1
|
Ooi JSY, Lim CR, Hua CX, Ng JF, New SY. DNA Hairpins and Stabilization of Gold Nanoparticles: Effect of Stem Length and Toehold Composition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15200-15207. [PMID: 37851548 DOI: 10.1021/acs.langmuir.3c01748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
This study investigates the effect of DNA hairpins on the stabilization of gold nanoparticles (AuNPs) against salt-induced aggregation (SIA) in label-free colorimetric biosensors. AuNPs were incubated with DNA hairpins of varying stem lengths and toehold sequences, followed by the addition of NaCl, before being subjected to ultraviolet-visible (UV-vis) measurement. Results showed that hairpins with longer stems generally provide better stabilization of AuNPs (18-bp >14-bp >10-bp). No improvement was observed for 14- and 18-bp hairpins with a toehold beyond 8A, which may be attributed to saturated adsorption of hairpins on the gold surface. For 14-bp hairpins with an 8-mer homopolymeric toehold, we observed a stabilization trend of A > C > G > T, similar to the reported trend of ssDNA. For variants containing ≥50% adenine as terminal bases, introducing cytosine or guanine as preceding bases could also result in strong stabilization. As the proportion of adenine decreases, variants with guanine or thymine provide less protection against SIA, especially for guanine-rich hairpins (≥6G) that could form G-quadruplexes. Such findings could serve as guidelines for researchers to design suitable DNA hairpins for label-free AuNP-based biosensors.
Collapse
Affiliation(s)
- Jessica S Y Ooi
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Cher Ryn Lim
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Chai Xian Hua
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Jeck Fei Ng
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor's University, No. 1 Jalan Taylor's, 47500 Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Siu Yee New
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| |
Collapse
|
2
|
Zhang X, Zhang Z, Xue X, Fan T, Tan C, Liu F, Tan Y, Jiang Y. PROTAC Degrader of Estrogen Receptor α Targeting DNA-Binding Domain in Breast Cancer. ACS Pharmacol Transl Sci 2022; 5:1109-1118. [PMID: 36407946 PMCID: PMC9667539 DOI: 10.1021/acsptsci.2c00109] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Indexed: 12/24/2022]
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) are a powerful class of drugs that selectively degrade the proteins of interest (POIs) through cellular ubiquitination mechanisms. Estrogen receptor α (ERα) plays a vital role in the pathogenesis and treatment of breast cancer. In this work, the DNA-binding domain (DBD) of ERα was selected as the target to avoid drug resistance caused by the ligand-binding domain (LBD) of ERα. The estrogen response element (ERE), a natural DNA sequence binding with DBD of ERα, was chosen as a recognized unit of PROTAC. Therefore, we designed a nucleic acid-conjugated PROTAC, ERE-PROTAC, via a click reaction, in which the ERE sequence recruits ERα and the typical small molecule VH032 recruits the von Hippel-Lindau (VHL) E3 ligase. The proposed ERE-PROTAC showed to efficiently and reversibly degrade ERα in different breast cancer cells by targeting the DBD, indicating its potential to overcome the current resistance caused by LBD mutations.
Collapse
Affiliation(s)
| | | | - Xiaoqi Xue
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Tingting Fan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Chunyan Tan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Feng Liu
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Ying Tan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| |
Collapse
|
3
|
Yaraki MT, Zahed Nasab S, Zare I, Dahri M, Moein Sadeghi M, Koohi M, Tan YN. Biomimetic Metallic Nanostructures for Biomedical Applications, Catalysis, and Beyond. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c00285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Shima Zahed Nasab
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 143951561, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz 7178795844, Iran
| | - Mohammad Dahri
- Student Research Committee, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345, Iran
| | - Mohammad Moein Sadeghi
- Student Research Committee, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345, Iran
| | - Maedeh Koohi
- Department of Chemistry, Faculty of Science, University of Zanjan, Zanjan 45371-38791, Islamic Republic of Iran
| | - Yen Nee Tan
- Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K
- Newcastle Research and Innovation Institute, Newcastle University in Singapore, 80 Jurong East Street 21, No. 05-04, 609607, Singapore
| |
Collapse
|
4
|
Tavakkoli Yaraki M, Hu F, Daqiqeh Rezaei S, Liu B, Tan YN. Metal-enhancement study of dual functional photosensitizers with aggregation-induced emission and singlet oxygen generation. NANOSCALE ADVANCES 2020; 2:2859-2869. [PMID: 36132415 PMCID: PMC9419615 DOI: 10.1039/d0na00182a] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/09/2020] [Indexed: 05/10/2023]
Abstract
Photosensitizers with aggregation-induced emission (AIE-PS) are attractive for image-guided photodynamic therapy due to their dual functional role in generating singlet oxygen and producing high fluorescent signal in the aggregated state. However, their brightness and treatment efficiency maybe limited in current practice. Herein we report the first systematic investigation on the metal-enhanced fluorescence (MEF) and singlet oxygen generation (ME-SOG) ability of our newly synthesized AIE-photosensitizers. The Ag@AIE-PS of varied sizes were prepared via layer-by-layer assembly with controlled distance between silver nanoparticles (AgNPs) and AIE-PS. A maximum of 6-fold enhancement in fluorescence and 2-fold increment in SOG were observed for the 85nmAg@AIE-PS. Comprehensive characterization and simulation were conducted to unravel the plasmon-enhancement mechanisms of Ag@AIE-PS. Results show that MEF of AIE-PS is determined by the enhanced electric field around AgNPs, while ME-SOG is dictated by the scattering efficiency of the metal core, where bigger AgNPs would result in larger enhancement factor. Furthermore, the optimum distance between AgNPs and AIE-PS to achieve maximum SOG enhancement is shorter than that required for the highest MEF. The correlation of MEF and ME-SOG found in this study is useful for designing new a generation of AIE-photosensitizers with high brightness and treatment efficiency towards practical theranostic application in the future.
Collapse
Affiliation(s)
- Mohammad Tavakkoli Yaraki
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (ASTAR) 138634 Singapore
- Department Chemical and Biomolecular Engineering, National University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Fang Hu
- Department Chemical and Biomolecular Engineering, National University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Soroosh Daqiqeh Rezaei
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (ASTAR) 138634 Singapore
- Department of Mechanical Engineering, National University of Singapore 9 Engineering Drive 1 117575 Singapore
| | - Bin Liu
- Department Chemical and Biomolecular Engineering, National University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Yen Nee Tan
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (ASTAR) 138634 Singapore
- Faculty of Science, Agriculture & Engineering, Newcastle University Newcastle Upon Tyne NE1 7RU UK
| |
Collapse
|
5
|
Tavakkoli Yaraki M, Daqiqeh Rezaei S, Tan YN. Simulation guided design of silver nanostructures for plasmon-enhanced fluorescence, singlet oxygen generation and SERS applications. Phys Chem Chem Phys 2020; 22:5673-5687. [PMID: 32103209 DOI: 10.1039/c9cp06029d] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Plasmonic nanostructures such as gold and silver could alter the intrinsic properties of fluorophores, photosensitizers or Raman reporters in their close vicinity. In this study, we have conducted systematic simulations to provide insight for the design of silver nanostructures with appropriate geometrical features for metal-enhanced fluorescence (MEF), metal-enhanced singlet oxygen generation (ME-SOG) and surface-enhanced Raman scattering (SERS) applications. The size-dependent optical properties and electric field enhancement of single and dimeric nanocubes were simulated. The extinction spectra of silver nanocubes were analysed by the multipole expansion method. Results show that a suitable size of Ag nanocubes for MEF and ME-SOG can be selected based on their maximum light scattering yield, the excitation and emission wavelengths of a particular fluorophore/photosensitizer and their maximum spectral overlap. Simulations of the 'hot-spot' or gap distance between two silver nanocubes with different configurations (i.e., face-to-face, edge-to-edge and corner-to-corner) were also performed. A direct correlation was found between the size and enhanced electric field around the Ag nanocubes simulated under 15 common Raman laser wavelengths from the UV to near-infrared region. The maximum SERS enhancement factor can be achieved by selecting the silver nanocubes with the right orientation, suitable edge length and gap distance that give the highest electric field at a specific Raman laser wavelength. It was also found that the higher order of silver nanostructures, e.g., trimer and tetramer, can lead to better enhancement effects. These simulation results can serve as generic guidelines to rationally design metal-enhancement systems including MEF, ME-SOG and SERS for different application needs without cumbersome optimization and tedious trial-and-error experimentation.
Collapse
Affiliation(s)
- Mohammad Tavakkoli Yaraki
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 138634, Singapore
| | | | | |
Collapse
|
6
|
Zhao VXT, Wong TI, Zheng XT, Tan YN, Zhou X. Colorimetric biosensors for point-of-care virus detections. MATERIALS SCIENCE FOR ENERGY TECHNOLOGIES 2020; 3:237-249. [PMID: 33604529 PMCID: PMC7148662 DOI: 10.1016/j.mset.2019.10.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 05/05/2023]
Abstract
Colorimetric biosensors can be used to detect a particular analyte through color changes easily by naked eyes or simple portable optical detectors for quantitative measurement. Thus, it is highly attractive for point-of-care detections of harmful viruses to prevent potential pandemic outbreak, as antiviral medication must be administered in a timely fashion. This review paper summaries existing and emerging techniques that can be employed to detect viruses through colorimetric assay design with detailed discussion of their sensing principles, performances as well as pros and cons, with an aim to provide guideline on the selection of suitable colorimetric biosensors for detecting different species of viruses. Among the colorimetric methods for virus detections, loop-mediated isothermal amplification (LAMP) method is more favourable for its faster detection, high efficiency, cheaper cost, and more reliable with high reproducible assay results. Nanoparticle-based colorimetric biosensors, on the other hand, are most suitable to be fabricated into lateral flow or lab-on-a-chip devices, and can be coupled with LAMP or portable PCR systems for highly sensitive on-site detection of viruses, which is very critical for early diagnosis of virus infections and to prevent outbreak in a swift and controlled manner.
Collapse
Affiliation(s)
- Victoria Xin Ting Zhao
- College of Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Ten It Wong
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Xin Ting Zheng
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Yen Nee Tan
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
- Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
| | - Xiaodong Zhou
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| |
Collapse
|
7
|
Recent development of nucleic acid nanosensors to detect sequence-specific binding interactions: From metal ions, small molecules to proteins and pathogens. SENSORS INTERNATIONAL 2020; 1:100034. [PMID: 34766041 PMCID: PMC7434487 DOI: 10.1016/j.sintl.2020.100034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
DNA carries important genetic instructions and plays vital roles in regulating biological activities in living cells. Proteins such as transcription factors binds to DNA to regulate the biological functions of DNA, and similarly many drug molecules also bind to DNA to modulate its functions. Due to the importance of protein-DNA and drug-DNA binding, there has been intense effort in developing novel nanosensors in the same length scale as DNA, to effectively study these binding interactions in details. In addition, aptamers can be artificially selected to detect metal ions and pathogens such as bacteria and viruses, making nucleic acid nanosensors more versatile in detecting a large variety of analytes. In this minireview, we first explained the different types and binding modes of protein-DNA and drug-DNA interactions in the biological systems, as well as aptamer-target binding. This was followed by the review of five types of nucleic acid nanosensors based on optical or electrochemical detection. The five types of nucleic acid nanosensors utilizing colorimetric, dynamic light scattering (DLS), surface-enhanced Raman spectroscopy (SERS), fluorescence and electrochemical detections have been recently developed to tackle some of the challenges in high-throughput screening technology for large scale analysis, which is especially useful for drug development and mass screening for pandemic outbreak such as SARS or COVID-19.
Collapse
|
8
|
Recent advances in metallic nanobiosensors development: Colorimetric, dynamic light scattering and fluorescence detection. SENSORS INTERNATIONAL 2020. [DOI: 10.1016/j.sintl.2020.100049] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
9
|
Pallares RM, Thanh NTK, Su X. Quantifying the binding between proteins and open chromatin-like DNA sequences with gold nanorods. Chem Commun (Camb) 2019; 55:15041-15044. [PMID: 31696164 DOI: 10.1039/c9cc07511a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of transcription factors to DNA is one of the main mechanisms in gene regulation. While transcription factors frequently bind to unwrapped long DNA sequences known as open chromatin structures, most bioassays that study protein-DNA binding rely on short oligonucleotide probes. In this work, we develop a gold nanorod-based colorimetric assay for the binding of transcription factors to DNA in long open chromatin-like structures. After the determination of the binding affinity and stoichiometry, we explored the effect of the probe length on the assay performance and compared it to other established techniques.
Collapse
Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
| | | | | |
Collapse
|
10
|
Wang H, Rao H, Luo M, Xue X, Xue Z, Lu X. Noble metal nanoparticles growth-based colorimetric strategies: From monocolorimetric to multicolorimetric sensors. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.06.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
11
|
Assah E, Goh W, Zheng XT, Lim TX, Li J, Lane D, Ghadessy F, Tan YN. Rapid colorimetric detection of p53 protein function using DNA-gold nanoconjugates with applications for drug discovery and cancer diagnostics. Colloids Surf B Biointerfaces 2018; 169:214-221. [DOI: 10.1016/j.colsurfb.2018.05.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 12/11/2022]
|
12
|
Uliana CV, Peverari CR, Afonso AS, Cominetti MR, Faria RC. Fully disposable microfluidic electrochemical device for detection of estrogen receptor alpha breast cancer biomarker. Biosens Bioelectron 2017; 99:156-162. [PMID: 28755608 DOI: 10.1016/j.bios.2017.07.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/05/2017] [Accepted: 07/16/2017] [Indexed: 02/08/2023]
Abstract
A novel fully disposable microfluidic electrochemical array device (µFED) was developed and successfully applied for detection of the biomarker estrogen receptor alpha (ERα). The µFED was constructed using low-cost materials and an inexpensive home cutter printer enabled the manufacture of dozens of µFEDs in less than 2h, at a cost of less than US$ 0.20 in material per device. The µFED incorporates counter and reference electrodes and eight carbon-based working electrodes, which were modified with DNA sequences known as estrogen response elements (DNA-ERE), where ERα binds specifically. Paramagnetic particles heavily decorated with anti-ERα antibody and horseradish peroxidase (MP-Ab-HRP) were used to efficiently capture ERα from the sample solution. The ERα-MP-Ab-HRP bioconjugate formed was injected into the µFED and incubated with the DNA-ERE-modified electrodes, followed by amperometric detection with application of -0.2V vs. Ag|AgCl while a mixture of H2O2 and hydroquinone was injected into the microfluidic device. An ultralow limit of detection of 10.0 fg mL-1 was obtained with the proposed method. The performance of the assay, in terms of sensitivity and reproducibility, was studied using undiluted calf serum, and excellent recoveries in the range of 94.7-108% were achieved for the detection of ERα in MCF-7 cell lysate. The µFED system can be easily constructed and applied for multiplex biomarker detection, making the device an excellent cost-effective alternative for cancer diagnosis, especially in developing countries.
Collapse
Affiliation(s)
- Carolina V Uliana
- Department of Chemistry, Federal University of São Carlos, São Carlos 13565-905, SP, Brazil
| | - Camila R Peverari
- Department of Chemistry, Federal University of São Carlos, São Carlos 13565-905, SP, Brazil
| | - André S Afonso
- Institute of Science, Engineering and Technology, UFVJM, Teófilo Otoni 39803-371, MG, Brazil
| | - Marcia R Cominetti
- Department of Gerontology, Federal University of São Carlos, São Carlos 13565-905, SP, Brazil
| | - Ronaldo C Faria
- Department of Chemistry, Federal University of São Carlos, São Carlos 13565-905, SP, Brazil.
| |
Collapse
|
13
|
Zheng XT, Xu HV, Tan YN. Bioinspired Design and Engineering of Functional Nanostructured Materials for Biomedical Applications. ACS SYMPOSIUM SERIES 2017. [DOI: 10.1021/bk-2017-1253.ch007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- Xin Ting Zheng
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 138634
- Division of Chemical and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore 117543
| | - Hesheng Victor Xu
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 138634
- Division of Chemical and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore 117543
| | - Yen Nee Tan
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore 138634
- Division of Chemical and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore 117543
| |
Collapse
|
14
|
Bayle S, Chopineau J, Roig B, Habauzit D. Estrogen receptor preparation effects on the receptor–DNA interaction by surface plasmon resonance. Anal Bioanal Chem 2016; 408:8257-8262. [DOI: 10.1007/s00216-016-9967-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/06/2016] [Accepted: 09/22/2016] [Indexed: 12/22/2022]
|
15
|
Ahn J, Choi Y, Lee AR, Lee JH, Jung JH. A duplex DNA–gold nanoparticle probe composed as a colorimetric biosensor for sequence-specific DNA-binding proteins. Analyst 2016; 141:2040-5. [DOI: 10.1039/c6an00033a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The SPL-12-mediated change of Au aggregation via duplex DNA–SPL-12 interactions could be utilized for colorimetric sensing of SPL-12 using duplex DNA–Au.
Collapse
Affiliation(s)
- Junho Ahn
- Department of Chemistry and Research Institute of Natural Sciences
- Gyeongsang National University
- Jinju 660-701
- Korea
| | - Yeonweon Choi
- Department of Chemistry and Research Institute of Natural Sciences
- Gyeongsang National University
- Jinju 660-701
- Korea
| | - Ae-Ree Lee
- Department of Chemistry and Research Institute of Natural Sciences
- Gyeongsang National University
- Jinju 660-701
- Korea
| | - Joon-Hwa Lee
- Department of Chemistry and Research Institute of Natural Sciences
- Gyeongsang National University
- Jinju 660-701
- Korea
| | - Jong Hwa Jung
- Department of Chemistry and Research Institute of Natural Sciences
- Gyeongsang National University
- Jinju 660-701
- Korea
| |
Collapse
|
16
|
Seow N, Tan YN, Yung LYL, Su X. DNA-Directed Assembly of Nanogold Dimers: A Unique Dynamic Light Scattering Sensing Probe for Transcription Factor Detection. Sci Rep 2015; 5:18293. [PMID: 26678946 PMCID: PMC4683372 DOI: 10.1038/srep18293] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/13/2015] [Indexed: 12/16/2022] Open
Abstract
We have developed a unique DNA-assembled gold nanoparticles (AuNPs) dimer for dynamic light scattering (DLS) sensing of transcription factors, exemplified by estrogen receptor (ER) that binds specifically to a double-stranded (ds) DNA sequence containing estrogen response element (ERE). Here, ERE sequence is incorporated into the DNA linkers to bridge the AuNPs dimer for ER binding. Coupled with DLS, this AuNP dimer-based DLS detection system gave distinct readout of a single ‘complex peak’ in the presence of the target molecule (i.e., ER). This unique signature marked the first time that such nanostructures can be used to study transcription factor-DNA interactions, which DLS alone cannot do. This was also unlike previously reported AuNP-DLS assays that gave random and broad distribution of particles size upon target binding. In addition, the ERE-containing AuNP dimers could also suppress the light-scattering signal from the unbound proteins and other interfering factors (e.g., buffer background), and has potential for sensitive detection of target proteins in complex biological samples such as cell lysates. In short, the as-developed AuNP dimer probe coupled with DLS is a simple (mix and test), rapid (readout in ~5 min) and sensitive (low nM levels of ER) platform to detect sequence-specific protein-DNA binding event.
Collapse
Affiliation(s)
- Nianjia Seow
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, Singapore 119260, Singapore
| | - Yen Nee Tan
- Institute of Material Research and Engineering, ASTAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
| | - Lin-Yue Lanry Yung
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, Singapore 119260, Singapore
| | - Xiaodi Su
- Institute of Material Research and Engineering, ASTAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
| |
Collapse
|
17
|
Li N, Su X, Lu Y. Nanomaterial-based biosensors using dual transducing elements for solution phase detection. Analyst 2015; 140:2916-43. [PMID: 25763412 DOI: 10.1039/c4an02376e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Biosensors incorporating nanomaterials have demonstrated superior performance compared to their conventional counterparts. Most reported sensors use nanomaterials as a single transducer of signals, while biosensor designs using dual transducing elements have emerged as new approaches to further improve overall sensing performance. This review focuses on recent developments in nanomaterial-based biosensors using dual transducing elements for solution phase detection. The review begins with a brief introduction of the commonly used nanomaterial transducers suitable for designing dual element sensors, including quantum dots, metal nanoparticles, upconversion nanoparticles, graphene, graphene oxide, carbon nanotubes, and carbon nanodots. This is followed by the presentation of the four basic design principles, namely Förster Resonance Energy Transfer (FRET), Amplified Fluorescence Polarization (AFP), Bio-barcode Assay (BCA) and Chemiluminescence (CL), involving either two kinds of nanomaterials, or one nanomaterial and an organic luminescent agent (e.g. organic dyes, luminescent polymers) as dual transducers. Biomolecular and chemical analytes or biological interactions are detected by their control of the assembly and disassembly of the two transducing elements that change the distance between them, the size of the fluorophore-containing composite, or the catalytic properties of the nanomaterial transducers, among other property changes. Comparative discussions on their respective design rules and overall performances are presented afterwards. Compared with the single transducer biosensor design, such a dual-transducer configuration exhibits much enhanced flexibility and design versatility, allowing biosensors to be more specifically devised for various purposes. The review ends by highlighting some of the further development opportunities in this field.
Collapse
Affiliation(s)
- Ning Li
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, 117602 Singapore.
| | | | | |
Collapse
|
18
|
Lukman S, Moh Aung KM, Liang Lim MG, Hong S, Tan SK, Cheung E, Su X. Hybrid assembly of DNA-coated gold nanoparticles with water soluble conjugated polymers for studying protein–DNA interaction and ligand inhibition. RSC Adv 2014. [DOI: 10.1039/c3ra46752j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
|
19
|
Lukman S, Aung KMM, Liu J, Liu B, Su X. Hybrid sensor using gold nanoparticles and conjugated polyelectrolytes for studying sequence rule in protein-DNA interactions. ACS APPLIED MATERIALS & INTERFACES 2013; 5:12725-12734. [PMID: 24221695 DOI: 10.1021/am404120q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein-DNA interactions play center roles in many biological processes. Studying sequence specific protein-DNA interactions and revealing sequence rules require sensitive and quantitative methodologies that are capable of capturing subtle affinity difference with high accuracy and in a high throughput manner. In this study, double stranded DNA-conjugated gold nanoparticles (dsDNA-AuNPs) and water-soluble conjugated polyelectrolytes (CPEs) are used as cooperative sensing elements to construct a suit of hybrid sensors for detecting protein-DNA interactions, exploiting the differential Förster resonance energy transfer (FRET) with and without protein binding. Through a proper selection of CPEs in terms of charge properties relative to the charge of dsDNA-AuNPs and emission wavelengths relative to the AuNP extinction peak, the hybrid sensors can be constructed into "light-on", "light-off", and "two-way" models. Protein binding can be detected by fluorescence recovery, fluorescence quenching, or both ways, respectively. The "two-way" sensor allows for detection of proteins of any charge properties or unknown charge properties. With estrogen receptor (ERα and ERβ), their consensus DNA (5'-GGTCAnnnTGACC-5') element, and all 15 possible singly mutated elements (i.e., 3 possible base substitutions at each of 1 to 5 positions from left to right of the 5' end half site, GGTCA), we have demonstrated the accuracy of the hybrids sensors for determination of binding affinity constant, binding stoichiometry, and site- and nucleotide-specific binding energy matrix. The in vitro binding energy determined by the hybrid sensors correlates very well with the energy matrix computed from in vivo genome-wide ERα binding data using Thermodynamic Modeling of ChIP-Seq (rank correlation coefficient 0.98). The high degree of correlation of the in vitro energy matrix versus the in vivo matrix renders the new method a highly reliable alternative for understanding in vivo protein binding in the whole genome.
Collapse
Affiliation(s)
- Steven Lukman
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR) , Singapore
| | | | | | | | | |
Collapse
|
20
|
Aung KMM, New SY, Hong S, Sutarlie L, Lim MGL, Tan SK, Cheung E, Su X. Studying forkhead box protein A1-DNA interaction and ligand inhibition using gold nanoparticles, electrophoretic mobility shift assay, and fluorescence anisotropy. Anal Biochem 2013; 448:95-104. [PMID: 24291642 DOI: 10.1016/j.ab.2013.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 11/11/2013] [Accepted: 11/17/2013] [Indexed: 10/26/2022]
Abstract
Forkhead box protein 1 (FoxA1) is a member of the forkhead family of winged helix transcription factors that plays pivotal roles in the development and differentiation of multiple organs and in the regulation of estrogen-stimulated genes. Conventional analytical methods-electrophoretic mobility shift assay (EMSA) and fluorescence anisotropy (FA)-as well as a gold nanoparticles (AuNPs)-based assay were used to study DNA binding properties of FoxA1 and ligand interruption of FoxA1-DNA binding. In the AuNPs assay, the distinct ability of protein-DNA complex to protect AuNPs against salt-induced aggregation was exploited to screen sequence selectivity and determine the binding affinity constant based on AuNPs color change and absorbance spectrum shift. Both conventional EMSA and FA and the AuNPs assay suggested that FoxA1 binds to DNA in a core sequence-dependent manner and the flanking sequence also played a role to influence the affinity. The EMSA and AuNPs were found to be more sensitive than FA in differentiation of sequence-dependent affinity. With the addition of a spin filtration step, AuNPs assay has been extended for studying small molecular ligand inhibition of FoxA1-DNA interactions enabling drug screening. The results correlate very well with those obtained using FA.
Collapse
Affiliation(s)
- Khin Moh Moh Aung
- Institute of Materials Research and Engineering, Agency for Science, Technology, and Research (A(*)STAR), Singapore
| | - Siu Yee New
- Institute of Materials Research and Engineering, Agency for Science, Technology, and Research (A(*)STAR), Singapore
| | - Shuzhen Hong
- Cancer Biology and Pharmacology, Genome Institute of Singapore, Agency for Science, Technology, and Research (A(*)STAR), Singapore
| | - Laura Sutarlie
- Institute of Materials Research and Engineering, Agency for Science, Technology, and Research (A(*)STAR), Singapore
| | - Michelle Gek Liang Lim
- Cancer Biology and Pharmacology, Genome Institute of Singapore, Agency for Science, Technology, and Research (A(*)STAR), Singapore
| | - Si Kee Tan
- Cancer Biology and Pharmacology, Genome Institute of Singapore, Agency for Science, Technology, and Research (A(*)STAR), Singapore
| | - Edwin Cheung
- Cancer Biology and Pharmacology, Genome Institute of Singapore, Agency for Science, Technology, and Research (A(*)STAR), Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore.
| | - Xiaodi Su
- Institute of Materials Research and Engineering, Agency for Science, Technology, and Research (A(*)STAR), Singapore.
| |
Collapse
|
21
|
Gao T, Ning L, Li C, Wang H, Li G. A colorimetric method for protein assay via exonuclease III-assisted signal attenuation strategy and specific DNA-protein interaction. Anal Chim Acta 2013; 788:171-6. [PMID: 23845497 DOI: 10.1016/j.aca.2013.06.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/16/2013] [Accepted: 06/19/2013] [Indexed: 01/01/2023]
Abstract
Taking advantage of exonuclease III (Exo III)-assisted signal attenuation strategy and the protection of DNA from Exo III-mediated digestion by specific DNA-protein interaction, a colorimetric method is proposed in this paper for protein assay. Specifically, in the absence of target protein, Exo III-assisted signal attenuation can be achieved by digesting the report DNA in a complex formed by the hybridization of a report DNA and a probe DNA. Nevertheless, in the presence of target protein, the binding of the analyte to the probe DNA will inhibit the Exo III-assisted nucleotides cleavage, so that cyclic signal attenuation is blocked. Therefore, a bridge can be established between the concentration of target protein and the degree of the attenuation of the obtained signal, and the relationship can be shown by the surface plasmon changes caused by the report DNA-induced aggregation of DNA-modified gold nanoparticles (AuNPs). Our method can also have considerable sensitivity and selectivity, which has been demonstrated by the assay of human α-thrombin. Furthermore, by simply changing the sequence of the probe DNA, we can expand the application of our method to not only aptamer binding proteins but also DNA binding proteins, thus we have also used this method to analyze a specific serological marker for systemic lupus erythematosus (SLE) in this study. With a broad detection range of 1.3-133 nM and a detection limit of 0.61 nM (S/N=3), it may hold great promise for clinical application.
Collapse
Affiliation(s)
- Tao Gao
- Department of Biochemistry and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
| | | | | | | | | |
Collapse
|
22
|
An exonuclease III protection-based electrochemical method for estrogen receptor assay. Int J Mol Sci 2013; 14:10298-306. [PMID: 23681011 PMCID: PMC3676839 DOI: 10.3390/ijms140510298] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/25/2013] [Accepted: 05/10/2013] [Indexed: 12/23/2022] Open
Abstract
Estrogen receptor (ER), expressed in approximately 80% of primary breast cancer cells, has proven to be a valuable predictive factor of the disease. Herein, by making use of the specific binding of ER to its DNA response elements, we propose an Exonuclease III (Exo III) protection-based electrochemical method for detecting ER proteins. In this assay, the presence of ER can protect the duplex DNA molecules immobilized on an electrode surface from Exo III-catalyzed digestion, resulting in an increased electrochemical signal. Experimental results have revealed that the proposed method can allow the quantification of ER in the range of 0.5 to 100 nM with a satisfactory detection limit of 0.38 nM. Furthermore, since this approach can also be employed to detect ER directly in nuclear extracts, it may be of great use in biomedical applications in the future.
Collapse
|
23
|
|
24
|
Colorimetric assay of matrix metalloproteinase activity based on metal-induced self-assembly of carboxy gold nanoparticles. Biosens Bioelectron 2013; 41:833-9. [DOI: 10.1016/j.bios.2012.10.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/06/2012] [Accepted: 10/08/2012] [Indexed: 12/27/2022]
|
25
|
The pH-dependent interaction of silver nanoparticles and hydrogen peroxide: A new platform for visual detection of iodide with ultra-sensitivity. Talanta 2013; 107:146-53. [DOI: 10.1016/j.talanta.2012.12.029] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/14/2012] [Accepted: 12/21/2012] [Indexed: 11/17/2022]
|
26
|
Tan YN, Lee KH, Su X. A study of DNA design dependency of segmented DNA-induced gold nanoparticle aggregation towards versatile bioassay development. RSC Adv 2013. [DOI: 10.1039/c3ra44661a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
|
27
|
James AE, Driskell JD. Monitoring gold nanoparticle conjugation and analysis of biomolecular binding with nanoparticle tracking analysis (NTA) and dynamic light scattering (DLS). Analyst 2013; 138:1212-8. [DOI: 10.1039/c2an36467k] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
28
|
Vilela D, González MC, Escarpa A. Sensing colorimetric approaches based on gold and silver nanoparticles aggregation: Chemical creativity behind the assay. A review. Anal Chim Acta 2012; 751:24-43. [DOI: 10.1016/j.aca.2012.08.043] [Citation(s) in RCA: 393] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 08/20/2012] [Accepted: 08/25/2012] [Indexed: 10/27/2022]
|
29
|
Xu W, Xie X, Li D, Yang Z, Li T, Liu X. Ultrasensitive colorimetric DNA detection using a combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA). SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:1846-50. [PMID: 22461378 DOI: 10.1002/smll.201200263] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Indexed: 05/18/2023]
Abstract
A combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA) is used for the rapid, colorimetric detection of DNA. The integration of rolling circle amplification into the NEANA approach allows for detection of oligonucleotides with arbitrary sequences at ultralow concentrations.
Collapse
Affiliation(s)
- Wei Xu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | | | | | | | | | | |
Collapse
|
30
|
Zhang J, Wang X, Yang X. Colorimetric determination of hypochlorite with unmodified gold nanoparticles through the oxidation of a stabilizer thiol compound. Analyst 2012; 137:2806-12. [DOI: 10.1039/c2an35239g] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
31
|
Zhang J, Yang C, Wang X, Yang X. Colorimetric recognition and sensing of nitrite with unmodified gold nanoparticles based on a specific diazo reaction with phenylenediamine. Analyst 2012; 137:3286-92. [DOI: 10.1039/c2an35204d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
32
|
Zhang J, Xu X, Yang X. Highly specific colorimetric recognition and sensing of sulfide with glutathione-modified gold nanoparticle probe based on an anion-for-molecule ligand exchange reaction. Analyst 2012; 137:1556-8. [DOI: 10.1039/c2an16307a] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
33
|
Piao JY, Chung DS. Novel colorimetric assay of LSD1 activity using gold nanoparticles. Analyst 2012; 137:2669-73. [DOI: 10.1039/c2an16286e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Affinity analysis of DNA aptamer-peptide interactions using gold nanoparticles. Anal Biochem 2011; 421:725-31. [PMID: 22214880 DOI: 10.1016/j.ab.2011.12.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/28/2011] [Accepted: 12/02/2011] [Indexed: 11/22/2022]
Abstract
Gold nanoparticles (AuNPs) were used as colorimetric probe and fluorescence quencher for affinity analysis of DNA aptamers toward their target mucin 1 (MUC1) peptide. Single-stranded DNA (ssDNA) aptamer-coated AuNPs showed increased stability (i.e., more resistant to aggregation induced by NaCl) in the presence of their target peptide due to the increase in steric protection conferred by the ssDNA-peptide complexes formed on the AuNPs. Based on changes in the UV-vis extinction spectrum of AuNPs (a measure of AuNPs aggregation) and fluorescence restoration of CY5-ssDNA upon ssDNA-peptide complex formation, the formation of the complexes and ssDNA sequence-dependent dissociation constant (K(d)) were determined. Besides the UV-vis and fluorescence measurements, the hydrodynamic diameters, zeta potential measurements, and transmission electron microscopy (TEM) images of AuNPs after various coatings supported the assay principle. The methodology presented herein provides a rapid and sensitive alternative solution for the identification of high affinity binders from systematic evolution of ligands by exponential enrichment (SELEX).
Collapse
|
35
|
Abstract
The field of radiation oncology has evolved, especially in the past 20 years. Advances in technology, particularly in computing power, software, and imaging, have fueled contributions to cancer care. It is currently fashionable to say that many of these advances have only served to increase costs of care without clear evidence of benefit, and certainly, efforts to evaluate the value of radiation oncology treatments are needed. However, it is undeniable that the future of radiation oncology depends on discovering such advances and to demonstrate that these increase the therapeutic index of treatment. Across the global radiation oncology community, investigations are proceeding in which innovative means are being used to achieve this goal. We review some of these novel methods to improve the therapeutic index of radiation therapy.
Collapse
|
36
|
Xie X, Xu W, Li T, Liu X. Colorimetric detection of HIV-1 ribonuclease H activity by gold nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1393-1396. [PMID: 21438149 DOI: 10.1002/smll.201002150] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 01/24/2011] [Indexed: 05/30/2023]
Affiliation(s)
- Xiaoji Xie
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore.
| | | | | | | |
Collapse
|
37
|
Zhang X, Kong X, Fan W, Du X. Iminodiacetic acid-functionalized gold nanoparticles for optical sensing of myoglobin via Cu2+ coordination. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:6504-6510. [PMID: 21488608 DOI: 10.1021/la200177e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A novel gold nanoparticle (AuNP)-based optical sensing system has been developed for the detection of myoglobin (Mb), which is of significant importance for early disease diagnosis. Two thiol molecules containing an iminodiacetic acid moiety (IDA) were synthesized. This detection is based on the Mb-induced aggregation of IDA-functionalized AuNPs resulting from the structures of Mb sandwiched between the functionalized AuNPs via Cu(2+) bridges in the coordination interactions of IDA-Cu(2+)-histidine residues available on the Mb surface, which was confirmed by UV-vis spectroscopy, transmission electron microscopy, dynamic light scattering, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The induction aggregation resulted in a red shift in plasmon resonance band of the AuNPs concomitant with a change in solution color from red to purple. The qualitative and quantitative detections of Mb can be achieved by colorimetric observations and UV-vis spectral measurements, respectively. The selectivity of protein assay with the functionalized AuNPs was further investigated, and it is found that the optical sensing of histidine-rich proteins is closely related to number and distribution of surface histidine residues as well as size of proteins.
Collapse
Affiliation(s)
- Xianfeng Zhang
- Key Laboratory of Mesoscopic Chemistry (Ministry of Education), and School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, PR China
| | | | | | | |
Collapse
|
38
|
Tan YN, Lee KH, Su X. Study of Single-Stranded DNA Binding Protein–Nucleic Acids Interactions using Unmodified Gold Nanoparticles and Its Application for Detection of Single Nucleotide Polymorphisms. Anal Chem 2011; 83:4251-7. [DOI: 10.1021/ac200525a] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yen Nee Tan
- Institute of Material Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
| | - Kwai Han Lee
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457
| | - Xiaodi Su
- Institute of Material Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
| |
Collapse
|
39
|
Zhang H, Wang L, Jiang W. Label free DNA detection based on gold nanoparticles quenching fluorescence of Rhodamine B. Talanta 2011; 85:725-9. [PMID: 21645765 DOI: 10.1016/j.talanta.2011.04.057] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 04/13/2011] [Accepted: 04/21/2011] [Indexed: 11/18/2022]
Abstract
A novel and sensitive label free DNA detection method using gold nanoparticles (GNPs) and Rhodamine B (RB) has been developed. The assay is based on the following two properties. One is the different adsorption properties of single-stranded and double-stranded DNA on GNPs in colloidal solution. The other is the different quenching ability of aggregated GNPs and dispersed GNPs on RB. Un-aggregated GNPs could effectively quench the fluorescence of RB. However, the quenching ability greatly decreases after GNPs aggregated. The hybridization of probe DNA and target DNA is monitored by the fluorescence detection after the RB is added to the solution. Under the optimal experimental conditions, the detection limit of this assay is 2.9×10(-13) mol L(-1).
Collapse
Affiliation(s)
- Hong Zhang
- School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China
| | | | | |
Collapse
|
40
|
Witzens J, Hochberg M. Optical detection of target molecule induced aggregation of nanoparticles by means of high-Q resonators. OPTICS EXPRESS 2011; 19:7034-7061. [PMID: 21503017 DOI: 10.1364/oe.19.007034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We theoretically investigate a novel scheme to detect target molecule induced, or suppressed, aggregation of nanoparticles. High-Q optical resonators are used to both optically trap gold nanoparticle clusters and to detect their presence via a shift in the resonance wavelength. The well depth of the optical trap is chosen to be relatively low compared to the thermal energy of the nanoparticles, so that trapping of single nanoparticles is marginal and results in a comparatively small wavelength shift. Aggregation of functionalized gold nanoparticles is mediated or suppressed via binding to a target molecule. The well depth for the resulting nanoparticle clusters scales much more favorably relative to Brownian motion, resulting in large nanoparticle concentration enhancements in the evanescent field region of the resonator. We predict a target molecule sensitivity in the tens of fM range. In order to predict the resonator response, a complete theory of time resolved nanoparticle cluster trapping dynamics is derived. In particular, the formalism of Kramers' escape time is adapted to 2D (silicon wire) and 3D (ring resonator) optical traps.
Collapse
Affiliation(s)
- Jeremy Witzens
- Integrated Photonics Group, RWTH Aachen University, Sommerfeldstr. 24, 52074 Aachen, Germany.
| | | |
Collapse
|
41
|
Wang X, Xu Y, Chen Y, Li L, Liu F, Li N. The gold-nanoparticle-based surface plasmon resonance light scattering and visual DNA aptasensor for lysozyme. Anal Bioanal Chem 2011; 400:2085-91. [PMID: 21461986 DOI: 10.1007/s00216-011-4943-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/20/2011] [Accepted: 03/21/2011] [Indexed: 11/25/2022]
Abstract
We developed a new simple and sensitive assay for lysozyme based on gold nanoparticle plasmon resonance light scattering (PRLS) measurement and naked-eye detection using for the first time the lysozyme DNA aptamer as the recognition element. Lysozyme DNA aptamer could stabilize gold nanoparticles (AuNPs) at high ionic strength. Introducing lysozyme to the system easily triggered the aggregation of AuNPs, producing a red-to-blue color change of the solution, red-shifted plasmon absorption, and enhanced plasmon resonance light scattering. The linear range was found to be 0.2∼4 nM for 0.7 nM AuNPs, 0.3∼6 nM for 1.4 nM AuNPs and 0.6∼8 nM for 2.1 nM AuNPs. About 0.1 nM lysozyme can produce an observable enhancement of PRLS signal. For visual detection, 1 nM lysozyme can produce a very distinctive color change. Satisfactory recoveries were obtained for simulated saliva and diluted urine samples, indicating that the method has potential for analyses of clinical samples. The simplicity and high sensitivity that are consistent with the resources and needs of many laboratories makes this method a good choice for routine analysis.
Collapse
Affiliation(s)
- Xinyi Wang
- Beijing National Laboratory for Molecular Sciences, Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | | | | | | | | | | |
Collapse
|
42
|
|
43
|
Aung KMM, Tan YN, Desai KV, Su X. Interrogating Oestrogen Receptor–DNA Interactions using Metallic Nanoparticles and Surface Plasmon Resonance Technique. Aust J Chem 2011. [DOI: 10.1071/ch11194] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Surface plasmon resonance (SPR) spectroscopy is an important technique for real-time measurement of biomolecular interactions on the solid–liquid interface. Metallic nanoparticles (mNP) have unique optical properties arising from localized SPR. They can be used as elegant colorimetric probes for studying biomolecular interactions in homogenous solution. In this study, we used the two techniques in parallel to study the binding interactions of oestrogen receptors (ERα and ERβ) with their response elements (ERE). First, we have validated the principle of a gold nanoparticle (AuNP)-based colorimetric assay that protein–DNA complexes are able to provide more electrosteric forces than protein alone, using AuNP of a range of particle size (10, 20, and 50 nm) and examined particle size-dependent assay performance for detecting ERβ–DNA interactions. Second, we have demonstrated the ability of this AuNP assay to discriminate subtle binding affinity difference of ERβ to a mutated ERE containing a single base pair alternation relative to that with a perfect ERE sequence. The accuracy and sensitivity of the AuNP assay for detecting sequence dependent binding are found comparable with the golden standard SPR assay. Third, through a parallel study, we have compared the performance of the AuNP assay and SPR assay for measuring a protein–DNA binding event when the protein is partially denatured or has lower reactivity. We found that the AuNP assay can detect protein–DNA complex formation and determine sequence specificity more easily owing presumably to the homogenouse phase binding nature. With this study we conclude that the AuNP-based assay is a valuable complementary technique to SPR for interrogating sequence-specific protein–DNA interactions.
Collapse
|
44
|
Yin Y, Cao Y, Xu Y, Li G. Colorimetric immunoassay for detection of tumor markers. Int J Mol Sci 2010; 11:5077-94. [PMID: 21614193 PMCID: PMC3100837 DOI: 10.3390/ijms11125077] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 11/24/2010] [Accepted: 11/25/2010] [Indexed: 11/16/2022] Open
Abstract
Tumor markers are substances, usually proteins, produced by the body in response to cancer growth, or by the cancer tissue itself. They can be detected in blood, urine, or tissue samples, and the discovery and detection of tumor markers may provide earlier diagnosis of cancer and improved therapeutic intervention. Colorimetric immunoassays for tumor marker detection have attracted considerable attention, due to their simplicity and high efficiency. The traditionally used colorimetric immunoassays for the detection of tumor markers are based on enzyme-linked immunosorbent assays, and the great achievement of nanotechnology has further opened opportunities for the development of such kind of immunoassays. This paper will summarize recent advances in the field of colorimetric immunoassays for detecting tumor markers, which is aimed to provide an overview in this field, as well as experimental guidance for the learner.
Collapse
Affiliation(s)
- Yongmei Yin
- Department of Oncology, Jiangsu Province Hospital, Nanjing 210029, China
- Authors to whom correspondence should be addressed; E-Mails: (Y.Y.); (G.L.); Tel.: +86-25-681-360-43, +86-25-835-935-96; Fax: +86-25-837-100-40, +86-25-835-925-10
| | - Ya Cao
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China; E-Mails: (Y.C.); (Y.X.)
| | - Yuanyuan Xu
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China; E-Mails: (Y.C.); (Y.X.)
| | - Genxi Li
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China; E-Mails: (Y.C.); (Y.X.)
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China
- Authors to whom correspondence should be addressed; E-Mails: (Y.Y.); (G.L.); Tel.: +86-25-681-360-43, +86-25-835-935-96; Fax: +86-25-837-100-40, +86-25-835-925-10
| |
Collapse
|
45
|
Tan YN, Su X, Zhu Y, Lee JY. Sensing of transcription factor through controlled-assembly of metal nanoparticles modified with segmented DNA elements. ACS NANO 2010; 4:5101-10. [PMID: 20704275 DOI: 10.1021/nn100943d] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have developed a unique metal nanoparticle (mNPs)-based assay to detect sequence-specific interactions between transcription factor and its corresponding DNA-binding elements. This assay exploits the interparticle-distance dependent optical properties of noble mNPs as sensing element and utilizes specific protein-DNA interactions to control the dispersion status of the mNPs. The assay involves two sets of double-stranded (ds)DNA modified-mNPs, each carrying a half site segment of a functional DNA sequence for the protein of interest. Each of these half sites is designed to contain a short complementary sticky end that introduces base-pairing forces to facilitate particle aggregation and to form a transient full dsDNA sequence. The detection of specific protein-DNA binding is founded on the premise that the mixture of these two sets of dsDNA-mNPs experiences a remarkable particle aggregation under certain salt conditions; whereas the aggregation can be retarded in the presence of a specific protein that binds and stabilizes the transient full dsDNA structure and therefore introduces steric protection forces between particles. We have demonstrated the concept using estrogen receptor α and its response elements, with gold and silver NPs as the sensing platform. UV-vis spectroscopy, transmission electron spectroscopy, and dynamic light scattering measurements were conducted to provide full characterization of the particle aggregation/dispersion mechanism. Differing from most of the mNP-based colorimetric sensors that are designed based on the analyte-induced aggregation mechanism, current protein binding-stabilization sensing strategy reduces the false signals caused by unrelated particle destabilizing effects. It is expected that this assay principle can be directed toward other transcription factors by simply changing the recognition sequence to form different segmented dsDNA-mNP constructs.
Collapse
Affiliation(s)
- Yen Nee Tan
- Institute of Material Research and Engineering, ASTAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
| | | | | | | |
Collapse
|