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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.
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Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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Pallares RM, Thanh NTK, Su X. Sensing of circulating cancer biomarkers with metal nanoparticles. NANOSCALE 2019; 11:22152-22171. [PMID: 31555790 DOI: 10.1039/c9nr03040a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The analysis of circulating cancer biomarkers, including cell-free and circulating tumor DNA, circulating tumor cells, microRNA and exosomes, holds promise in revolutionizing cancer diagnosis and prognosis using body fluid analysis, also known as liquid biopsy. To enable clinical application of these biomarkers, new analytical tools capable of detecting them in very low concentrations in complex sample matrixes are needed. Metal nanoparticles have emerged as extraordinary analytical scaffolds because of their unique optoelectronic properties and ease of functionalization. Hence, multiple analytical techniques have been developed based on these nanoparticles and their plasmonic properties. The aim of this review is to summarize and discuss the present development on the use of metal nanoparticles for the analysis of circulating cancer biomarkers. We examine how metal nanoparticles can be used as (1) analytical transducers in various sensing principles, such as aggregation induced colorimetric assays, plasmon resonance energy transfer, surface enhanced Raman spectroscopy, and refractive index sensing, and (2) signal amplification elements in surface plasmon resonance spectroscopy and electrochemical detection. We critically discuss the clinical relevance of each category of circulating biomarkers, followed by a thorough analysis of how these nanoparticle-based designs have overcome some of the main challenges that gold standard analytical techniques currently face, and what new directions the field may take in the future.
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Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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Panicker S, Ahmady IM, Almehdi AM, Workie B, Sahle-Demessie E, Han C, Chehimi MM, Mohamed AA. Gold-Aryl nanoparticles coated with polyelectrolytes for adsorption and protection of DNA against nuclease degradation. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4803] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Seema Panicker
- Center for Advanced Materials Research, Research Institute for Science and Engineering; University of Sharjah; Sharjah 27272 UAE
| | - Islam M. Ahmady
- Department of Applied Biology; University of Sharjah; Sharjah 27272 UAE
| | - Ahmed M. Almehdi
- Department of Chemistry; University of Sharjah; Sharjah 27272 UAE
| | - Bizuneh Workie
- Department of Chemistry; Delaware State University; 1200 North DuPont Highway, Dover Delaware 19901 USA
| | - Endalkachew Sahle-Demessie
- The U.S. Environmental Protection Agency, ORD, NRMRL, LMMD, MMB; 26 W. Martin Luther King Jr. Drive Cincinnati Ohio 45268 USA
| | - Changseok Han
- Department of Environmental Engineering; INHA University; Michuhol-gu, 100 Inha-ro Incheon 22212 Republic of Korea
| | | | - Ahmed A. Mohamed
- Center for Advanced Materials Research, Research Institute for Science and Engineering; University of Sharjah; Sharjah 27272 UAE
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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]
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Wang J, Lv F, Liu L, Ma Y, Wang S. Strategies to design conjugated polymer based materials for biological sensing and imaging. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2017.06.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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6
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Wei X, Chen Z, Tan L, Lou T, Zhao Y. DNA-Catalytically Active Gold Nanoparticle Conjugates-Based Colorimetric Multidimensional Sensor Array for Protein Discrimination. Anal Chem 2016; 89:556-559. [DOI: 10.1021/acs.analchem.6b04878] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiangcong Wei
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Zhengbo Chen
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Lulu Tan
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Tianhong Lou
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Yan Zhao
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
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Pallares RM, Bosman M, Thanh NTK, Su X. A plasmonic multi-logic gate platform based on sequence-specific binding of estrogen receptors and gold nanorods. NANOSCALE 2016; 8:19973-19977. [PMID: 27783084 DOI: 10.1039/c6nr07569j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A hybrid system made of gold nanorods (AuNRs) and double-stranded DNA (dsDNA) is used to build a versatile multi-logic gate platform, capable of performing six different logic operations. The sequence-specific binding of transcription factors to the DNA drives the optical response of the design.
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Affiliation(s)
- Roger M Pallares
- Department of Chemistry, University College London, London, WC1H 0AJ, UK and Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way. Innovis, #8-03, Singapore138634.
| | - Michel Bosman
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way. Innovis, #8-03, Singapore138634.
| | - Nguyen T K Thanh
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK and UCL Healthcare Biomagnetic and Nanomaterials Laboratories, 21 Albemarle Street, London W1S 4BS, UK.
| | - Xiaodi Su
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way. Innovis, #8-03, Singapore138634.
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9
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Gold Nanoparticle-Based Förster Resonance Energy Transfer (FRET) Analysis of Estrogen Receptor: DNA Interaction. Methods Mol Biol 2015. [PMID: 26585138 DOI: 10.1007/978-1-4939-3127-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Estrogen receptors play critical roles in regulating genes responsible for development and maintenance of reproductive tissues and other physiological function. The interaction of ERs with DNA sequences, known as estrogen response elements (EREs) (a palindromic repeat separated by three-base spacer, 5'GGTCAnnnTGACC-3'), is required for estrogen regulation of target gene expression. Here, we describe a simple "mix-and-measure"-based method for detecting ER:ERE interactions using ERE-immobilized metal nanoparticles and water-soluble conjugated polyelectrolytes (CPEs) as cooperative sensing elements. This method can differentiate the distinct DNA-binding affinity between ERα and ERβ, and determine ER:ERE-binding stoichiometry. This method can also accurately detect all 15 singly mutated EREs (i.e., three possible base substitutions at each of one to five positions from left to right of the 5' end half site, GGTCA) for their binding energy to ER. This method is compatible with 96-well plate format for high-throughput analysis.
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Wang P, Lin L, Guo Z, Chen J, Tian H, Chen X, Yang H. Highly Fluorescent Gene Carrier Based on Ag-Au Alloy Nanoclusters. Macromol Biosci 2015; 16:160-7. [DOI: 10.1002/mabi.201500235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 06/30/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Ping Wang
- College of Chemistry; Jilin University; Changchun 130012 China
| | - Lin Lin
- Key Laboratory of polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 China
| | - Zhaopei Guo
- Key Laboratory of polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 China
| | - Jie Chen
- Key Laboratory of polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 China
| | - Huayu Tian
- Key Laboratory of polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 China
| | - Xuesi Chen
- Key Laboratory of polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 China
| | - Hua Yang
- College of Chemistry; Jilin University; Changchun 130012 China
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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.
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Affiliation(s)
- Ning Li
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, 117602 Singapore.
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