Gold-Nanoparticle-Based Assay for Instantaneous Detection of Nuclear Hormone Receptor−Response Elements InteractionsClick to copy article linkArticle link copied!
Abstract
Gold nanoparticles (AuNPs) are widely used as colorimetric probes for biosensing, relying on their unique particle size-dependent and/or interparticle distance-dependent extinction spectrum and solution color. Herein, we describe an AuNP-based colorimetric assay to detect binding interactions between nuclear hormone receptors and their corresponding DNA-binding elements, particularly the human estrogen receptors (ERα and ERβ) and their cognate estrogen response elements (EREs). We found that the protein−DNA (ER−ERE) complexes can stabilize citrate anion-capped AuNPs against salt-induced aggregation to a larger extent than the protein (ER) or the DNA (ERE) alone, due to their unique molecular size and charge properties that provide a strong electrosteric protection. Moreover, our results show that the extent of stabilization is sequence-dependent and can distinguish a single base variation in the ERE associated with minor changes in protein−DNA binding affinity. With this assay, many important parameters of protein−DNA binding events (e.g., sequence selectivity, distinct DNA binding properties of protein subtypes, binding stoichiometry, and sequence-independent transient binding) can be determined instantly without using labels, tedious sample preparations, and sophisticated instrumentation. These benefits, in particular the high-throughput potential, could enable this assay to become the assay of choice to complement conventional techniques for large scale characterization of protein−DNA interactions, a key aspect in biological research.
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- Jessica S. Y. Ooi, Cher Ryn Lim, Chai Xian Hua, Jeck Fei Ng, Siu Yee New. DNA Hairpins and Stabilization of Gold Nanoparticles: Effect of Stem Length and Toehold Composition. Langmuir 2023, 39
(43)
, 15200-15207. https://doi.org/10.1021/acs.langmuir.3c01748
- Xinyan Zhang, Zhilin Zhang, Xiaoqi Xue, Tingting Fan, Chunyan Tan, Feng Liu, Ying Tan, Yuyang Jiang. PROTAC Degrader of Estrogen Receptor α Targeting DNA-Binding Domain in Breast Cancer. ACS Pharmacology & Translational Science 2022, 5
(11)
, 1109-1118. https://doi.org/10.1021/acsptsci.2c00109
- Mohammad Tavakkoli Yaraki, Shima Zahed Nasab, Iman Zare, Mohammad Dahri, Mohammad Moein Sadeghi, Maedeh Koohi, Yen Nee Tan. Biomimetic Metallic Nanostructures for Biomedical Applications, Catalysis, and Beyond. Industrial & Engineering Chemistry Research 2022, 61
(22)
, 7547-7593. https://doi.org/10.1021/acs.iecr.2c00285
- Xin Ting Zheng Hesheng Victor Xu Yen Nee Tan . Bioinspired Design and Engineering of Functional Nanostructured Materials for Biomedical Applications. 2017, 123-152. https://doi.org/10.1021/bk-2017-1253.ch007
- Steven Lukman, Khin Moh Moh Aung, Jie Liu, Bin Liu, and Xiaodi Su . Hybrid Sensor Using Gold Nanoparticles and Conjugated Polyelectrolytes for Studying Sequence Rule in Protein–DNA Interactions. ACS Applied Materials & Interfaces 2013, 5
(23)
, 12725-12734. https://doi.org/10.1021/am404120q
- Yen Nee Tan, Kwai Han Lee, and Xiaodi Su . Study of Single-Stranded DNA Binding Protein–Nucleic Acids Interactions using Unmodified Gold Nanoparticles and Its Application for Detection of Single Nucleotide Polymorphisms. Analytical Chemistry 2011, 83
(11)
, 4251-4257. https://doi.org/10.1021/ac200525a
- Xianfeng Zhang, Xianming Kong, Wenjuan Fan, and Xuezhong Du . Iminodiacetic Acid-Functionalized Gold Nanoparticles for Optical Sensing of Myoglobin via Cu2+ Coordination. Langmuir 2011, 27
(10)
, 6504-6510. https://doi.org/10.1021/la200177e
- Yen Nee Tan, Xiaodi Su, Yue Zhu, and Jim Yang Lee . Sensing of Transcription Factor through Controlled-Assembly of Metal Nanoparticles Modified with Segmented DNA Elements. ACS Nano 2010, 4
(9)
, 5101-5110. https://doi.org/10.1021/nn100943d
- Huan Du, Yanwen Jin, Xiaoke Zheng, Nansheng Cheng, Junbo Chen, Xiandeng Hou. A simple strategy based on combinatorial gold nanoparticle sizes for enhanced sensitivity in colorimetric bioanalysis. Journal of Materials Chemistry B 2023, 11
(17)
, 3851-3859. https://doi.org/10.1039/D3TB00024A
- Afagh Rastmanesh, Mohammad Tavakkoli Yaraki, Jinyu Wu, Zihao Wang, Prachi Ghoderao, Yongxiang Gao, Yen Nee Tan. Bioinspired micro/nanomotors towards a self-propelled noninvasive diagnosis and treatment of cancer. Molecular Systems Design & Engineering 2021, 6
(8)
, 566-593. https://doi.org/10.1039/D1ME00065A
- Mohammad Tavakkoli Yaraki, Fang Hu, Soroosh Daqiqeh Rezaei, Bin Liu, Yen Nee Tan. Metal-enhancement study of dual functional photosensitizers with aggregation-induced emission and singlet oxygen generation. Nanoscale Advances 2020, 2
(7)
, 2859-2869. https://doi.org/10.1039/D0NA00182A
- Mohammad Tavakkoli Yaraki, Soroosh Daqiqeh Rezaei, Eshu Middha, Yen Nee Tan. Synthesis and Simulation Study of Right Silver Bipyramids via Seed‐Mediated Growth cum Selective Oxidative Etching Approach. Particle & Particle Systems Characterization 2020, 37
(5)
https://doi.org/10.1002/ppsc.202000027
- Mohammad Tavakkoli Yaraki, Soroosh Daqiqeh Rezaei, Yen Nee Tan. Simulation guided design of silver nanostructures for plasmon-enhanced fluorescence, singlet oxygen generation and SERS applications. Physical Chemistry Chemical Physics 2020, 22
(10)
, 5673-5687. https://doi.org/10.1039/C9CP06029D
- Victoria Xin Ting Zhao, Ten It Wong, Xin Ting Zheng, Yen Nee Tan, Xiaodong Zhou. Colorimetric biosensors for point-of-care virus detections. Materials Science for Energy Technologies 2020, 3 , 237-249. https://doi.org/10.1016/j.mset.2019.10.002
- Xin Ting Zheng, Yen Nee Tan. 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. https://doi.org/10.1016/j.sintl.2020.100034
- Mohammad Tavakkoli Yaraki, Yen Nee Tan. Recent advances in metallic nanobiosensors development: Colorimetric, dynamic light scattering and fluorescence detection. Sensors International 2020, 1 , 100049. https://doi.org/10.1016/j.sintl.2020.100049
- Roger M. Pallares, Nguyen Thi Kim Thanh, Xiaodi Su. Quantifying the binding between proteins and open chromatin-like DNA sequences with gold nanorods. Chemical Communications 2019, 55
(100)
, 15041-15044. https://doi.org/10.1039/C9CC07511A
- Hongqiang Wang, Honghong Rao, Minyue Luo, Xin Xue, Zhonghua Xue, Xiaoquan Lu. Noble metal nanoparticles growth-based colorimetric strategies: From monocolorimetric to multicolorimetric sensors. Coordination Chemistry Reviews 2019, 398 , 113003. https://doi.org/10.1016/j.ccr.2019.06.020
- Roger M. Pallares, Laura Sutarlie, Nguyễn T.K. Thanh, Xiaodi Su. Fluorescence sensing of protein-DNA interactions using conjugated polymers and graphene oxide. Sensors and Actuators B: Chemical 2018, 271 , 97-103. https://doi.org/10.1016/j.snb.2018.05.105
- Enock Assah, Walter Goh, Xin Ting Zheng, Ting Xiang Lim, Jun Li, David Lane, Farid Ghadessy, Yen Nee Tan. Rapid colorimetric detection of p53 protein function using DNA-gold nanoconjugates with applications for drug discovery and cancer diagnostics. Colloids and Surfaces B: Biointerfaces 2018, 169 , 214-221. https://doi.org/10.1016/j.colsurfb.2018.05.007
- Carolina V. Uliana, Camila R. Peverari, André S. Afonso, Marcia R. Cominetti, Ronaldo C. Faria. Fully disposable microfluidic electrochemical device for detection of estrogen receptor alpha breast cancer biomarker. Biosensors and Bioelectronics 2018, 99 , 156-162. https://doi.org/10.1016/j.bios.2017.07.043
- W. L. Goh, E. Assah, X. T. Zheng, D. P. Lane, F. J. Ghadessy, Y. N. Tan. Transcription Factors as Detection and Diagnostic Biomarkers in Cancer. 2017, 31-58. https://doi.org/10.1007/978-981-10-4726-8_2
- Nianjia Seow, Yen Nee Tan, Lin-Yue Lanry Yung, Xiaodi Su. DNA-Directed Assembly of Nanogold Dimers: A Unique Dynamic Light Scattering Sensing Probe for Transcription Factor Detection. Scientific Reports 2016, 5
(1)
https://doi.org/10.1038/srep18293
- Sandrine Bayle, Joel Chopineau, Benoit Roig, Denis Habauzit. Estrogen receptor preparation effects on the receptor–DNA interaction by surface plasmon resonance. Analytical and Bioanalytical Chemistry 2016, 408
(29)
, 8257-8262. https://doi.org/10.1007/s00216-016-9967-0
- Khin Moh Moh Aung, Michelle Gek Liang Lim, Shuzhen Hong, Edwin Cheung, Xiaodi Su. Determination of DNA Binding Behavior of FoxA1 Constructs Using a Gold Nanoparticle-Based High Throughput Assay. Journal of Molecular and Engineering Materials 2016, 04
(03)
, 1640012. https://doi.org/10.1142/S2251237316400128
- Hesheng Victor Xu, Xin Ting Zheng, Beverly Yin Leng Mok, Salwa Ali Ibrahim, Yong Yu, Yen Nee Tan. Molecular Design of Bioinspired Nanostructures for Biomedical Applications: Synthesis, Self-Assembly and Functional Properties. Journal of Molecular and Engineering Materials 2016, 04
(01)
, 1640003. https://doi.org/10.1142/S2251237316400037
- Junho Ahn, Yeonweon Choi, Ae-Ree Lee, Joon-Hwa Lee, Jong Hwa Jung. A duplex DNA–gold nanoparticle probe composed as a colorimetric biosensor for sequence-specific DNA-binding proteins. The Analyst 2016, 141
(6)
, 2040-2045. https://doi.org/10.1039/C6AN00033A
- A.A.I. Khalil. Development of double-pulse lasers ablation system for generating gold ion source under applying an electric field. Optics & Laser Technology 2015, 75 , 105-114. https://doi.org/10.1016/j.optlastec.2015.06.015
- Ning Li, Xiaodi Su, Yi Lu. Nanomaterial-based biosensors using dual transducing elements for solution phase detection. The Analyst 2015, 140
(9)
, 2916-2943. https://doi.org/10.1039/C4AN02376E
- . Molecular Plasmonics: Life Sciences Applications. 2014, 117-156. https://doi.org/10.1002/9783527649686.ch6
- Laura Sutarlie, Khin Moh Moh Aung, Michelle Gek Liang Lim, Steven Lukman, Edwin Cheung, Xiaodi Su. Studying Protein–DNA Complexes Using Gold Nanoparticles by Exploiting Particle Aggregation, Refractive Index Change, and Fluorescence Quenching and Enhancement Principles. Plasmonics 2014, 9
(4)
, 753-763. https://doi.org/10.1007/s11468-013-9655-2
- Khin Moh Moh Aung, Siu Yee New, Shuzhen Hong, Laura Sutarlie, Michelle Gek Liang Lim, Si Kee Tan, Edwin Cheung, Xiaodi Su. Studying forkhead box protein A1–DNA interaction and ligand inhibition using gold nanoparticles, electrophoretic mobility shift assay, and fluorescence anisotropy. Analytical Biochemistry 2014, 448 , 95-104. https://doi.org/10.1016/j.ab.2013.11.017
- Steven Lukman, Khin Moh Moh Aung, Michelle Gek Liang Lim, Shuzhen Hong, Si Kee Tan, Edwin Cheung, Xiaodi Su. Hybrid assembly of DNA-coated gold nanoparticles with water soluble conjugated polymers for studying protein–DNA interaction and ligand inhibition. RSC Advances 2014, 4
(17)
, 8883. https://doi.org/10.1039/c3ra46752j
- Tao Gao, Limin Ning, Chao Li, Haiyan Wang, Genxi Li. A colorimetric method for protein assay via exonuclease III-assisted signal attenuation strategy and specific DNA–protein interaction. Analytica Chimica Acta 2013, 788 , 171-176. https://doi.org/10.1016/j.aca.2013.06.029
- Yue Liu, ChengZhi Huang. Single scattering particles based analytical techniques. Chinese Science Bulletin 2013, 58
(17)
, 1969-1979. https://doi.org/10.1007/s11434-013-5707-4
- Mo-Yuan Shen, Cheng-Fu Chao, Yue-Jin Wu, Yu-Hsien Wu, Chin-Ping Huang, Yaw-Kuen Li. A design for fast and effective screening of hyaluronidase inhibitor using gold nanoparticles. Sensors and Actuators B: Chemical 2013, 181 , 605-610. https://doi.org/10.1016/j.snb.2013.02.054
- Sha Zhu, Ya Cao, Yuanyuan Xu, Yongmei Yin, Genxi Li. An Exonuclease III Protection-Based Electrochemical Method for Estrogen Receptor Assay. International Journal of Molecular Sciences 2013, 14
(5)
, 10298-10306. https://doi.org/10.3390/ijms140510298
- Gae Baik Kim, Kun Hee Kim, Yeon Hee Park, Sungho Ko, Young-Pil Kim. Colorimetric assay of matrix metalloproteinase activity based on metal-induced self-assembly of carboxy gold nanoparticles. Biosensors and Bioelectronics 2013, 41 , 833-839. https://doi.org/10.1016/j.bios.2012.10.025
- Guang-Li Wang, Xiao-Ying Zhu, Yu-Ming Dong, Huan-Jun Jiao, Xiu-Ming Wu, Zai-Jun Li. The pH-dependent interaction of silver nanoparticles and hydrogen peroxide: A new platform for visual detection of iodide with ultra-sensitivity. Talanta 2013, 107 , 146-153. https://doi.org/10.1016/j.talanta.2012.12.029
- Susan Buckhout-White, Mario Ancona, Kelly Boeneman Gemmill, Ellen R. Goldman, Igor L. Medintz. Characterizing Functionalized DNA for Use in Nanomedicine. 2013, 11-41. https://doi.org/10.1007/978-3-642-36853-0_2
- Andre E. James, Jeremy D. Driskell. Monitoring gold nanoparticle conjugation and analysis of biomolecular binding with nanoparticle tracking analysis (NTA) and dynamic light scattering (DLS). The Analyst 2013, 138
(4)
, 1212. https://doi.org/10.1039/c2an36467k
- Yen Nee Tan, Kwai Han Lee, Xiaodi Su. A study of DNA design dependency of segmented DNA-induced gold nanoparticle aggregation towards versatile bioassay development. RSC Advances 2013, 3
(44)
, 21604. https://doi.org/10.1039/c3ra44661a
- Diana Vilela, María Cristina González, Alberto Escarpa. Sensing colorimetric approaches based on gold and silver nanoparticles aggregation: Chemical creativity behind the assay. A review. Analytica Chimica Acta 2012, 751 , 24-43. https://doi.org/10.1016/j.aca.2012.08.043
- Wei Xu, Xiaoji Xie, Dawei Li, Zhaoqi Yang, Tianhu Li, Xiaogang Liu. Ultrasensitive Colorimetric DNA Detection using a Combination of Rolling Circle Amplification and Nicking Endonuclease‐Assisted Nanoparticle Amplification (NEANA). Small 2012, 8
(12)
, 1846-1850. https://doi.org/10.1002/smll.201200263
- Lihan Tan, Koon Gee Neoh, En-Tang Kang, Woo-Seok Choe, Xiaodi Su. Affinity analysis of DNA aptamer–peptide interactions using gold nanoparticles. Analytical Biochemistry 2012, 421
(2)
, 725-731. https://doi.org/10.1016/j.ab.2011.12.007
- Jing Yu Piao, Doo Soo Chung. Novel colorimetric assay of LSD1 activity using gold nanoparticles. The Analyst 2012, 137
(11)
, 2669. https://doi.org/10.1039/c2an16286e
- Jia Zhang, Xiaowen Xu, Xiurong Yang. Highly specific colorimetric recognition and sensing of sulfide with glutathione-modified gold nanoparticle probe based on an anion-for-molecule ligand exchange reaction. The Analyst 2012, 137
(7)
, 1556. https://doi.org/10.1039/c2an16307a
- Jia Zhang, Cheng Yang, Xiaolei Wang, Xiurong Yang. Colorimetric recognition and sensing of nitrite with unmodified gold nanoparticles based on a specific diazo reaction with phenylenediamine. The Analyst 2012, 137
(14)
, 3286. https://doi.org/10.1039/c2an35204d
- Jia Zhang, Xiaolei Wang, Xiurong Yang. Colorimetric determination of hypochlorite with unmodified gold nanoparticles through the oxidation of a stabilizer thiol compound. The Analyst 2012, 137
(12)
, 2806. https://doi.org/10.1039/c2an35239g
- Hong Zhang, Lei Wang, Wei Jiang. Label free DNA detection based on gold nanoparticles quenching fluorescence of Rhodamine B. Talanta 2011, 85
(1)
, 725-729. https://doi.org/10.1016/j.talanta.2011.04.057
- Xinyi Wang, Yao Xu, Yang Chen, Limei Li, Feng Liu, Na Li. The gold-nanoparticle-based surface plasmon resonance light scattering and visual DNA aptasensor for lysozyme. Analytical and Bioanalytical Chemistry 2011, 400
(7)
, 2085-2091. https://doi.org/10.1007/s00216-011-4943-1
- Xiaoji Xie, Wei Xu, Tianhu Li, Xiaogang Liu. Colorimetric Detection of HIV‐1 Ribonuclease H Activity by Gold Nanoparticles. Small 2011, 7
(10)
, 1393-1396. https://doi.org/10.1002/smll.201002150
- Michelle Alonso-Basanta, Christina Chapman, Jay F. Dorsey, Ramesh Rengan, Stephen M. Hahn. A Glimpse of the Future. The Cancer Journal 2011, 17
(3)
, 190-194. https://doi.org/10.1097/PPO.0b013e3182216bc0
- Jeremy Witzens, Michael Hochberg. Optical detection of target molecule induced aggregation of nanoparticles by means of high-Q resonators. Optics Express 2011, 19
(8)
, 7034. https://doi.org/10.1364/OE.19.007034
- Xuejia Xue, Feng Wang, Xiaogang Liu. Emerging functional nanomaterials for therapeutics. Journal of Materials Chemistry 2011, 21
(35)
, 13107. https://doi.org/10.1039/c1jm11401h
- Khin Moh Moh Aung, Yen Nee Tan, Kartiki Vasant Desai, Xiaodi Su. Interrogating Oestrogen Receptor–DNA Interactions using Metallic Nanoparticles and Surface Plasmon Resonance Technique. Australian Journal of Chemistry 2011, 64
(9)
, 1288. https://doi.org/10.1071/CH11194
- Xiaodi Su. Noble Metal Nanoparticles as Colorimetric Probes for Biological Analysis. 2010, 183-214. https://doi.org/10.1201/b10450-7
- Yongmei Yin, Ya Cao, Yuanyuan Xu, Genxi Li. Colorimetric Immunoassay for Detection of Tumor Markers. International Journal of Molecular Sciences 2010, 11
(12)
, 5077-5094. https://doi.org/10.3390/ijms11125077
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