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Vaz R, Valpradinhos B, Frasco MF, Sales MGF. Emerging Optical Materials in Sensing and Discovery of Bioactive Compounds. SENSORS (BASEL, SWITZERLAND) 2021; 21:5784. [PMID: 34502675 PMCID: PMC8434157 DOI: 10.3390/s21175784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 11/16/2022]
Abstract
Optical biosensors are used in numerous applications and analytical fields. Advances in these sensor platforms offer high sensitivity, selectivity, miniaturization, and real-time analysis, among many other advantages. Research into bioactive natural products serves both to protect against potentially dangerous toxic compounds and to promote pharmacological innovation in drug discovery, as these compounds have unique chemical compositions that may be characterized by greater safety and efficacy. However, conventional methods for detecting these biomolecules have drawbacks, as they are time-consuming and expensive. As an alternative, optical biosensors offer a faster, simpler, and less expensive means of detecting various biomolecules of clinical interest. In this review, an overview of recent developments in optical biosensors for the detection and monitoring of aquatic biotoxins to prevent public health risks is first provided. In addition, the advantages and applicability of these biosensors in the field of drug discovery, including high-throughput screening, are discussed. The contribution of the investigated technological advances in the timely and sensitive detection of biotoxins while deciphering the pathways to discover bioactive compounds with great health-promoting prospects is envisaged to meet the increasing demands of healthcare systems.
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Affiliation(s)
- Raquel Vaz
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal; (R.V.); (M.G.F.S.)
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Beatriz Valpradinhos
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Manuela F. Frasco
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal; (R.V.); (M.G.F.S.)
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Maria Goreti F. Sales
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal; (R.V.); (M.G.F.S.)
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal
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2
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Li G, Panday SK, Peng Y, Alexov E. SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions. Bioinformatics 2021; 37:3760-3765. [PMID: 34343273 DOI: 10.1093/bioinformatics/btab567] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/28/2021] [Accepted: 07/31/2021] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Mutations that alter protein-DNA interactions may be pathogenic and cause diseases. Therefore, it is extremely important to quantify the effect of mutations on protein-DNA binding free energy to reveal the molecular origin of diseases and to assist the development of treatments. Although several methods that predict the change of protein-DNA binding affinity upon mutations in the binding protein were developed, the effect of DNA mutations was not considered yet. RESULTS Here, we report a new version of SAMPDI, the SAMPDI-3D, which is a gradient boosting decision tree machine learning method to predict the change of the protein-DNA binding free energy caused by mutations in both the binding protein and the bases of the corresponding DNA. The method is shown to achieve Pearson correlation coefficient of 0.76 and 0.80 in a benchmarking test against experimentally determined change of the binding free energy caused by mutations in the binding protein or DNA, respectively. Furthermore, three datasets collected from literature were used to do blind benchmark for SAMPDI-3D and it is shown that it outperforms all existing state-of-the-art methods. The method is very fast allowing for genome-scale investigations. AVAILABILITY It is available as a web server and a stand-code at http://compbio.clemson.edu/SAMPDI-3D/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gen Li
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | | | - Yunhui Peng
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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3
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Patel M, Patel D, Datta S, Singh U. An immunochemistry-based screen for chemical inhibitors of DNA-protein interactions and its application to human CGGBP1. BMC Cancer 2020; 20:1016. [PMID: 33081720 PMCID: PMC7576722 DOI: 10.1186/s12885-020-07526-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Inhibition of DNA-binding of proteins by small-molecule chemicals holds immense potential in manipulating the activities of DNA-binding proteins. Such a chemical inhibition of DNA-binding of proteins can be used to modulate processes such as replication, transcription, DNA repair and maintenance of epigenetic states. This prospect is currently challenged with the absence of robust and generic protocols to identify DNA-protein interactions. Additionally, much of the current approaches to designing inhibitors requires structural information of the target proteins. METHODS We have developed a simple dot blot and immunodetection-based assay to screen chemical libraries for inhibitors of DNA-protein interactions. The assay has been applied to a library of 1685 FDA-approved chemicals to discover inhibitors of CGGBP1, a multifunctional DNA-binding protein with no known structure. Additional in vitro and in cellulo assays have been performed to verify and supplement the findings of the screen. RESULTS Our primary screen has identified multiple inhibitors of direct or indirect interactions between CGGBP1 and genomic DNA. Of these, one inhibitor, Givinostat, was found to inhibit direct DNA-binding of CGGBP1 in the secondary screen using purified recombinant protein as the target. DNA and chromatin immunoprecipitation assays reinforced the findings of the screen that Givinostat inhibits CGGBP1-DNA binding. CONCLUSIONS The assay we have described successfully identifies verifiable inhibitors of DNA-binding of protein; in this example, the human CGGBP1. This assay is customizable for a wide range of targets for which primary antibodies are available. It works with different sources of the target protein, cell lysates or purified recombinant preparations and does not require special equipment, DNA modifications or protein structural data. This assay is scalable and highly adaptable with the potential to discover inhibitors of transcription factors with implications in cancer biology.
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Affiliation(s)
- Manthan Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Divyesh Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Subhamoy Datta
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Umashankar Singh
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.
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Villanueva R, Romero-Tamayo S, Laplaza R, Martínez-Olivan J, Velázquez-Campoy A, Sancho J, Ferreira P, Medina M. Redox- and Ligand Binding-Dependent Conformational Ensembles in the Human Apoptosis-Inducing Factor Regulate Its Pro-Life and Cell Death Functions. Antioxid Redox Signal 2019; 30:2013-2029. [PMID: 30450916 DOI: 10.1089/ars.2018.7658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aims: The human apoptosis-inducing factor (hAIF) supports OXPHOS biogenesis and programmed cell death, with missense mutations producing neurodegenerative phenotypes. hAIF senses the redox environment of cellular compartments, stabilizing a charge transfer complex (CTC) dimer that modulates the protein interaction network. In this context, we aimed to evaluate the subcellular pH, CTC formation, and pathogenic mutations effects on hAIF stability, and a thermal denaturation high-throughput screening (HTS) assay to discover AIF binders. Results: Apoptotic hAIFΔ1-101 is not stable at intermembrane mitochondrial space (IMS) pH, but the 77-101 residues confer stability to the mitochondrial isoform. hAIF and its CTC populate different conformational ensembles with redox switch to the CTC producing a less stable and compact protein. The pathogenic G308E, ΔR201, and E493V mutations modulate hAIF stability; particularly, ΔR201 causes a population shift to a less stable conformation that remodels active site structure and dynamics. We have identified new molecules that modulate the hAIF reduced nicotinamide adenine dinucleotide (NADH)/oxidized nicotinamide adenine dinucleotide (NAD+) association/dissociation equilibrium and regulate its catalytic efficiency. Innovation: Biophysical methods allow evaluating the regulation of hAIF functional ensembles and to develop an HTS assay to discover small molecules that might modulate hAIF stability and activities. Conclusions: The mitochondrial soluble 54-77 portion stabilizes hAIF at the IMS pH. NADH-redox-linked conformation changes course with strong NAD+ binding and protein dimerization, but they produce a negative impact in overall hAIF stability. Loss of functionality in the R201 deletion is due to distortion of the active site architecture. We report molecules that may serve as leads in the development of hAIF bioactive compounds.
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Affiliation(s)
- Raquel Villanueva
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Silvia Romero-Tamayo
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Ruben Laplaza
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,2 Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan Martínez-Olivan
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,3 Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.,4 Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,5 Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Javier Sancho
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,4 Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Patricia Ferreira
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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5
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Mishra A, Pant P, Mrinal N, Jayaram B. A computational protocol for the discovery of lead molecules targeting DNA unique to pathogens. Methods 2017; 131:4-9. [PMID: 28733089 DOI: 10.1016/j.ymeth.2017.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/11/2017] [Accepted: 07/18/2017] [Indexed: 12/19/2022] Open
Abstract
With the rapid emergence of drug resistant pathogens, it has become imperative to develop alternative medications as well as find new drug targets to overcome this crisis. Hence, this has become prime focus of several academic laboratories and pharmaceutical companies. Here, we report a computational protocol for identifying unique DNA sequence(s) in the pathogen which is absent in human and related non-pathogenic strains of the microbe. In order to use the unique sequence as drug target, the protocol, in the second step, uses virtual screening against a million compound library to identify candidate small molecules which can bind to these unique DNA targets in the pathogen only. Theoretically the molecules identified after screening should not bind to human DNA. This methodology is demonstrated on Mycobacterium tuberculosis H37Rv, wherein a new octamer sequence present only in H37Rv has been identified and a few candidate small molecules as potential drug have been proposed. Being fast and cost effective, this protocol could be of importance in generating new potential drug candidates against infectious organisms for further experimental studies. This methodology is freely available at http://www.scfbio-iitd.res.in/PSDDF/.
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Affiliation(s)
- Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Pradeep Pant
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India; Department of Chemistry, Indian Institute of Technology Delhi, India
| | - Nirotpal Mrinal
- Laboratory of Molecular Biology, South Asian University, New Delhi, India
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India; Department of Chemistry, Indian Institute of Technology Delhi, India.
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Diouf B, Lin W, Goktug A, Grace CRR, Waddell MB, Bao J, Shao Y, Heath RJ, Zheng JJ, Shelat AA, Relling MV, Chen T, Evans WE. Alteration of RNA Splicing by Small-Molecule Inhibitors of the Interaction between NHP2L1 and U4. SLAS DISCOVERY 2017; 23:164-173. [PMID: 28985478 DOI: 10.1177/2472555217735035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Splicing is an important eukaryotic mechanism for expanding the transcriptome and proteome, influencing a number of biological processes. Understanding its regulation and identifying small molecules that modulate this process remain a challenge. We developed an assay based on time-resolved fluorescence resonance energy transfer (TR-FRET) to detect the interaction between the protein NHP2L1 and U4 RNA, which are two key components of the spliceosome. We used this assay to identify small molecules that interfere with this interaction in a high-throughput screening (HTS) campaign. Topotecan and other camptothecin derivatives were among the top hits. We confirmed that topotecan disrupts the interaction between NHP2L1 and U4 by binding to U4 and inhibits RNA splicing. Our data reveal new functions of known drugs that could facilitate the development of therapeutic strategies to modify splicing and alter gene function.
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Affiliation(s)
- Barthelemy Diouf
- 1 Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,2 Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenwei Lin
- 3 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Asli Goktug
- 3 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christy R R Grace
- 4 Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Brett Waddell
- 5 Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ju Bao
- 1 Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,2 Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Youming Shao
- 6 Protein Production Facility, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard J Heath
- 6 Protein Production Facility, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jie J Zheng
- 7 Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Anang A Shelat
- 3 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- 1 Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,2 Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- 3 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- 1 Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,2 Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
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7
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Noguchi F, Inui S, Fedele C, Shackleton M, Itami S. Calcium-Dependent Enhancement by Extracellular Acidity of the Cytotoxicity of Mitochondrial Inhibitors against Melanoma. Mol Cancer Ther 2017; 16:936-947. [DOI: 10.1158/1535-7163.mct-15-0235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/30/2015] [Accepted: 02/08/2017] [Indexed: 11/16/2022]
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Inan H, Poyraz M, Inci F, Lifson MA, Baday M, Cunningham BT, Demirci U. Photonic crystals: emerging biosensors and their promise for point-of-care applications. Chem Soc Rev 2017; 46:366-388. [PMID: 27841420 PMCID: PMC5529146 DOI: 10.1039/c6cs00206d] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in clinical settings worldwide. The implementation of biosensors at the point-of-care (POC), such as at primary clinics or the bedside, faces impediments because they may require highly trained personnel, have long assay times, large sizes, and high instrumental cost. Thus, there exists a need to develop inexpensive, reliable, user-friendly, and compact biosensing systems at the POC. Biosensors incorporated with photonic crystal (PC) structures hold promise to address many of the aforementioned challenges facing the development of new POC diagnostics. Currently, PC-based biosensors have been employed for detecting a variety of biotargets, such as cells, pathogens, proteins, antibodies, and nucleic acids, with high efficiency and selectivity. In this review, we provide a broad overview of PCs by explaining their structures, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-based biosensors incorporated with emerging technologies, including telemedicine, flexible and wearable sensing, smart materials and metamaterials. Finally, we discuss current challenges associated with existing biosensors, and provide an outlook for PC-based biosensors and their promise at the POC.
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Affiliation(s)
- Hakan Inan
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA.
| | - Muhammet Poyraz
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA. and Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Fatih Inci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA.
| | - Mark A Lifson
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA.
| | - Murat Baday
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA.
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Utkan Demirci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA. and Department of Electrical Engineering (by courtesy), Stanford University, Stanford, CA, USA
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Fabini E, Zambelli B, Mazzei L, Ciurli S, Bertucci C. Surface plasmon resonance and isothermal titration calorimetry to monitor the Ni(II)-dependent binding of Helicobacter pylori NikR to DNA. Anal Bioanal Chem 2016; 408:7971-7980. [DOI: 10.1007/s00216-016-9894-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/28/2016] [Accepted: 08/17/2016] [Indexed: 02/03/2023]
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10
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Kong X, Ye B, Yang Z, Chen B, Ling Y. Simultaneous detection of platelet-specific antibodies based on a photonic crystal-encoded suspension array. Clin Chim Acta 2016; 458:72-7. [PMID: 27129630 DOI: 10.1016/j.cca.2016.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 04/20/2016] [Accepted: 04/25/2016] [Indexed: 12/01/2022]
Abstract
BACKGROUND The appearance of antibodies to platelets in the blood is an important cause of immune thrombocytopenia (ITP), and platelet glycoprotein (GP)-specific antibody detection may be helpful to diagnose this condition. METHODS Photonic crystal microspheres with different distinct reflection spectra were coated with anti-GPIIb, -GPIIIa, -GPIb and -GPIX monoclonal antibodies (MoAbs) to create a photonic crystal-encoded suspension array (PCSA). Fluorescein isothiocyanate-labelled goat anti-human IgG was added to detect human IgG simultaneously. The detection results were analysed by fluorescence microscopy. Parallel MoAb immobilization of platelet antigen (MAIPA) was used as a reference test. Both methods were used to analyse 63 clinical samples including serum from 32 ITP patients and 31 healthy humans. RESULTS The PCSA showed greater sensitivity than MAIPA in detecting anti-GPIIb (75.0% vs 31.1%) and GPIIIa (84.4% vs 40.6%) antibodies and similar sensitivity as MAIPA in detecting anti-GPIb (37.5% vs 34.4%) and GPIX (50.0% vs 40.8%) antibodies. The MAIPA and PCSA tests had similar specificity. The PCSA detected higher dilutions of serum containing anti-GPIIIa antibody or anti-GPIIb antibody than did MAIPA. The entire testing process was controlled within 3.5h. CONCLUSIONS The PCSA assay described has comparable or better sensitivity and specificity compared to the MAIPA and is more rapid.
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Affiliation(s)
- Xin Kong
- The Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, Changzhou, Jiangsu 213000, China
| | - Baofen Ye
- State Key Laboratory of Bioelectronics Southeast University, Nanjing 210096, China
| | - Zixue Yang
- State Key Laboratory of Bioelectronics Southeast University, Nanjing 210096, China; Department of Hematology, Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Baoan Chen
- Department of Hematology, Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Yun Ling
- The Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, Changzhou, Jiangsu 213000, China; Department of Hematology, Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China.
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11
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Cunningham B, Zhang M, Zhuo Y, Kwon L, Race C. Recent Advances in Biosensing With Photonic Crystal Surfaces: A Review. IEEE SENSORS JOURNAL 2016; 16:3349-3366. [PMID: 27642265 PMCID: PMC5021450 DOI: 10.1109/jsen.2015.2429738] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Photonic crystal surfaces that are designed to function as wavelength-selective optical resonators have become a widely adopted platform for label-free biosensing, and for enhancement of the output of photon-emitting tags used throughout life science research and in vitro diagnostics. While some applications, such as analysis of drug-protein interactions, require extremely high resolution and the ability to accurately correct for measurement artifacts, others require sensitivity that is high enough for detection of disease biomarkers in serum with concentrations less than 1 pg/ml. As the analysis of cells becomes increasingly important for studying the behavior of stem cells, cancer cells, and biofilms under a variety of conditions, approaches that enable high resolution imaging of live cells without cytotoxic stains or photobleachable fluorescent dyes are providing new tools to biologists who seek to observe individual cells over extended time periods. This paper will review several recent advances in photonic crystal biosensor detection instrumentation and device structures that are being applied towards direct detection of small molecules in the context of high throughput drug screening, photonic crystal fluorescence enhancement as utilized for high sensitivity multiplexed cancer biomarker detection, and label-free high resolution imaging of cells and individual nanoparticles as a new tool for life science research and single-molecule diagnostics.
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Affiliation(s)
- B.T. Cunningham
- Dept. of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign
| | - M. Zhang
- Dept. of Physics, University of Illinois at Urbana-Champaign
| | - Y. Zhuo
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign
| | - L. Kwon
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign
| | - C. Race
- Dept. of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign
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12
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Lifson MA, Miller BL. Photonic Crystals as Robust Label-Free Biosensors. PHOTONIC MATERIALS FOR SENSING, BIOSENSING AND DISPLAY DEVICES 2016. [DOI: 10.1007/978-3-319-24990-2_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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13
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Aki S, Endo T, Sueyoshi K, Hisamoto H. Plasticized poly(vinyl chloride)-based photonic crystal for ion sensing. Anal Chem 2014; 86:11986-91. [PMID: 25397688 DOI: 10.1021/ac503447m] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we, for the first time, developed a plasticized poly(vinyl chloride) (PVC)-based two-dimensional photonic crystal (2D-PhC) optical sensor using nanoimprint lithography (NIL), which can perform highly sensitive, fast, and selective ion sensing based on ion extraction. Concerning the principle of response, present plasticized PVC-based PhC works as a waveguide and a grating. Incident light was guided in the bulk of plasticized PVC and, then, guided light of a specific wavelength was diffracted by a periodic nanostructure. The guided and diffracted light intensity changes of PVC-based PhCs possessing various thicknesses were monitored at 580 nm; then, we found that the 0.35 μm-thick PhC film exhibited the highest diffraction intensity. For the ion-sensing application, potassium-selective sensing elements involving potassium ionophore and lipophilic dye were dissolved in a plasticized PVC-based PhC, and the K(+)-selective response was successfully observed by monitoring the diffracted peak intensity change. The present 2D-PhC optical sensor exhibited a fast response within 5 s (95% response time) due to the use of thin film, and sensitivity was 20 times higher than that of a PVC plane-film optical sensor, due to efficient collection of diffracted light by employing a periodic nanostructure of the photonic crystal.
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Affiliation(s)
- Shoma Aki
- Department of Applied Chemistry, Osaka Prefecture University , 1-1 Gakuencho, Naka-ku, Sakai, Osaka 599-8531, Japan
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Wyhs N, Walker D, Giovinazzo H, Yegnasubramanian S, Nelson WG. Time-Resolved Fluorescence Resonance Energy Transfer Assay for Discovery of Small-Molecule Inhibitors of Methyl-CpG Binding Domain Protein 2. JOURNAL OF BIOMOLECULAR SCREENING 2014; 19:1060-9. [PMID: 24608100 PMCID: PMC4183726 DOI: 10.1177/1087057114526433] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 02/10/2014] [Indexed: 01/23/2023]
Abstract
Methylated DNA binding proteins such as Methyl-CpG Binding Domain Protein 2 (MBD2) can transduce DNA methylation alterations into a repressive signal by recruiting transcriptional co-repressor complexes. Interfering with MBD2 could lead to reactivation of tumor suppressor genes and therefore represents an attractive strategy for epigenetic therapy. We developed and compared fluorescence polarization (FP) and time-resolved fluorescence resonance energy transfer (TR-FRET)-based high-throughput screening (HTS) assays to identify small-molecule inhibitors of the interaction between the methyl binding domain of MBD2 (MBD2-MBD) and methylated DNA. Although both assays performed well in 96-well format, the TR-FRET assay (Z' factor = 0.58) emerged as a superior screening strategy compared with FP (Z' factor = 0.08) when evaluated in an HTS 384-well plate format. Using TR-FRET, we screened the Sigma LOPAC library for MBD2-MBD inhibitors and identified four compounds that also validated in a dose-response series. This included two known DNA intercalators (mitoxantrone and idarubicin) among two other inhibitory compounds (NF449 and aurintricarboxylic acid). All four compounds also inhibited the binding of SP-1, a transcription factor with a GC-rich binding sequence, to a methylated oligonucleotide, demonstrating that the activity was nonspecific. Our results provide proof of principle for using TR-FRET-based HTS to identify small-molecule inhibitors of MBD2 and other DNA-protein interactions.
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Affiliation(s)
- Nicolas Wyhs
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Walker
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hugh Giovinazzo
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - William G Nelson
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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15
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Shen K, Jiang G, Mao W, Baig S, Wang MR. Fabrication of two kinds of eight-fold photonic quasi-crystals assisted by a specially designed prism. APPLIED OPTICS 2013; 52:6474-6480. [PMID: 24085122 DOI: 10.1364/ao.52.006474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/24/2013] [Indexed: 06/02/2023]
Abstract
We demonstrate that two kinds of 2D eight-fold photonic quasi-crystals (PQCs) can be fabricated by a specially designed prism via single-exposure holographic lithography. The prism with five continuous side surfaces out of common eight symmetrical side surfaces, plus a top surface, is well designed for PQC fabrication. Compared with the traditional method of setting up eight free-space beams in the half-space for an eight-fold PQC fabrication, our specially designed prism reduces the number of beams, avoids the differences of beam-to-beam phases, and simplifies the fabrication process. The theory and computer simulation confirm the patterns of two kinds of PQCs by a single prism illumination recording. Further, these quasi-crystal patterns are successfully verified by experimental results under a scanning electron microscope. In addition, these samples show some good properties, such as uniformity over large area, the implementation of a single defect by underexposure, and symmetry break of the eight dots. Our special prism-assisted holographic lithography technique provides a base for further investigating the optical properties of these novel structures.
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16
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Senveli SU, Tigli O. Biosensors in the small scale: methods and technology trends. IET Nanobiotechnol 2013; 7:7-21. [PMID: 23705288 DOI: 10.1049/iet-nbt.2012.0005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This study presents a review on biosensors with an emphasis on recent developments in the field. A brief history accompanied by a detailed description of the biosensor concepts is followed by rising trends observed in contemporary micro- and nanoscale biosensors. Performance metrics to quantify and compare different detection mechanisms are presented. A comprehensive analysis on various types and subtypes of biosensors are given. The fields of interest within the scope of this review are label-free electrical, mechanical and optical biosensors as well as other emerging and popular technologies. Especially, the latter half of the last decade is reviewed for the types, methods and results of the most prominently researched detection mechanisms. Tables are provided for comparison of various competing technologies in the literature. The conclusion part summarises the noteworthy advantages and disadvantages of all biosensors reviewed in this study. Furthermore, future directions that the micro- and nanoscale biosensing technologies are expected to take are provided along with the immediate outlook.
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Affiliation(s)
- Sukru U Senveli
- Department of Electrical and Computer Engineering, University of Miami, Coral Gables, FL 33146, USA
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17
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Design optimization of structural parameters for highly sensitive photonic crystal label-free biosensors. SENSORS 2013; 13:3232-41. [PMID: 23470487 PMCID: PMC3658742 DOI: 10.3390/s130303232] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/11/2013] [Accepted: 03/01/2013] [Indexed: 11/17/2022]
Abstract
The effects of structural design parameters on the performance of nano-replicated photonic crystal (PC) label-free biosensors were examined by the analysis of simulated reflection spectra of PC structures. The grating pitch, duty, scaled grating height and scaled TiO2 layer thickness were selected as the design factors to optimize the PC structure. The peak wavelength value (PWV), full width at half maximum of the peak, figure of merit for the bulk and surface sensitivities, and surface/bulk sensitivity ratio were also selected as the responses to optimize the PC label-free biosensor performance. A parametric study showed that the grating pitch was the dominant factor for PWV, and that it had low interaction effects with other scaled design factors. Therefore, we can isolate the effect of grating pitch using scaled design factors. For the design of PC-label free biosensor, one should consider that: (1) the PWV can be measured by the reflection peak measurement instruments, (2) the grating pitch and duty can be manufactured using conventional lithography systems, and (3) the optimum design is less sensitive to the grating height and TiO2 layer thickness variations in the fabrication process. In this paper, we suggested a design guide for highly sensitive PC biosensor in which one select the grating pitch and duty based on the limitations of the lithography and measurement system, and conduct a multi objective optimization of the grating height and TiO2 layer thickness for maximizing performance and minimizing the influence of parameter variation. Through multi-objective optimization of a PC structure with a fixed grating height of 550 nm and a duty of 50%, we obtained a surface FOM of 66.18 RIU−1 and an S/B ratio of 34.8%, with a grating height of 117 nm and TiO2 height of 210 nm.
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Li N, Cheng XR, Brahmendra A, Prashar A, Endo T, Guyard C, Terebiznik M, Kerman K. Photonic crystals on copolymer film for bacteria detection. Biosens Bioelectron 2013; 41:354-8. [DOI: 10.1016/j.bios.2012.08.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 08/21/2012] [Accepted: 08/24/2012] [Indexed: 10/28/2022]
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Holdgate G, Geschwindner S, Breeze A, Davies G, Colclough N, Temesi D, Ward L. Biophysical methods in drug discovery from small molecule to pharmaceutical. Methods Mol Biol 2013; 1008:327-355. [PMID: 23729258 DOI: 10.1007/978-1-62703-398-5_12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Biophysical methods have become established in many areas of drug discovery. Application of these methods was once restricted to a relatively small number of scientists using specialized, low throughput technologies and methods. Now, automated high-throughput instruments are to be found in a growing number of laboratories. Many biophysical methods are capable of measuring the equilibrium binding constants between pairs of molecules crucial for molecular recognition processes, encompassing protein-protein, protein-small molecule, and protein-nucleic acid interactions, and several can be used to measure the kinetic or thermodynamic components controlling these biological processes. For a full characterization of a binding process, determinations of stoichiometry, binding mode, and any conformational changes associated with such interactions are also required. The suite of biophysical methods that are now available represents a powerful toolbox of techniques which can effectively deliver this full characterization.The aim of this chapter is to provide the reader with an overview of the drug discovery process and how biophysical methods, such as surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), nuclear magnetic resonance, mass spectrometry (MS), and thermal unfolding methods can answer specific questions in order to influence project progression and outcomes. The selection of these examples is based upon the experiences of the authors at AstraZeneca, and relevant approaches are highlighted where they have utility in a particular drug discovery scenario.
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Pal S, Fauchet PM, Miller BL. 1-D and 2-D photonic crystals as optical methods for amplifying biomolecular recognition. Anal Chem 2012; 84:8900-8. [PMID: 22947038 PMCID: PMC3491098 DOI: 10.1021/ac3012945] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Label-free sensing strategies are an intensely studied and increasingly used alternative to signal amplification via fluorescent labels and enzymatic methods. This article discusses one class of optical sensors, termed "photonic crystals", that effectively amplify binding events (such as analyte capture) via strong light-matter interactions.
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Affiliation(s)
- Sudeshna Pal
- Department of Electrical and Computer Engineering, University of Rochester, Rochester, New York 14642
- Department of Mechanical, Materials, and Aerospace Engineering University of Central Florida, Orlando, Florida 32816
| | - Philippe M. Fauchet
- Department of Electrical and Computer Engineering, University of Rochester, Rochester, New York 14642
- Department of Electrical Engineering and Computer Science Vanderbilt University, Nashville, Tennessee 37235
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, New York 14642
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21
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Sensitive detection of glucose in human serum with oligonucleotide modified gold nanoparticles by using dynamic light scattering technique. Biosens Bioelectron 2012; 41:880-3. [PMID: 23084753 DOI: 10.1016/j.bios.2012.09.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/25/2012] [Accepted: 09/12/2012] [Indexed: 11/21/2022]
Abstract
Dynamic light scattering based sensor for glucose was developed with oligonucleotide functionalized gold nanoparticles (Oligo-AuNPs). Oligonucleotide 5'-SH-(A)(12)-AGACAAGAGAGG-3' (Oligo 1) modified AuNPs and oligonucleotide 5'-CAACAGAGAACG-(A)(12)-HS-3' (Oligo 2) modified AuNPs could hybridize with oligonulceotide 5'-CGTTCTCTGTTGCCTCTCTTGTCT-3' (Oligo 3), which resulted in the aggregation of Oligo-AuNPs probes, and triggered the increase of their average diameter. However, Oligo 3 could be cleaved into DNA fragments by the mixture of glucose, glucose oxidase (GOD) and Fe(2+), and the DNA fragments could not hybridize with Oligo-AuNPs probes. Under the conditions of 3.7 nM Oligo 1-AuNPs, 3.7 nM Oligo 2-AuNPs, 8.0 μg/mL GOD, 100 nM Oligo 3 and 900 nM Fe(2+), the average diameter of Oligo-AuNPs probes decreased linearly with the increasing concentration of glucose over the range from 50 pmol/L to 5.0 nmol/L, with a detection limit of 38 pmol/L (3σ/slope). Moreover, five sugars had no effect on the average diameter of mixture of Oligo-AuNPs probes, GOD and Fe(2+), which demonstrated the good selectivity of the assay.
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22
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Threm D, Nazirizadeh Y, Gerken M. Photonic crystal biosensors towards on-chip integration. JOURNAL OF BIOPHOTONICS 2012; 5:601-616. [PMID: 22678992 DOI: 10.1002/jbio.201200039] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/24/2012] [Accepted: 05/02/2012] [Indexed: 06/01/2023]
Abstract
Photonic crystal technology has attracted large interest in the last years. The possibility to generate highly sensitive sensor elements with photonic crystal structures is very promising for medical or environmental applications. The low-cost fabrication on the mass scale is as advantageous as the compactness and reliability of photonic crystal biosensors. The possibility to integrate microfluidic channels together with photonic crystal structures allows for highly compact devices. This article reviews different types of photonic crystal sensors including 1D photonic crystal biosensors, biosensors with photonic crystal slabs, photonic crystal waveguide biosensors and biosensors with photonic crystal microcavities. Their applications in biomolecular and pathogen detection are highlighted. The sensitivities and the detection limits of the different biosensors are compared. The focus is on the possibilities to integrate photonic crystal biosensors on-chip.
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Affiliation(s)
- Daniela Threm
- Institute of Electrical and Information Engineering, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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23
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Breuer S, Chang MW, Yuan J, Torbett BE. Identification of HIV-1 inhibitors targeting the nucleocapsid protein. J Med Chem 2012; 55:4968-77. [PMID: 22587465 DOI: 10.1021/jm201442t] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The HIV-1 nucleocapsid (NC) is a RNA/DNA binding protein encoded within the Gag polyprotein, which is critical for the selection and chaperoning of viral genomic RNA during virion assembly. RNA/DNA binding occurs through a highly conserved zinc-knuckle motif present in NC. Given the necessity of NC-viral RNA/DNA interaction for viral replication, identification of compounds that disrupt the NC-RNA/DNA interaction may have value as an antiviral strategy. To identify small molecules that disrupt NC-viral RNA/DNA binding, a high-throughput fluorescence polarization assay was developed and a library of 14,400 diverse, druglike compounds was screened. Compounds that disrupted NC binding to a fluorescence-labeled DNA tracer were next evaluated by differential scanning fluorimetry to identify compounds that must bind to NC or Gag to impart their effects. Two compounds were identified that inhibited NC-DNA interaction, specifically bound NC with nanomolar affinity, and showed modest anti-HIV-1 activity in ex vivo cell assays.
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Affiliation(s)
- Sebastian Breuer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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24
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Endo T, Sato M, Kajita H, Okuda N, Tanaka S, Hisamoto H. Printed two-dimensional photonic crystals for single-step label-free biosensing of insulin under wet conditions. LAB ON A CHIP 2012; 12:1995-9. [PMID: 22543758 DOI: 10.1039/c2lc40066a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Two-dimensional photonic crystals (2D-PCs) fabricated on a cyclo-olefin polymer (COP) film using a printable photonics technology based on nano-imprint lithography (NIL) were used for label-free biosensing of insulin under wet conditions. In general, 2D-PC-based biosensing involves a complicated dry-up procedure after biosensing reactions on the 2D-PCs to obtain a high sensitivity through the large difference in refractive index. Therefore, it can be difficult to achieve simple operation involving single-step analysis. Performance of the biosensing under wet conditions would simplify the operational procedure. For label-free biosensing of insulin under wet conditions, the Fresnel reflection intensity change was used instead of the wavelength shift, which is the commonly used sensing signal. By detecting changes in refractive index caused by specific interactions between the antigen and antibody as the Fresnel reflection intensity changes, physiologically important concentrations of insulin could be detected, even under wet conditions. These results suggest that low-cost printed 2D-PCs offer great potential for single-step label-free biosensing through the introduction of a sample solution.
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Affiliation(s)
- Tatsuro Endo
- Analytical Chemistry Group, Department of Applied Chemistry, Osaka Prefecture University, Sakai-shi, Osaka, Japan.
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25
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Battle CH, Jayawickramarajah J. Supramolecular Approaches for Inhibition of Protein-Protein and Protein-DNA Interactions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Affiliation(s)
- Matthew S. Luchansky
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
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Liu JN, Schulmerich MV, Bhargava R, Cunningham BT. Optimally designed narrowband guided-mode resonance reflectance filters for mid-infrared spectroscopy. OPTICS EXPRESS 2011; 19:24182-97. [PMID: 22109445 PMCID: PMC3482905 DOI: 10.1364/oe.19.024182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/27/2011] [Accepted: 10/31/2011] [Indexed: 05/19/2023]
Abstract
An alternative to the well-established Fourier transform infrared (FT-IR) spectrometry, termed discrete frequency infrared (DFIR) spectrometry, has recently been proposed. This approach uses narrowband mid-infrared reflectance filters based on guided-mode resonance (GMR) in waveguide gratings, but filters designed and fabricated have not attained the spectral selectivity (≤ 32 cm(-1)) commonly employed for measurements of condensed matter using FT-IR spectroscopy. With the incorporation of dispersion and optical absorption of materials, we present here optimal design of double-layer surface-relief silicon nitride-based GMR filters in the mid-IR for various narrow bandwidths below 32 cm(-1). Both shift of the filter resonance wavelengths arising from the dispersion effect and reduction of peak reflection efficiency and electric field enhancement due to the absorption effect show that the optical characteristics of materials must be taken into consideration rigorously for accurate design of narrowband GMR filters. By incorporating considerations for background reflections, the optimally designed GMR filters can have bandwidth narrower than the designed filter by the antireflection equivalence method based on the same index modulation magnitude, without sacrificing low sideband reflections near resonance. The reported work will enable use of GMR filters-based instrumentation for common measurements of condensed matter, including tissues and polymer samples.
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Affiliation(s)
- Jui-Nung Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
| | - Matthew V. Schulmerich
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
| | - Rohit Bhargava
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
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28
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Leavens FMV, Churchill CDM, Wang S, Wetmore SD. Evaluating how discrete water molecules affect protein-DNA π-π and π(+)-π stacking and T-shaped interactions: the case of histidine-adenine dimers. J Phys Chem B 2011; 115:10990-1003. [PMID: 21809837 DOI: 10.1021/jp205424z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Changes in the magnitude of (M06-2X/6-31+G(d,p)) π-π stacking and T-shaped (nucleobase-edge and amino acid-edge) interactions between (neutral or protonated) histidine (His) and adenine (A) dimers upon microsolvation with up to four discrete water molecules were determined. A variety of histidine-water interactions were considered including conventional (N-H···O, N···H-O, C-H···O) hydrogen bonding and nonconventional (X-H···π (neutral His) or lone-pair···π (protonated His)) contacts. Overall, the effects of discrete His-H(2)O interactions on the neutral histidine-adenine π-π contacts are negligible (<3 kJ mol(-1) or 15%) regardless of the type of water binding, the number of water molecules bound, or the His-A dimer (stacked or (amino acid- or nucleobase-edge) T-shaped) configuration. This suggests that previously reported gas-phase binding strengths for a variety of neutral amino acid-nucleobase dimers are likely relevant for a wide variety of (microsolvated) environments. In contrast, the presence of water decreases the histidine-adenine π(+)-π interaction by up to 15 kJ mol(-1) (or 30%) for all water binding modes and orientations, as well as different stacked and T-shaped His(+)-A dimers. Regardless of the larger effect of discrete histidine-water interactions on the magnitude of the π(+)-π compared with π-π interactions, the π(+)-π binding strengths remain substantially larger than the corresponding π-π contacts. These findings emphasize the distinct nature of π(+)-π and π-π interactions and suggest that π(+)-π contacts can provide significant stabilization in biological systems relative to π-π contacts under many different environmental conditions.
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Affiliation(s)
- Fern M V Leavens
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4
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Narasimhan K, Pillay S, Bin Ahmad NR, Bikadi Z, Hazai E, Yan L, Kolatkar PR, Pervushin K, Jauch R. Identification of a polyoxometalate inhibitor of the DNA binding activity of Sox2. ACS Chem Biol 2011; 6:573-81. [PMID: 21344919 DOI: 10.1021/cb100432x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aberrant expression of transcription factors is a frequent cause of disease, yet drugs that modulate transcription factor protein-DNA interactions are presently unavailable. To this end, the chemical tractability of the DNA binding domain of the stem cell inducer and oncogene Sox2 was explored in a high-throughput fluorescence anisotropy screen. The screening revealed a Dawson polyoxometalate (K(6)[P(2)Mo(18)O(62)]) as a direct and nanomolar inhibitor of the DNA binding activity of Sox2. The Dawson polyoxometalate (Dawson-POM) was found to be selective for Sox2 and related Sox-HMG family members when compared to unrelated paired and zinc finger DNA binding domains. [(15)N,(1)H]-Transverse relaxation optimized spectroscopy (TROSY) experiments coupled with docking studies suggest an interaction site of the POM on the Sox2 surface that enabled the rationalization of its inhibitory activity. The unconventional molecular scaffold of the Dawson-POM and its inhibitory mode provides strategies for the development of drugs that modulate transcription factors.
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Affiliation(s)
- Kamesh Narasimhan
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Shubhadra Pillay
- School of Biological sciences, Nanyang Technological University, Singapore 637551
| | | | - Zsolt Bikadi
- Virtua Drug Research and Development Ltd., Budapest 1015, Hungary
| | - Eszter Hazai
- Virtua Drug Research and Development Ltd., Budapest 1015, Hungary
| | - Li Yan
- School of Biological sciences, Nanyang Technological University, Singapore 637551
| | - Prasanna R. Kolatkar
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Konstantin Pervushin
- School of Biological sciences, Nanyang Technological University, Singapore 637551
| | - Ralf Jauch
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672
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Vela L, Lowe PN, Gerstenmaier J, Laing LG, Stimmel JB, Orband-Miller LA, Martin JJ. Validation of an optical microplate label-free platform in the screening of chemical libraries for direct binding to a nuclear receptor. Assay Drug Dev Technol 2011; 9:532-48. [PMID: 21438675 DOI: 10.1089/adt.2010.0345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Optical microplate-based biosensors combine the advantages of label-free detection with industry-standard assay laboratory infrastructure and scalability. A plate-based label-free platform allows the same basic platform to be used to quantify molecular interactions of macromolecules and to screen and characterize drug-like small-molecule interactions. The ligand-binding domain of orphan estrogen-related nuclear receptor-γ (ERRγ) is utilized, as a model system of a challenging type of target, to illustrate the rapid development and utility of a range of biochemical assay formats on these biosensors. Formats in which either the domain, or a peptide derived from its cognate corepressor, RIP140, were immobilized were utilized. The direct binding of small drug molecules to the domain was characterized using immobilized domain. Subsequent addition of peptide distinguished whether compounds acted as either antagonists of peptide binding, or as agonists promoting a ternary complex. The format with peptide immobilized gave a more sensitive procedure for establishing the effect of compounds on the domain-peptide interaction. Using a direct-binding format, a diverse chemical library of 1,408 compounds in DMSO was screened for ability to bind to biosensors coated with ERRγ ligand-binding domain. Hits were then characterized using the other biosensor assay formats. The standard requirements for a full primary screening campaign were fulfilled by the acceptable hit-rate, quality-performance parameters, and throughput of the direct-binding assay format. Such a format allows direct screening of targets, such as orphan receptors, without the requirement for prior knowledge of a validated ligand.
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Affiliation(s)
- Laura Vela
- Screening and Compound Profiling, GlaxoSmithKline, Tres Cantos, Spain
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Heeres JT, Hergenrother PJ. High-throughput screening for modulators of protein–protein interactions: use of photonic crystal biosensors and complementary technologies. Chem Soc Rev 2011; 40:4398-410. [DOI: 10.1039/b923660k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Morgan AW, Chan LL, Sendemir-Urkmez A, Cunningham BT, Jamison RD. Detection of growth factor binding to gelatin and heparin using a photonic crystal optical biosensor. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2010. [DOI: 10.1016/j.msec.2010.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Cunningham BT. Photonic Crystal Surfaces as a General Purpose Platform for Label-Free and Fluorescent Assays. ACTA ACUST UNITED AC 2010; 15:120-135. [PMID: 20383277 DOI: 10.1016/j.jala.2009.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Photonic crystal surfaces can be designed to provide a wide range of functions that are used to perform biochemical and cell-based assays. Detection of the optical resonant reflections from photonic crystal surfaces enables high sensitivity label-free biosensing, while the enhanced electromagnetic fields that occur at resonant wavelengths can be used to enhance the detection sensitivity of any surface-based fluorescence assay. Fabrication of photonic crystals from inexpensive plastic materials over large surface areas enables them to be incorporated into standard formats that include microplates, microarrays, and microfluidic channels. This report reviews the design of photonic crystal biosensors, their associated detection instrumentation, and biological applications. Applications including small molecule high throughput screening, cell membrane integrin activation, gene expression analysis, and protein biomarker detection are highlighted. Recent results in which photonic crystal surfaces are used for enhancing the detection of Surface-Enhanced Raman Spectroscopy, and the development of high resolution photonic crystal-based laser biosensors are also described.
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Affiliation(s)
- Brian T Cunningham
- Department of Electrical and Computer Engineering Department of Bioengineering University of Illinois at Urbana-Champaign
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Heeres JT, Kim SH, Leslie BJ, Lidstone EA, Cunningham BT, Hergenrother PJ. Identifying modulators of protein-protein interactions using photonic crystal biosensors. J Am Chem Soc 2010; 131:18202-3. [PMID: 19968284 DOI: 10.1021/ja907066r] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inhibitors and activators of protein-protein interactions are valuable as biological probes and medicinal agents but are often difficult to identify. Herein we describe a high-throughput assay, based upon photonic crystal (PC) biosensors, for the identification of modulators of protein-protein interactions. Through the use of a d-biotin-tris-NTA (BTN) hybrid compound, any His6-tagged protein can be immobilized on the surface of a PC biosensor. Binding of the bound protein to its cognate partner is detected via a shift in the peak wavelength value. We demonstrate this assay with three protein-protein pairs (caspase-9-XIAP, caspase-7-XIAP, FKBP12-FRB) and their small molecule modulators.
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Affiliation(s)
- James T Heeres
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Chan LL, Lidstone EA, Finch KE, Heeres JT, Hergenrother PJ, Cunningham BT. A Method for Identifying Small-Molecule Aggregators Using Photonic Crystal Biosensor Microplates. ACTA ACUST UNITED AC 2009; 14:348-359. [PMID: 20930952 DOI: 10.1016/j.jala.2009.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Small molecules identified through high-throughput screens are an essential element in pharmaceutical discovery programs. It is now recognized that a substantial fraction of small molecules exhibit aggregating behavior leading to false positive results in many screening assays, typically due to nonspecific attachment to target proteins. Therefore, the ability to efficiently identify compounds within a screening library that aggregate can streamline the screening process by eliminating unsuitable molecules from further consideration. In this work, we show that photonic crystal (PC) optical biosensor microplate technology can be used to identify and quantify small-molecule aggregation. A group of aggregators and nonaggregators were tested using the PC technology, and measurements were compared with those gathered by three alternative methods: dynamic light scattering (DLS), an α-chymotrypsin colorimetric assay, and scanning electron microscopy (SEM). The PC biosensor measurements of aggregation were confirmed by visual observation using SEM, and were in general agreement with the α-chymotrypsin assay. DLS measurements, in contrast, demonstrated inconsistent readings for many compounds that are found to form aggregates in shapes, very different from the classical spherical particles assumed in DLS modeling. As a label-free detection method, the PC biosensor aggregation assay is simple to implement and provides a quantitative direct measurement of the mass density of material adsorbed to the transducer surface, whereas the microplate-based sensor format enables compatibility with high-throughput automated liquid-handling methods used in pharmaceutical screening.
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Affiliation(s)
- Leo L Chan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL
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Block ID, Mathias PC, Jones SI, Vodkin LO, Cunningham BT. Optimizing the spatial resolution of photonic crystal label-free imaging. APPLIED OPTICS 2009; 48:6567-6574. [PMID: 19956311 DOI: 10.1364/ao.48.006567] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A theory is derived to describe the relationship between photonic crystal (PC) label-free imaging resolution and PC resonance spectral linewidth and location. PCs are fabricated and patterned with a resolution standard photomask in order to verify this relationship experimentally. Two distinct linear resolutions of <1 microm and 3.5 microm are demonstrated in orthogonal directions on a single device, where the former is limited by the imaging system optics and the latter is constrained by finite resonant mode propagation. In order to illustrate the utility of improved design control, the spectral response of a PC is optimized for label-free imaging of immobilized DNA capture spots on a microarray.
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Affiliation(s)
- Ian D Block
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Block ID, Mathias PC, Ganesh N, Jones SI, Dorvel BR, Chaudhery V, Vodkin LO, Bashir R, Cunningham BT. A detection instrument for enhanced-fluorescence and label-free imaging on photonic crystal surfaces. OPTICS EXPRESS 2009; 17:13222-35. [PMID: 19654728 PMCID: PMC2804394 DOI: 10.1364/oe.17.013222] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We report on the design and demonstration of an optical imaging system capable of exciting surface-bound fluorophores within the resonant evanescent electric field of a photonic crystal surface and gathering fluorescence emission that is directed toward the imaging objective by the photonic crystal. The system also has the ability to quantify shifts in the local resonance angle induced by the adsorption of biomolecules on the photonic crystal surface for label-free biomolecular imaging. With these two capabilities combined within a single detection system, we demonstrate label-free images self-registered to enhanced fluorescence images with 328x more sensitive fluorescence detection relative to a glass surface. This technique is applied to a DNA microarray where label-free quantification of immobilized capture DNA enables improved quality control and subsequent enhanced fluorescence detection of dye-tagged hybridized DNA yields 3x more genes to be detected versus commercially available microarray substrates.
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Affiliation(s)
- Ian D. Block
- Dept. of Electrical Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Patrick C. Mathias
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Nikhil Ganesh
- Dept. of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Sarah I. Jones
- Dept. of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Brian R. Dorvel
- Dept. of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Vikram Chaudhery
- Dept. of Electrical Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Lila O. Vodkin
- Dept. of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rashid Bashir
- Dept. of Electrical Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Dept. of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Brian T. Cunningham
- Dept. of Electrical Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL USA
- B.T. Cunningham, tel: +1-217-265-6291;
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Hauschild KE, Stover JS, Boger DL, Ansari AZ. CSI-FID: high throughput label-free detection of DNA binding molecules. Bioorg Med Chem Lett 2009; 19:3779-82. [PMID: 19435662 PMCID: PMC2760306 DOI: 10.1016/j.bmcl.2009.04.097] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 04/16/2009] [Accepted: 04/20/2009] [Indexed: 11/16/2022]
Abstract
Determining the sequence specifity of DNA binding molecules is a non-trivial task. Here we describe the development of a platform for assaying the sequence specificity of DNA ligands using label free detection on high density DNA microarrays. This is achieved by combining Cognate Site Identification (CSI) with Fluorescence Intercalation Displacement (FID) to create CSI-FID. We use the well-studied small molecule DNA ligand netropsin to develop this high throughput platform. Analysis of the DNA binding properties of protein- and small molecule-based libraries with CSI-FID will advance the development of genome-anchored molecules for therapeutic purposes.
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Affiliation(s)
- Karl E Hauschild
- Genome Center of Wisconsin, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Qavi AJ, Washburn AL, Byeon JY, Bailey RC. Label-free technologies for quantitative multiparameter biological analysis. Anal Bioanal Chem 2009; 394:121-35. [PMID: 19221722 PMCID: PMC2667559 DOI: 10.1007/s00216-009-2637-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 01/12/2009] [Accepted: 01/20/2009] [Indexed: 11/26/2022]
Abstract
In the postgenomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We describe the fundamental principles of these different methods and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application.
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Affiliation(s)
- Abraham J. Qavi
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Adam L. Washburn
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Ji-Yeon Byeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
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Rutledge LR, Durst HF, Wetmore SD. Evidence for Stabilization of DNA/RNA−Protein Complexes Arising from Nucleobase−Amino Acid Stacking and T-Shaped Interactions. J Chem Theory Comput 2009; 5:1400-10. [DOI: 10.1021/ct800567q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Holly F. Durst
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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