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Fitzgerald P, Cochrane WG, Paegel BM. Dose-Response Activity-Based DNA-Encoded Library Screening. ACS Med Chem Lett 2023; 14:1295-1303. [PMID: 37736190 PMCID: PMC10510511 DOI: 10.1021/acsmedchemlett.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/04/2023] [Indexed: 09/23/2023] Open
Abstract
Dose-response, or "conforming" behavior, increases confidence in a screening hit's authenticity. Here, we demonstrate dose-response solid-phase DNA-encoded library (DEL) screening. Compound dose in microfluidic droplets is modulated via the UV intensity of photocleavage from DEL beads. A 55,296-member DEL was screened at different UV intensities against model enzyme drug targets factor Xa (FXa) and autotaxin (ATX). Both screens yielded photochemical dose-dependent hit rates (FXa hit rates of 0.08/0.05% at 100/30% UV exposure; ATX hit rates of 0.24/0.08% at 100/20% UV exposure). FXa hits contained structures reflective of FXa inhibitors and four hits inhibited FXa (IC50 = 4.2 ± 0.1, 7.4 ± 0.3, 9.0 ± 0.3, and 19 ± 2 μM.) The top ATX hits (two dihydrobenzamidazolones and a tetrahydroisoquinoline) were validated as inhibitors (IC50 = 7 ± 2, 13 ± 2, and 1 ± 0.3 μM). Photochemical dose-response DEL screening data prioritized hits for synthesis, the rate-limiting step in DEL lead identification.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Wesley G. Cochrane
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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2
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Functional Peptides from One-bead One-compound High-throughput Screening Technique. Chem Res Chin Univ 2023. [DOI: 10.1007/s40242-023-2356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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3
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Ge P, Yang M, Bouchard JL, Dzamko N, Lewis SJG, Halliday GM, Doran TM. Chemoselective Bioconjugation of Amyloidogenic Protein Antigens to PEGylated Microspheres Enables Detection of α-Synuclein Autoantibodies in Human Plasma. Bioconjug Chem 2022; 33:301-310. [PMID: 35020392 DOI: 10.1021/acs.bioconjchem.1c00530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The misfolding and subsequent aggregation of amyloidogenic proteins is a classic pathological hallmark of neurodegenerative diseases. Aggregates of the α-synuclein protein (αS) are implicated in Parkinson's disease (PD) pathogenesis, and naturally occurring autoantibodies to these aggregates are proposed to be potential early-stage biomarkers to facilitate the diagnosis of PD. However, upon misfolding, αS forms a multitude of quaternary structures of varying functions that are unstable ex vivo. Thus, when used as a capture agent in enzyme-linked immunosorbent assays (ELISAs), significant variance among laboratories has prevented the development of these valuable diagnostic tests. We reasoned that those conflicting results arise due to the high nonspecific binding and amyloid nucleation that are typical of ELISA platforms. In this work, we describe a multiplexed, easy-to-operate immunoassay that is generally applicable to quantify the levels of amyloid proteins and their binding partners, named Oxaziridine-Assisted Solid-phase Immunosorbent (OASIS) assay. The assay is built on a hydrophilic poly(ethylene glycol) scaffold that inhibits aggregate nucleation, which we show reduces assay variance when compared to similar ELISA measurements. To validate our OASIS assay in patient-derived samples, we measured the levels of naturally occurring antibodies against the αS monomer and oligomers in a cohort of donor plasma from patients diagnosed with PD. Using OASIS assays, we observed significantly higher titers of immunoglobulin G antibody recognizing αS oligomers in PD patients compared to those in healthy controls, while there was no significant difference in naturally occurring antibodies against the αS monomer. In addition to its development into a blood test to potentially predict or monitor PD, we anticipate that the OASIS assay will be of high utility for studies aimed at understanding protein misfolding, its pathology and symptomology in PD, and other neurodegenerative diseases.
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Affiliation(s)
- Peng Ge
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mu Yang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jacob L Bouchard
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Nicolas Dzamko
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Simon J G Lewis
- Parkinson's Disease Research Clinic, Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Glenda M Halliday
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Todd M Doran
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
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4
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Cochrane WG, Malone ML, Dang VQ, Cavett V, Satz AL, Paegel BM. Activity-Based DNA-Encoded Library Screening. ACS COMBINATORIAL SCIENCE 2019; 21:425-435. [PMID: 30884226 DOI: 10.1021/acscombsci.9b00037] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Robotic high-throughput compound screening (HTS) and, increasingly, DNA-encoded library (DEL) screening are driving bioactive chemical matter discovery in the postgenomic era. HTS enables activity-based investigation of highly complex targets using static compound libraries. Conversely, DEL grants efficient access to novel chemical diversity, although screening is limited to affinity-based selections. Here, we describe an integrated droplet-based microfluidic circuit that directly screens solid-phase DELs for activity. An example screen of a 67 100-member library for inhibitors of the phosphodiesterase autotaxin yielded 35 high-priority structures for nanomole-scale synthesis and validation (20 active), guiding candidate selection for synthesis at scale (5/5 compounds with IC50 values of 4-10 μM). We further compared activity-based hits with those of an analogous affinity-based DEL selection. This miniaturized screening platform paves the way toward applying DELs to more complex targets (signaling pathways, cellular response) and represents a distributable approach to small molecule discovery.
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Affiliation(s)
| | | | | | | | - Alexander L. Satz
- Roche Pharma Research and Early Development (pRED) Roche Innovation Center Basel F. Hoffman-La Roche Ltd Grenzacherstrasse 124 CH-4070 Basel Switzerland
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5
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Komnatnyy VV, Nielsen TE, Qvortrup K. Bead-based screening in chemical biology and drug discovery. Chem Commun (Camb) 2018; 54:6759-6771. [PMID: 29888365 DOI: 10.1039/c8cc02486c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput screening is an important component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds requires assays amenable to miniaturisation and automization. Combinatorial chemistry holds a unique promise to deliver structurally diverse libraries for early drug discovery. Among the various library forms, the one-bead-one-compound (OBOC) library, where each bead carries many copies of a single compound, holds the greatest potential for the rapid identification of novel hits against emerging drug targets. However, this potential has not yet been fully realized due to a number of technical obstacles. In this feature article, we review the progress that has been made in bead-based library screening and its application to the discovery of bioactive compounds. We identify the key challenges of this approach and highlight key steps needed for making a greater impact in the field.
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Affiliation(s)
- Vitaly V Komnatnyy
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
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6
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Xu G, Shi C, Guo D, Wang L, Ling Y, Han X, Luo J. Functional-segregated coumarin-containing telodendrimer nanocarriers for efficient delivery of SN-38 for colon cancer treatment. Acta Biomater 2015; 21:85-98. [PMID: 25910639 DOI: 10.1016/j.actbio.2015.04.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/25/2015] [Accepted: 04/16/2015] [Indexed: 12/17/2022]
Abstract
Four coumarin-containing telodendrimers (denoted as P-I, P-II, P-III and P-IV) were designed and synthesized to self-assemble into the corresponding nanoparticles. Of those, two nanoparticles (P-II and P-IV micelles) were screened and selected for targeted drug delivery of 7-ethyl-10-hydroxy camptothecin (SN-38), a prominent and efficacious anticancer agent, for the treatment of colon cancers. The nanoparticle encapsulation significantly increased the solubility of SN-38 in aqueous solution. Dynamic light scattering (DLS) showed the size of these SN-38 nanoparticles to be around 50 nm, and rod-shaped micelles were observed using transmission electron microscopy (TEM). These two novel nanoformulations of SN-38/P-II and SN-38/P-IV were found to exhibit similar in vitro cytotoxic activity against colon cancer cells as the free drug (SN-38 in DMSO) and were 500-fold more potent than irinotecan (a prodrug of SN-38). In addition, near infrared fluorescent (NIRF) optical imaging was utilized to monitor the tumor targeted delivery of SN-38/NPs via co-loading a NIRF dye. It was demonstrated that these NPs preferentially accumulated in tumors when compared to healthy tissue. A pharmacokinetics study showed that SN-38 micelle formulations had a longer circulating time in blood than irinotecan. Furthermore, SN-38 loaded nanoformulations exhibit superior anti-tumor efficacy when compared with irinotecan at equivalent SN-38 dose in HT-29 human colon cancer xenograft models.
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Affiliation(s)
- Gaofei Xu
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY 13210, United States; Department of Applied Chemistry, Science College, China Agricultural University, Beijing 100193, China
| | - Changying Shi
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Dandan Guo
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Lili Wang
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Yun Ling
- Department of Applied Chemistry, Science College, China Agricultural University, Beijing 100193, China
| | - Xiaobing Han
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Juntao Luo
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY 13210, United States.
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7
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Label-free detection microarray for novel peptide ligands screening base on MS–SPRi combination. Talanta 2015; 134:705-711. [DOI: 10.1016/j.talanta.2014.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/30/2022]
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8
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Chemoselective tarantula toxins report voltage activation of wild-type ion channels in live cells. Proc Natl Acad Sci U S A 2014; 111:E4789-96. [PMID: 25331865 DOI: 10.1073/pnas.1406876111] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Electrically excitable cells, such as neurons, exhibit tremendous diversity in their firing patterns, a consequence of the complex collection of ion channels present in any specific cell. Although numerous methods are capable of measuring cellular electrical signals, understanding which types of ion channels give rise to these signals remains a significant challenge. Here, we describe exogenous probes which use a novel mechanism to report activity of voltage-gated channels. We have synthesized chemoselective derivatives of the tarantula toxin guangxitoxin-1E (GxTX), an inhibitory cystine knot peptide that binds selectively to Kv2-type voltage gated potassium channels. We find that voltage activation of Kv2.1 channels triggers GxTX dissociation, and thus GxTX binding dynamically marks Kv2 activation. We identify GxTX residues that can be replaced by thiol- or alkyne-bearing amino acids, without disrupting toxin folding or activity, and chemoselectively ligate fluorophores or affinity probes to these sites. We find that GxTX-fluorophore conjugates colocalize with Kv2.1 clusters in live cells and are released from channels activated by voltage stimuli. Kv2.1 activation can be detected with concentrations of probe that have a trivial impact on cellular currents. Chemoselective GxTX mutants conjugated to dendrimeric beads likewise bind live cells expressing Kv2.1, and the beads are released by channel activation. These optical sensors of conformational change are prototype probes that can indicate when ion channels contribute to electrical signaling.
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9
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Shao Y, Shi C, Xu G, Guo D, Luo J. Photo and redox dual responsive reversibly cross-linked nanocarrier for efficient tumor-targeted drug delivery. ACS APPLIED MATERIALS & INTERFACES 2014; 6:10381-92. [PMID: 24921150 PMCID: PMC4094256 DOI: 10.1021/am501913m] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/12/2014] [Indexed: 05/25/2023]
Abstract
To develop a feasible and efficient nanocarrier for potential clinical application, a series of photo and redox dual responsive reversibly cross-linked micelles have been developed for the targeted anticancer drug delivery. The nanocarrier can be cross-linked efficiently via a clean, efficient, and controllable coumarin photodimerization within the nanocarrier, which simplify the formulation process and quality control prior clinical use and improve the in vivo stability for tumor targeting. At the same time, cross-linking of nanocarrier could be cleaved via the responsiveness of the built-in disulfide cross-linkage to the redox tumor microenvironment for on-demand drug release. Coumarin and disulfide bond was introduced into a linear-dendritic copolymer (named as telodendrimer) precisely via peptide chemistry. The engineered nanocarrier possesses good drug loading capacity and stability, and exhibits a safer profile as well as similar anticancer effects compared with free drug in cell culture. The in vivo and ex vivo small animal imaging revealed the preferred tumor accumulation and the prolonged tumor residency of the payload delivered by the cross-linked micelles compared to the non-cross-linked micelles and free drug surrogate because of the increased stability.
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Affiliation(s)
- Yu Shao
- Department
of Pharmacology, SUNY Upstate Cancer Research Institute, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
| | - Changying Shi
- Department
of Pharmacology, SUNY Upstate Cancer Research Institute, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
| | - Gaofei Xu
- Department
of Pharmacology, SUNY Upstate Cancer Research Institute, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
- Department
of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - DanDan Guo
- Department
of Pharmacology, SUNY Upstate Cancer Research Institute, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
| | - Juntao Luo
- Department
of Pharmacology, SUNY Upstate Cancer Research Institute, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
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10
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Sun YS, Fei Y, Luo J, Dixon S, Landry JP, Lam KS, Zhu X. Generating Encoded Compound Libraries for Fabricating Microarrays as a High-Throughput Protein Ligand Discovery Platform. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.840728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yung-Shin Sun
- a Department of Physics , Fu-Jen Catholic University , New Taipei City , Taiwan
| | - Yiyan Fei
- b Department of Optical Science and Engineering , Fudan University , Shanghai , China
- c Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Ultra-Precision Optical Manufacturing Engineering Center , Fudan University , Shanghai , China
| | - Juntao Luo
- d Department of Pharmacology , Upstate Cancer Research Institute, State University of New York Upstate Medical University , Syracuse , New York , USA
| | - Seth Dixon
- e Division of Hematology and Oncology, Department of Internal Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
| | - James P. Landry
- f Department of Physics , University of California at Davis , Davis , California , USA
| | - Kit S. Lam
- e Division of Hematology and Oncology, Department of Internal Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
- g Department of Biochemistry and Molecular Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
| | - Xiangdong Zhu
- f Department of Physics , University of California at Davis , Davis , California , USA
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11
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Vokkaliga S, Jeong J, LaCourse WR, Kalivretenos A. Synthesis of amide libraries with immobilized HOBt. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.03.097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Townsend JB, Shaheen F, Liu R, Lam KS. Jeffamine derivatized TentaGel beads and poly(dimethylsiloxane) microbead cassettes for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound combinatorial small molecule libraries. ACTA ACUST UNITED AC 2010; 12:700-12. [PMID: 20593859 DOI: 10.1021/cc100083f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method to efficiently immobilize and partition large quantities of microbeads in an array format in microfabricated poly(dimethylsiloxane) (PDMS) cassette for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound (OBOC) combinatorial libraries is described. Commercially available Jeffamine triamine T-403 (∼440 Da) was derivatized such that two of its amino groups were protected by Fmoc and the remaining amino group capped with succinic anhydride to generate a carboxyl group. This resulting trifunctional hydrophilic polymer was then sequentially coupled two times to the outer layer of topologically segregated bilayer TentaGel (TG) beads with solid phase peptide synthesis chemistry resulting in beads with increased loading capacity, hydrophilicity, and porosity at the outer layer. We have found that such bead configuration can facilitate ultrahigh-throughput in situ releasable solution-phase screening of OBOC libraries. An encoded releasable OBOC small molecule library was constructed on Jeffamine derivatized TG beads with library compounds tethered to the outer layer via a disulfide linker and coding tags in the interior of the beads. Compound-beads could be efficiently loaded (5-10 min) into a 5 cm diameter Petri dish containing a 10,000-well PDMS microbead cassette, such that over 90% of the microwells were each filled with only one compound-bead. Jurkat T-lymphoid cancer cells suspended in Matrigel were then layered over the microbead cassette to immobilize the compound-beads. After 24 h of incubation at 37 °C, dithiothreitol was added to trigger the release of library compounds. Forty-eight hours later, MTT reporter assay was used to identify regions of reduced cell viability surrounding each positive bead. From a total of about 20,000 beads screened, 3 positive beads were detected and physically isolated for decoding. A strong consensus motif was identified for these three positive compounds. These compounds were resynthesized and found to be cytotoxic (IC(50) 50-150 μM) against two T-lymphoma cell lines and less so against the MDA-MB 231 breast cancer cell line. This novel ultrahigh-throughput OBOC releasable method can potentially be adapted to many existing 96- or 384-well solution-phase cell-based or biochemical assays.
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Affiliation(s)
- Jared B Townsend
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, University of California Davis Cancer Center, University of California Davis, 4501 X Street, Sacramento, California 95817, USA
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13
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Jun BH, Baek J, Kang H, Park YJ, Jeong DH, Lee YS. Preparation of polydiacetylene immobilized optically encoded beads. J Colloid Interface Sci 2010; 355:29-34. [PMID: 21194704 DOI: 10.1016/j.jcis.2010.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 12/01/2010] [Accepted: 12/02/2010] [Indexed: 10/18/2022]
Abstract
Polydiacetylene (PDA), which can change the chromic and fluorescence properties by inducing environmental perturbations, is immobilized on planar solid supports for many biological applications. In this work, we immobilize PDA onto optically encoded spherical beads (PDA-SERS beads). The prepared PDA immobilized beads (36 μm) exhibit a blue color without fluorescence. By inducing stress, their color and fluorescence properties are changed to red with fluorescence. The SERS spectra of the PDA-SERS beads can be recognized over the PDA background. Moreover, our PDA immobilization methods are successfully applied to silica-surface SERS-encoded beads (5 μm) and proven to also be useful in fluorescence encoding systems.
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Affiliation(s)
- Bong-Hyun Jun
- School of Chemical and Biological Engineering, Seoul National University, Seoul 151-747, Republic of Korea
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