitable as a diagnostic tool for monitoring the oligodeoxyribonucleotide (ODN) structural behavior in solution. Preliminary experiments, performed on the quadruplex formed by the ODN sequence TGGGGT, showed that the OT can be used as a probe for ODN structuration by monitoring the medium viscosity changes associated with ODN folding-unfolding processes.
Collapse
Affiliation(s)
- Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università di Napoli Federico II, Faculty of Pharmacy, via Domenico Montesano 49, Naples 80131, Italy.
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Warsinke A. Electrochemical biochips for protein analysis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 109:155-93. [PMID: 17928973 DOI: 10.1007/10_2007_079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Proteins bear important functions for most life processes. It is estimated that the human proteome comprises more than 250,000 proteins. Over the last years, highly sophisticated and powerful instruments have been developed that allow their detection and characterization with great precision and sensitivity. However, these instruments need well-equipped laboratories and a well-trained staff. For the determination of proteins in a hospital, in a doctor's office, or at home, low-budget protein analysis methods are needed that are easy to perform. In addition, for a proteomic approach, highly parallel measurements with small sample sizes are required. Biochips are considered as promising tools for such applications. The following chapter describes electrochemical biochips for protein analysis that use antibodies or aptamers as recognition elements.
Collapse
Affiliation(s)
- Axel Warsinke
- University of Potsdam, Institute of Biochemistry and Biology, iPOC Research Group, Karl-Liebknecht-Strasse 24-25, D-14476 Golm, Germany.
| |
Collapse
|
41
|
Willner I, Cheglakov Z, Weizmann Y, Sharon E. Analysis of DNA and single-base mutations using magnetic particles for purification, amplification and DNAzyme detection. Analyst 2008; 133:923-7. [DOI: 10.1039/b802015a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
42
|
Petraccone L, Erra E, Randazzo A, Giancola C. Energetic aspects of locked nucleic acids quadruplex association and dissociation. Biopolymers 2007; 83:584-94. [PMID: 16944520 DOI: 10.1002/bip.20591] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The design of modified nucleic acid aptamers is improved by considering thermodynamics and kinetics of their association/dissociation processes. Locked Nucleic Acids (LNA) is a promising class of nucleic acid analogs. In this work the thermodynamic and kinetic properties of a LNA quadruplex formed by the TGGGT sequence, containing only conformationally restricted LNA residues, are reported and compared to those of 2'-OMe-RNA (O-RNA) and DNA quadruplexes. The thermodynamic analysis indicates that the sugar-modified quadruplexes (LNA and O-RNA) are stabilized by entropic effects. The kinetic analysis shows that LNA and O-RNA quadruplexes are characterized by a slower dissociation and a faster association with respect to DNA quadruplex. Interestingly, the LNA quadruplex formation process shows a second-order kinetics with respect to single strand concentration and has a negative activation energy. To explain these data, a mechanism for tetramer formation with two intermediate states was proposed.
Collapse
Affiliation(s)
- Luigi Petraccone
- Dipartimento di Scienze Farmaceutiche, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy
| | | | | | | |
Collapse
|
43
|
Joachimi A, Mayer G, Hartig JS. A new anticoagulant-antidote pair: control of thrombin activity by aptamers and porphyrins. J Am Chem Soc 2007; 129:3036-7. [PMID: 17319665 DOI: 10.1021/ja0677822] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Astrid Joachimi
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | | | | |
Collapse
|
44
|
Warsinke A, Nagel B. Towards Separation‐Free Electrochemical Affinity Sensors by Using Antibodies, Aptamers, and Molecularly Imprinted Polymers—A Review. ANAL LETT 2006. [DOI: 10.1080/00032710600853903] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
45
|
Cheglakov Z, Weizmann Y, Beissenhirtz MK, Willner I. Ultrasensitive detection of DNA by the PCR-Induced generation of DNAzymes: the DNAzyme primer approach. Chem Commun (Camb) 2006:3205-7. [PMID: 17028744 DOI: 10.1039/b605205c] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultrasensitive detection of DNA is achieved by PCR-induced evolution of a DNAzyme.
Collapse
Affiliation(s)
- Zoya Cheglakov
- Institute of Chemistry and Farkas Center for Light-Induced Processes, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | | | | | | |
Collapse
|
46
|
Clark J, Smith SS. Application of Nanoscale Bioassemblies to Clinical Laboratory Diagnostics. Adv Clin Chem 2006; 41:23-48. [PMID: 28682750 DOI: 10.1016/s0065-2423(05)41002-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This chapter summarizes progress in several approaches and devices that will improve and augment existing diagnostic techniques. The term bionanotechnology has been used to describe the science that supports the construction of nanoscale bioassemblies. In each of the present applications to diagnostics, bionanotechnological devices play a largely passive role. Cell surface targeting with an antibody, a growth factor, or a small molecule ligand achieves a new level of sophistication, however, it is still a passive approach. While the induced conformational changes associated with the binding of dendrimers or molecular beacons are somewhat more complex responses to the local environment, they are still largely passive mechanistically. Dynamic devices that change color with time of incubation based on the presence or absence of secondary or tertiary cellular markers within a population exhibiting a primary marker would be of considerable utility. Dynamic nanoscale devices of this type await the application of the rules of assembly associated with the scaffolds described earlier and perhaps the discovery and application of new rules of assembly and new scaffolds.
Collapse
Affiliation(s)
- Jarrod Clark
- City of Hope National Medical Center and Beckman Research Institute, Duarte, California
| | - Steven S Smith
- City of Hope National Medical Center and Beckman Research Institute, Duarte, California
| |
Collapse
|
47
|
Oliviero G, Amato J, Borbone N, Galeone A, Varra M, Piccialli G, Mayol L. Unusual monomolecular DNA quadruplex structures using bunch-oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:739-41. [PMID: 16248027 DOI: 10.1081/ncn-200060048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The chemical synthesis of several G-rich bunch-oligonucleotides and the structural characterization of the corresponding monomolecular G-quadruplexes (I-IV) have been reported. The synthetic method allow the achievement of monomolecular DNA quadruplex structures having unusual and predeterminable oligodeoxyribonucleotide (ODN) strand orientation.
Collapse
Affiliation(s)
- Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università di Napoli Federico II, Napoli, Italy.
| | | | | | | | | | | | | |
Collapse
|
48
|
Borbone N, Oliviero G, Galeone A, Piccialli G, Varra M, Mayol L. A bunch-oligonucleotide forming stable monomolecular quadruplex containing a T-tetrad. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:443-6. [PMID: 16247967 DOI: 10.1081/ncn-200059989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The chemical synthesis of bunch-ODN I and II prone to form quadruplex structures containing G-and T-tetrads has been reported. Structural studies were performed by 1H-NMR and CD melting experiments.
Collapse
Affiliation(s)
- Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Napoli, Italy.
| | | | | | | | | | | |
Collapse
|
49
|
Ding X, Li J, Hu J, Li Q. Electrochemical study of the interaction between cytochrome c and DNA at a modified gold electrode. Anal Biochem 2005; 339:46-53. [PMID: 15766709 DOI: 10.1016/j.ab.2004.11.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Indexed: 11/29/2022]
Abstract
The direct electron transfer of surface-confined horse heart cytochrome c (Cyt c) was achieved using COOH-terminated alkanethiolate-modified gold electrode. Later DNA was immobilized on the two-layer modified electrode. The quantitative determination of DNA was explored and the interaction between cytochrome c and DNA was studied. The binding site sizes were determined to be 15 bp per Cyt c molecule with double-stranded (ds) DNA and 30 nucleotides binding one Cyt c molecule with single-stranded (ss) DNA. At the dsDNA/Cyt c/MUA/Au electrode, the rate constant of oxidation electron transfer k(s,ox)=1.59x10(-3)cms-1 was obtained, at the ssDNA/Cyt c/MUA/Au electrode, the value was 2.43x10(-3)ms-1 when the scan rate was 1.0V/s. The different electrodes were characterized with electrochemical quartz crystal microbalance and atomic force microscope.
Collapse
Affiliation(s)
- XiaoQin Ding
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | | | | | | |
Collapse
|
50
|
Cheng-Lin Z, Mei-Chuan L, Ping L, Yue-Zhong X, Yu-Xiao C, Fen-Fen Z, Xiao-Li W, Li-Tong J. Fabrication of ZnO Nanorod Modified Electrode and Its Application to the Direct Electrochemical Determination of Hemoglobin and Cytochromec. CHINESE J CHEM 2005. [DOI: 10.1002/cjoc.200590144] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|