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Potdar RP, Khollam YB, Shaikh SF, Raut RW, Pandit B, More PS. Evanescent wave sensor for potassium ion detection with special reference to agricultural application. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Toppo AL, Jujjavarapu SE. New insights for integration of nano particle with microfluidic systems for sensor applications. Biomed Microdevices 2022; 24:13. [PMID: 35171352 DOI: 10.1007/s10544-021-00598-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2021] [Indexed: 11/29/2022]
Abstract
A biosensor is a compact device, which utilizes biological derived recognition component, immobilized on a transducer to analyze an analyte. Nanoparticles with their unique chemical and physical properties are versatile in their applications to develop as sensors. Different nanoparticles play different roles in the sensing systems like metal and metal oxide nanoparticles. The application of Gold, Silver and Copper nanoparticles will be discussed in brief. The nanoparticles typically function as substrates for immobilization of biomolecules, as catalytic agent, electron transfer agent between electrode surface and the biomolecules, and as reactants. Microfluidic deals with manipulating very small volumes of fluids (micro and nanoliters). This miniaturized platform enhances control of flow conditions and mixing rate of fluids. The microfluidics improves the sensitivity of the analysis, and reduces the volumes of sample and reagent in the analysis. The review specifically aims at representing microfluidics-based sensors and nanoparticle based sensors. This review will also focus on probable merger of these two fields to take advantage of both the fields and this will help in pushing the boundaries of these fields further more.
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Affiliation(s)
- A L Toppo
- Deparment of Biotechnology, National Institute of Technology Raipur, Raipur, India
| | - S E Jujjavarapu
- Deparment of Biotechnology, National Institute of Technology Raipur, Raipur, India.
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Lv D, Xu J, Qi M, Wang D, Xu W, Qiu L, Li Y, Cao Y. A strategy of screening and binding analysis of bioactive components from traditional Chinese medicine based on surface plasmon resonance biosensor. J Pharm Anal 2021; 12:500-508. [PMID: 35811628 PMCID: PMC9257445 DOI: 10.1016/j.jpha.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/11/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
Elucidating the active components of traditional Chinese medicine (TCM) is essential for understanding the mechanisms of TCM and promote its rational use as well as TCM-derived drug development. Recent studies have shown that surface plasmon resonance (SPR) technology is promising in this field. In the present study, we propose an SPR-based integrated strategy to screen and analyze the major active components of TCM. We used Radix Paeoniae Alba (RPA) as an example to identify the compounds that can account for its anti-inflammatory mechanism via tumor necrosis factor receptor type 1 (TNF-R1). First, RPA extraction was analyzed using an SPR-based screening system, and the potential active ingredients were collected, enriched, and identified as paeoniflorin and paeonol. Next, the affinity constants of paeoniflorin and paeonol were determined as 4.9 and 11.8 μM, respectively. Then, SPR-based competition assays and molecular docking were performed to show that the two compounds could compete with tumor necrosis factor-α (TNF-α) while binding to the subdomain 1 site of TNF-R1. Finally, in biological assays, the two compounds suppressed cytotoxicity and apoptosis induced by TNF-α in the L929 cell line. These findings prove that SPR technology is a useful tool for determining the active ingredients of TCM at the molecular level and can be used in various aspects of drug development. The SPR-based integrated strategy is reliable and feasible in TCM studies and will shed light on the elucidation of the pharmacological mechanism of TCM and facilitate its modernization. A surface plasmon resonance-based integrated strategy was established to analyze traditional Chinese medicine. Surface plasmon resonance technology can be used for ligand screening, affinity detection, and binding site confirmation. Paeoniflorin and paeonol were identified as TNF-R1-bound ingredients in RPA.
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Affiliation(s)
- Diya Lv
- Center for Instrumental Analysis, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Jin Xu
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Minyu Qi
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Dongyao Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Weiheng Xu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Lei Qiu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Yinghua Li
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- Corresponding author.
| | - Yan Cao
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
- Corresponding author.
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Puscasu A, Zanchetta M, Posocco B, Bunka D, Tartaggia S, Toffoli G. Development and validation of a selective SPR aptasensor for the detection of anticancer drug irinotecan in human plasma samples. Anal Bioanal Chem 2021; 413:1225-1236. [PMID: 33404749 DOI: 10.1007/s00216-020-03087-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 11/28/2022]
Abstract
In this work, a surface plasmon resonance (SPR)-based assay for the quantification of antineoplastic drug irinotecan in human plasma samples has been developed for the first time. The selective binding of irinotecan with an aptamer receptor, operating in human plasma, allowed to set-up a novel analytical methodology to detect the drug in the analytical range of interest by using SPR as detection technique. After hybridizing the aptamer to the sensing platform and optimizing the sample preparation procedure, a quantitative assay was validated according to FDA regulatory guidelines. The analytical working range was found between 100 and 7500 ng mL-1 with negligible interferences from plasma components and co-medication associated with the administration of irinotecan. The utility of the new SPR assay was confirmed by analyzing plasma samples in parallel with LC-MS as reference technique, providing a new analytical tool for the therapeutic drug monitoring of irinotecan in patients under chemotherapy regimens.
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Affiliation(s)
- Adelina Puscasu
- Clinical and Experimental Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, Aviano (PN), 33081, Italy
| | - Martina Zanchetta
- Clinical and Experimental Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, Aviano (PN), 33081, Italy.,Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127, Trieste, Italy
| | - Bianca Posocco
- Clinical and Experimental Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, Aviano (PN), 33081, Italy
| | - David Bunka
- Aptamer Group, Suite 2.78 - 2.91, Bio Centre, Innovation Way, Heslington, York, YO10 5NY, UK
| | - Stefano Tartaggia
- Clinical and Experimental Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, Aviano (PN), 33081, Italy.
| | - Giuseppe Toffoli
- Clinical and Experimental Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, Aviano (PN), 33081, Italy
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de Oliveira Vitarelli M, Elias MC. Quantifying the Affinity of Trypanosoma cruzi RPA-1 to the Single-Stranded DNA Overhang of the Telomere Using Surface Plasmon Resonance. Methods Mol Biol 2021; 2281:217-228. [PMID: 33847961 DOI: 10.1007/978-1-0716-1290-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Surface plasmon resonance (SPR) biosensors provide real-time binding affinity measurements between a pair of biomolecules, characterizing its interaction dynamics. An example of Trypanosoma cruzi's RPA-1 and a single-stranded DNA telomere sequence is presented with detailed guidelines and fundamentals for SPR technology.
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Affiliation(s)
- Marcela de Oliveira Vitarelli
- Cell Cycle Laboratory, Butantan Institute, São Paulo, SP, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, SP, Brazil
| | - Maria Carolina Elias
- Cell Cycle Laboratory, Butantan Institute, São Paulo, SP, Brazil.
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, SP, Brazil.
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Tang X, Zhang Z, Fang M, Han Y, Wang G, Wang S, Xue M, Li Y, Zhang L, Wu J, Yang B, Mwangi J, Lu Q, Du X, Lai R. Transferrin plays a central role in coagulation balance by interacting with clotting factors. Cell Res 2020; 30:119-132. [PMID: 31811276 PMCID: PMC7015052 DOI: 10.1038/s41422-019-0260-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/15/2019] [Indexed: 01/01/2023] Open
Abstract
Coagulation balance is maintained through fine-tuned interactions among clotting factors, whose physiological concentrations vary substantially. In particular, the concentrations of coagulation proteases (pM to nM) are much lower than their natural inactivator antithrombin (AT, ~ 3 μM), suggesting the existence of other coordinators. In the current study, we found that transferrin (normal plasma concentration ~40 μM) interacts with fibrinogen, thrombin, factor XIIa (FXIIa), and AT with different affinity to maintain coagulation balance. Normally, transferrin is sequestered by binding with fibrinogen (normal plasma concentration ~10 μM) at a molar ratio of 4:1. In atherosclerosis, abnormally up-regulated transferrin interacts with and potentiates thrombin/FXIIa and blocks AT's inactivation effect on coagulation proteases by binding to AT, thus inducing hypercoagulability. In the mouse model, transferrin overexpression aggravated atherosclerosis, whereas transferrin inhibition via shRNA knockdown or treatment with anti-transferrin antibody or designed peptides interfering with transferrin-thrombin/FXIIa interactions alleviated atherosclerosis. Collectively, these findings identify that transferrin is an important clotting regulator and an adjuster in the maintenance of coagulation balance and modifies the coagulation cascade.
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Affiliation(s)
- Xiaopeng Tang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204, Kunming, Yunnan, China
| | - Zhiye Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Mingqian Fang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204, Kunming, Yunnan, China
| | - Yajun Han
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Gan Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Sheng Wang
- Key Laboratory of Molecular Biophysics, Huazhong University of Science and Technology, Ministry of Education, College of Life Science and Technology, 430070, Wuhan, Hubei, China
| | - Min Xue
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204, Kunming, Yunnan, China
| | - Yaxiong Li
- Department of Cardiovascular Surgery, Yan'an Affiliated Hospital of Kunming Medical University, 650041, Kunming, Yunnan, China
| | - Li Zhang
- Department of Cardiovascular Surgery, Yan'an Affiliated Hospital of Kunming Medical University, 650041, Kunming, Yunnan, China
| | - Jian Wu
- Department of Cardiovascular Surgery, Yan'an Affiliated Hospital of Kunming Medical University, 650041, Kunming, Yunnan, China
| | - Biqing Yang
- Department of Laboratory, Dehong People's Hospital, 678400, Dehong, Yunnan, China
| | - James Mwangi
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204, Kunming, Yunnan, China
| | - Qiumin Lu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Xiaoping Du
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China.
- Institute for Drug Discovery and Development, Chinese Academy of Sciences, 201203, Shanghai, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China.
- Sino-African Joint Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China.
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, Hubei, China.
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Khavani M, Izadyar M, Housaindokht MR. RNA aptasensor based on gold nanoparticles for selective detection of neomycin B, molecular approach. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-019-01708-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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8
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Kusrini E, Hashim F, Gunawan C, Mann R, Azmi WNNWN, Amin NM. Anti-amoebic activity of acyclic and cyclic-samarium complexes on Acanthamoeba. Parasitol Res 2018. [DOI: 10.1007/s00436-018-5814-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Laughlin-Toth S, Carter EK, Ivanov I, Wilson WD. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences. Nucleic Acids Res 2017; 45:1297-1306. [PMID: 28180310 PMCID: PMC5388402 DOI: 10.1093/nar/gkw1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by an allosteric mechanism. In an effort to broaden sequence recognition of DNA-targeted-small-molecules to include both A·T and G·C base pairs, we recently discovered that the heterocyclic diamidine, DB2277, forms a strong monomer complex with a DNA sequence containing 5΄-AAAGTTT-3΄. Competition mass spectrometry and surface plasmon resonance identified new monomer complexes, as well as unexpected binding of two DB2277 with certain sequences. Inherent microstructural differences within the experimental DNAs were identified through computational analyses to understand the molecular basis for recognition. These findings emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recognition and offer new avenues to design synthetic small molecules for effective regulation of gene-expression.
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Affiliation(s)
- Sarah Laughlin-Toth
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - E Kathleen Carter
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
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Tiwari R, Haque L, Bhuiya S, Das S. Third strand stabilization of poly(U)·poly(A)* poly(U) triplex by the naturally occurring flavone luteolin: A multi-spectroscopic approach. Int J Biol Macromol 2017; 103:692-700. [PMID: 28545966 DOI: 10.1016/j.ijbiomac.2017.05.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 01/17/2023]
Abstract
Naturally occurring flavonoid luteolin (LTN) was found to interact with double stranded poly(A).poly(U) and triple stranded poly(U)·poly(A)*poly(U) with association constants of the order of 104M-1. The association was monitored by various spectroscopic and viscometric techniques. Non-cooperative binding was observed for the association of LTN with two different polymorphic forms of RNA. Intercalation mode of binding was confirmed by fluorescence quenching and viscometric experiments. Thermal melting profiles indicated greater stabilization of the Hoogsteen base paired third strand (∼16°C) compared to Watson-Crick double strand (∼5°C) of RNA by LTN. Since the interaction of naturally occurring small molecules with RNA is an active area of research, this study has led to great openings to explore LTN as RNA targeted therapeutic agent.
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Affiliation(s)
- Richa Tiwari
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Sutanwi Bhuiya
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Suman Das
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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11
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Pett L, Kiakos K, Satam V, Patil P, Laughlin-Toth S, Gregory M, Bowerman M, Olson K, Savagian M, Lee M, Lee M, Wilson WD, Hochhauser D, Hartley JA. Modulation of topoisomerase IIα expression and chemosensitivity through targeted inhibition of NF-Y:DNA binding by a diamino p-anisyl-benzimidazole (Hx) polyamide. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:617-629. [PMID: 27750031 PMCID: PMC5757371 DOI: 10.1016/j.bbagrm.2016.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Sequence specific polyamide HxIP 1, targeted to the inverted CCAAT Box 2 (ICB2) on the topoisomerase IIα (topo IIα) promoter can inhibit NF-Y binding, re-induce gene expression and increase sensitivity to etoposide. To enhance biological activity, diamino-containing derivatives (HxI*P 2 and HxIP* 3) were synthesised incorporating an alkyl amino group at the N1-heterocyclic position of the imidazole/pyrrole. METHODS DNase I footprinting was used to evaluate DNA binding of the diamino Hx-polyamides, and their ability to disrupt the NF-Y:ICB2 interaction assessed using EMSAs. Topo IIα mRNA (RT-PCR) and protein (Immunoblotting) levels were measured following 18h polyamide treatment of confluent A549 cells. γH2AX was used as a marker for etoposide-induced DNA damage after pre-treatment with HxIP* 3 and cell viability was measured using Cell-Titer Glo®. RESULTS Introduction of the N1-alkyl amino group reduced selectivity for the target sequence 5'-TACGAT-3' on the topo IIα promoter, but increased DNA binding affinity. Confocal microscopy revealed both fluorescent diamino polyamides localised in the nucleus, yet HxI*P 2 was unable to disrupt the NF-Y:ICB2 interaction and showed no effect against the downregulation of topo IIα. In contrast, inhibition of NF-Y binding by HxIP* 3 stimulated dose-dependent (0.1-2μM) re-induction of topo IIα and potentiated cytotoxicity of topo II poisons by enhancing DNA damage. CONCLUSIONS Polyamide functionalisation at the N1-position offers a design strategy to improve drug-like properties. Dicationic HxIP* 3 increased topo IIα expression and chemosensitivity to topo II-targeting agents. GENERAL SIGNIFICANCE Pharmacological modulation of topo IIα expression has the potential to enhance cellular sensitivity to clinically-used anticancer therapeutics. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Luke Pett
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London, WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London, WC1E 6BT, UK
| | - Vijay Satam
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Pravin Patil
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Sarah Laughlin-Toth
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Matthew Gregory
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Michael Bowerman
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Kevin Olson
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Mia Savagian
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Megan Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Moses Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States; Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Daniel Hochhauser
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London, WC1E 6BT, UK
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London, WC1E 6BT, UK.
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Schneider HJ. Spatial mismatch, non-additive binding energies and selectivity in supramolecular complexes. Org Biomol Chem 2017; 15:2146-2151. [DOI: 10.1039/c6ob02755e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A geometric mismatch in supramolecular complexes often leads to deviations from the additivity of binding energies with the consequence of large changes in selectivity and binding mode.
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Affiliation(s)
- Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes
- D 66123 Saarbrücken
- Germany
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Mehdizadeh Aghdam E, Sinn M, Tarhriz V, Barzegar A, Hartig JS, Hejazi MS. TPP riboswitch characterization in Alishewanella tabrizica and Alishewanella aestuarii and comparison with other TPP riboswitches. Microbiol Res 2016; 195:71-80. [PMID: 28024528 DOI: 10.1016/j.micres.2016.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/15/2016] [Accepted: 11/05/2016] [Indexed: 11/18/2022]
Abstract
Riboswitches are located in non-coding areas of mRNAs and act as sensors of cellular small molecules, regulating gene expression in response to ligand binding. The TPP riboswitch is the most widespread riboswitch occurring in all three domains of life. However, it has been rarely characterized in environmental bacteria other than Escherichia coli and Bacillus subtilis. In this study, TPP riboswitches located in the 5' UTR of thiC operon from Alishewanella tabrizica and Alishewanella aestuarii were identified and characterized. Moreover, affinity analysis of TPP binding to the TPP aptamer domains originated from A. tabrizica, A. aestuarii, E.coli, and B. subtilis were studied and compared using In-line probing and Surface Plasmon Resonance (SPR). TPP binding to the studied RNAs from A. tabrizica and A. aestuarii caused distinctive changes of the In-line cleavage pattern, demonstrating them as functional TPP riboswitches. With dissociation constant of 2-4nM (depending on the method utilized), the affinity of TPP binding was highest in A. tabrizica, followed by the motifs sourced from A. aestuarii, E. coli, and B. subtilis. The observed variation in their TPP-binding affinity might be associated with adaptation to the different environments of the studied bacteria.
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Affiliation(s)
- Elnaz Mehdizadeh Aghdam
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Vahideh Tarhriz
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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15
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Depletion of tyrosyl DNA phosphodiesterase 2 activity enhances etoposide-mediated double-strand break formation and cell killing. DNA Repair (Amst) 2016; 43:38-47. [DOI: 10.1016/j.dnarep.2016.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/20/2022]
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16
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Xu Y, Zheng Z. Direct RNA detection without nucleic acid purification and PCR: Combining sandwich hybridization with signal amplification based on branched hybridization chain reaction. Biosens Bioelectron 2016; 79:593-9. [DOI: 10.1016/j.bios.2015.12.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/09/2015] [Accepted: 12/15/2015] [Indexed: 01/22/2023]
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17
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Harika NK, Paul A, Stroeva E, Chai Y, Boykin DW, Germann MW, Wilson WD. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition. Nucleic Acids Res 2016; 44:4519-27. [PMID: 27131382 PMCID: PMC4889958 DOI: 10.1093/nar/gkw353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/17/2016] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents.
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Affiliation(s)
- Narinder K Harika
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ekaterina Stroeva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Yun Chai
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
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18
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Interaction of small molecules with fungal laccase: A Surface Plasmon Resonance based study. Enzyme Microb Technol 2016; 82:110-114. [DOI: 10.1016/j.enzmictec.2015.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 07/17/2015] [Accepted: 09/08/2015] [Indexed: 11/24/2022]
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19
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Selection of Single-Stranded DNA Molecular Recognition Elements against Exotoxin A Using a Novel Decoy-SELEX Method and Sensitive Detection of Exotoxin A in Human Serum. BIOMED RESEARCH INTERNATIONAL 2015; 2015:417641. [PMID: 26636098 PMCID: PMC4655287 DOI: 10.1155/2015/417641] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/09/2015] [Accepted: 10/12/2015] [Indexed: 12/04/2022]
Abstract
Exotoxin A is one of the virulence factors of Pseudomonas aeruginosa, a bacterium that can cause infections resulting in adverse health outcomes and increased burden to health care systems. Current methods of diagnosing P. aeruginosa infections are time consuming and can require significant preparation of patient samples. This study utilized a novel variation of the Systematic Evolution of Ligand by Exponential Enrichment, Decoy-SELEX, to identify an Exotoxin A specific single-stranded DNA (ssDNA) molecular recognition element (MRE). Its emphasis is on increasing stringency in directing binding toward free target of interest and at the same time decreasing binding toward negative targets. A ssDNA MRE with specificity and affinity was identified after fourteen rounds of Decoy-SELEX. Utilizing surface plasmon resonance measurements, the determined equilibrium dissociation constant (Kd) of the MRE is between 4.2 µM and 4.5 µM, and is highly selective for Exotoxin A over negative targets. A ssDNA MRE modified sandwich enzyme-linked immunosorbent assay (ELISA) has been developed and achieved sensitive detection of Exotoxin A at nanomolar concentrations in human serum. This study has demonstrated the proof-of-principle of using a ssDNA MRE as a clinical diagnostic tool.
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20
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Janssen BMG, van Ommeren SPFI, Merkx M. Efficient Synthesis of Peptide and Protein Functionalized Pyrrole-Imidazole Polyamides Using Native Chemical Ligation. Int J Mol Sci 2015; 16:12631-47. [PMID: 26053396 PMCID: PMC4490465 DOI: 10.3390/ijms160612631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/25/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023] Open
Abstract
The advancement of DNA-based bionanotechnology requires efficient strategies to functionalize DNA nanostructures in a specific manner with other biomolecules, most importantly peptides and proteins. Common DNA-functionalization methods rely on laborious and covalent conjugation between DNA and proteins or peptides. Pyrrole-imidazole (Py-Im) polyamides, based on natural minor groove DNA-binding small molecules, can bind to DNA in a sequence specific fashion. In this study, we explore the use of Py-Im polyamides for addressing proteins and peptides to DNA in a sequence specific and non-covalent manner. A generic synthetic approach based on native chemical ligation was established that allows efficient conjugation of both peptides and recombinant proteins to Py-Im polyamides. The effect of Py-Im polyamide conjugation on DNA binding was investigated by Surface Plasmon Resonance (SPR). Although the synthesis of different protein-Py-Im-polyamide conjugates was successful, attenuation of DNA affinity was observed, in particular for the protein-Py-Im-polyamide conjugates. The practical use of protein-Py-Im-polyamide conjugates for addressing DNA structures in an orthogonal but non-covalent manner, therefore, remains to be established.
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Affiliation(s)
- Brian M G Janssen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Sven P F I van Ommeren
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
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21
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Wang S, Aston K, Koeller KJ, Harris GD, Rath NP, Bashkin JK, Wilson WD. Modulation of DNA-polyamide interaction by β-alanine substitutions: a study of positional effects on binding affinity, kinetics and thermodynamics. Org Biomol Chem 2015; 12:7523-36. [PMID: 25141096 DOI: 10.1039/c4ob01456a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hairpin polyamides (PAs) are an important class of sequence-specific DNA minor groove binders, and frequently employ a flexible motif, β-alanine (β), to reduce the molecular rigidity to maintain the DNA recognition register. To better understand the diverse effects that β can have on DNA-PA binding affinity, selectivity, and especially kinetics, which have rarely been reported, we have initiated a detailed study for an eight-heterocyclic hairpin PA and its β derivatives with their cognate and mutant sequences. With these derivatives, all internal pyrroles of the parent PA are systematically substituted with single or double βs. A set of complementary experiments have been conducted to evaluate the molecular interactions in detail: UV-melting, biosensor-surface plasmon resonance, circular dichroism and isothermal titration calorimetry. The β substitutions generally weaken the binding affinities of these PAs with cognate DNA, and have large and diverse influences on PA binding kinetics in a position- and number-dependent manner. The DNA base mutations have also shown positional effects on the binding of a single PA. Besides the β substitutions, the monocationic Dp group [3-(dimethylamino)propylamine] in parent PA has been modified into a dicationic Ta group (3,3'-diamino-N-methyldipropylamine) to minimize the frequently observed PA aggregation with ITC experiments. The results clearly show that the Ta modification not only maintains the DNA binding mode and affinity of PA, but also significantly reduces PA aggregation and allows the complete thermodynamic signature of eight-ring hairpin PA to be determined for the first time. This combined set of results significantly extends our understanding of the energetic basis of specific DNA recognition by PAs.
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Affiliation(s)
- Shuo Wang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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22
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Paul A, Nanjunda R, Kumar A, Laughlin S, Nhili R, Depauw S, Deuser SS, Chai Y, Chaudhary AS, David-Cordonnier MH, Boykin DW, Wilson WD. Mixed up minor groove binders: Convincing A·T specific compounds to recognize a G·C base pair. Bioorg Med Chem Lett 2015; 25:4927-4932. [PMID: 26051649 DOI: 10.1016/j.bmcl.2015.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 01/08/2023]
Abstract
DNA minor-groove-binding compounds have limited biological applications, in part due to problems with sequence specificity that cause off-target effects. A model to enhance specificity has been developed with the goal of preparing compounds that bind to two AT sites separated by G·C base pairs. Compounds of interest were probed using thermal melting, circular dichroism, mass spectrometry, biosensor-SPR, and molecular modeling methods. A new minor groove binder that can strongly and specifically recognize a single G·C base pair with flanking AT sequences has been prepared. This multi-site DNA recognition mode offers novel design principles to recognize entirely new DNA motifs.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Rupesh Nanjunda
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Sarah Laughlin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Raja Nhili
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - Sabine Depauw
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - Shelby Sheldon Deuser
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Yun Chai
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Arpana S Chaudhary
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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23
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Aptamer Microarrays—Current Status and Future Prospects. MICROARRAYS 2015; 4:115-32. [PMID: 27600216 PMCID: PMC4996391 DOI: 10.3390/microarrays4020115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/16/2022]
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24
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Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance. Methods Mol Biol 2015; 1334:313-32. [PMID: 26404159 DOI: 10.1007/978-1-4939-2877-4_20] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biosensor-surface plasmon resonance (SPR) technology has emerged as a powerful label-free approach for the study of nucleic acid interactions in real time. The method provides simultaneous equilibrium and kinetic characterization for biomolecular interactions with low sample requirements and without the need for external probes. A detailed and practical guide for protein-DNA interaction analyses using biosensor-SPR methods is presented. Details of SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips and samples, experimental design, quantitative and qualitative data analyses and presentation. A specific example of the interaction of a transcription factor with DNA is provided with results evaluated by both kinetic and steady-state SPR methods.
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25
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Paul A, Chai Y, Boykin DW, Wilson WD. Understanding mixed sequence DNA recognition by novel designed compounds: the kinetic and thermodynamic behavior of azabenzimidazole diamidines. Biochemistry 2014; 54:577-87. [PMID: 25495885 PMCID: PMC4303320 DOI: 10.1021/bi500989r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sequence-specific recognition of DNA by small organic molecules offers a potentially effective approach for the external regulation of gene expression and is an important goal in cell biochemistry. Rational design of compounds from established modules can potentially yield compounds that bind strongly and selectively with specific DNA sequences. An initial approach is to start with common A·T bp recognition molecules and build in G·C recognition units. Here we report on the DNA interaction of a synthetic compound that specifically binds to a G·C bp in the minor groove of DNA by using an azabenzimidazole moiety. The detailed interactions were evaluated with biosensor-surface plasmon resonance (SPR), isothermal calorimetric (ITC), and mass spectrometry (ESI-MS) methods. The compound, DB2277, binds with single G·C bp containing sequences with sub-nanomolar potency and displays slow dissociation kinetics and high selectivity. A detailed thermodynamic and kinetic study at different experimental salt concentrations and temperatures shows that the binding free energy is salt concentration dependent but essentially temperature independent under our experimental conditions, and binding enthalpy is temperature dependent but salt concentration independent. The results show that in the proper compound structural context novel heterocyclic cations can be designed to strongly recognize complex DNA sequences.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303-3083, United States
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26
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Tang C, Paul A, Alam MP, Roy B, Wilson WD, Hecht SM. A short DNA sequence confers strong bleomycin binding to hairpin DNAs. J Am Chem Soc 2014; 136:13715-26. [PMID: 25188011 PMCID: PMC4183661 DOI: 10.1021/ja505733u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Bleomycins A5 and B2 were used to study the
structural features in hairpin DNAs conducive to strong BLM–DNA
interaction. Two members of a 10-hairpin DNA library previously found
to bind most tightly to these BLMs were subsequently noted to share
the sequence 5′-ACGC (complementary strand sequence 5′-GCGT).
Each underwent double-strand cleavage at five sites within, or near,
an eight base pair region of the DNA duplex which had been randomized
to create the original library. A new hairpin DNA library was selected
based on affinity for immobilized Fe(III)·BLM A5.
Two of the 30 newly identified DNAs also contained the sequence 5′-ACGC/5′-GCGT.
These DNAs bound to the Fe(II)·BLMs more tightly than any DNA
characterized previously. Surface plasmon resonance confirmed tight
Fe(III)·BLM B2 binding and gave an excellent fit for
a 1:1 binding model, implying the absence of significant secondary
binding sites. Fe(II)·BLM A5 was used to assess sites
of double-strand DNA cleavage. Both hairpin DNAs underwent double-strand
cleavage at five sites within or near the original randomized eight
base region. For DNA 12, four of the five double-strand
cleavages involved independent single-strand cleavage reactions; DNA 13 underwent double-strand DNA cleavage by independent single-strand
cleavages at all five sites. DNA 14, which bound Fe·BLM
poorly, was converted to a strong binder (DNA 15) by
insertion of the sequence 5′-ACGC/5′-GCGT. These findings
reinforce the idea that tighter DNA binding by Fe·BLM leads to
increased double-strand cleavage by a novel mechanism and identify
a specific DNA motif conducive to strong BLM binding and cleavage.
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Affiliation(s)
- Chenhong Tang
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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27
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Chai Y, Paul A, Rettig M, Wilson WD, Boykin DW. Design and synthesis of heterocyclic cations for specific DNA recognition: from AT-rich to mixed-base-pair DNA sequences. J Org Chem 2014; 79:852-66. [PMID: 24422528 PMCID: PMC3985508 DOI: 10.1021/jo402599s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 01/18/2023]
Abstract
The compounds synthesized in this research were designed with the goal of establishing a new paradigm for mixed-base-pair DNA sequence-specific recognition. The design scheme starts with a cell-permeable heterocyclic cation that binds to AT base pair sites in the DNA minor groove. Modifications were introduced in the original compound to include an H-bond accepting group to specifically recognize the G-NH that projects into the minor groove. Therefore, a series of heterocyclic cations substituted with an azabenzimidazole ring has been designed and synthesized for mixed-base-pair DNA recognition. The most successful compound, 12a, had an azabenzimidazole to recognize G and additional modifications for general minor groove interactions. It binds to the DNA site -AAAGTTT- more strongly than the -AAATTT- site without GC and indicates the design success. Structural modifications of 12a generally weakened binding. The interactions of the new compound with a variety of DNA sequences with and without GC base pairs were evaluated by thermal melting analysis, circular dichroism, fluorescence emission spectroscopy, surface plasmon resonance, and molecular modeling.
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Affiliation(s)
- Yun Chai
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ananya Paul
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Michael Rettig
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - W. David Wilson
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - David W. Boykin
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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28
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Chai Y, Munde M, Kumar A, Mickelson L, Lin S, Campbell NH, Banerjee M, Akay S, Liu Z, Farahat AA, Nhili R, Depauw S, David-Cordonnier MH, Neidle S, Wilson WD, Boykin DW. Structure-dependent binding of arylimidamides to the DNA minor groove. Chembiochem 2013; 15:68-79. [PMID: 24323836 DOI: 10.1002/cbic.201300622] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Indexed: 12/12/2022]
Abstract
Heterocyclic diamidines are strong DNA minor-groove binders and have excellent antiparasitic activity. To extend the biological activity of these compounds, a series of arylimidamides (AIAs) analogues, which have better uptake properties in Leishmania and Trypanosoma cruizi than diamidines, was prepared. The binding of the AIAs to DNA was investigated by Tm , fluorescence displacement titration, circular dichroism, DNase I footprinting, biosensor surface plasmon resonance, X-ray crystallography and molecular modeling. These compounds form 1:1 complexes with AT sequences in the DNA minor groove, and the binding strength varies with substituent size, charge and polarity. These substituent-dependent structure and properties provide a SAR that can be used to estimate K values for binding to DNA in this series. The structural results and molecular modeling studies provide an explanation for the differences in binding affinities for AIAs.
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Affiliation(s)
- Yun Chai
- Department of Chemistry, Georgia State University, 50 Decatur St. SE., Atlanta, GA 30303 (USA)
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29
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Urtasun N, Baieli MF, Romasanta PN, Fernández MM, Malchiodi EL, Cascone O, Wolman FJ, Miranda MV. Triazinic dye ligand selection by surface plasmon resonance for recombinant lactoferricin purification. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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Briscoe JL, Cho SY, Brener I. Defect-assisted plasmonic crystal sensor. OPTICS LETTERS 2013; 38:2569-71. [PMID: 23939114 PMCID: PMC4524508 DOI: 10.1364/ol.38.002569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We demonstrate enhanced sensitivity of a nanostructured plasmonic sensor that utilizes resonance in intentional structural defects within a plasmonic crystal. The measured sensitivity of the fabricated nanosensor is ~500 nm/RIU showing improvement over traditional nanohole array sensors. Furthermore, the defects provide an additional design parameter to increase sensitivity by engineering plasmon lifetime.
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Affiliation(s)
- Jayson L. Briscoe
- Klipsch School of Electrical and Computer Engineering, New Mexico State University, MSC 3-O, P.O. Box 30001, Las Cruces, NM 88003
| | - Sang-Yeon Cho
- Klipsch School of Electrical and Computer Engineering, New Mexico State University, MSC 3-O, P.O. Box 30001, Las Cruces, NM 88003
| | - Igal Brener
- Sandia National Laboratories, P.O. Box 5800, Albuquerque, NM 87185
- Center for Integrated Nanotechnologies, P.O. Box 5800, Albuquerque, NM 87185
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31
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Imaizumi Y, Kasahara Y, Fujita H, Kitadume S, Ozaki H, Endoh T, Kuwahara M, Sugimoto N. Efficacy of base-modification on target binding of small molecule DNA aptamers. J Am Chem Soc 2013; 135:9412-9. [PMID: 23734784 DOI: 10.1021/ja4012222] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Nucleic acid aptamers are receptors of single-stranded oligonucleotides that specifically bind to their targets. Significant interest is currently focused on development of small molecule aptamers owing to their applications in biosensing, diagnostics, and therapeutics involving low molecular weight biomarkers and drugs. Despite great potential for their diverse applications, relatively few aptamers that bind to small molecules have been reported, and methodologies to enhance and broaden their functions by expanding chemical repertories have barely been examined. Here we describe construction of a modified DNA library that includes (E)-5-(2-(N-(2-(N(6)-adeninyl)ethyl))carbamylvinyl)-uracil bases and discovery of high-affinity camptothecin-binding DNA aptamers using a systematic evolution of ligands by the exponential enrichment method. Our results are the first to demonstrate the superior efficacy of base modification on affinity enhancement and the usefulness of unnatural nucleic acid libraries for development of small molecule aptamers.
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Affiliation(s)
- Yuri Imaizumi
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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32
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Czerwinska I, Sato S, Takenaka S. Improving the affinity of naphthalene diimide ligand to telomeric DNA by incorporating Zn2+ ions into its dipicolylamine groups. Bioorg Med Chem 2012; 20:6416-22. [DOI: 10.1016/j.bmc.2012.08.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/23/2012] [Accepted: 08/23/2012] [Indexed: 10/27/2022]
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33
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Bashkin JK, Aston K, Ramos JP, Koeller KJ, Nanjunda R, He G, Dupureur CM, David Wilson W. Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine. Biochimie 2012; 95:271-9. [PMID: 23023196 DOI: 10.1016/j.biochi.2012.09.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 09/18/2012] [Indexed: 12/16/2022]
Abstract
Rules for polyamide-DNA recognition have proved invaluable for the design of sequence-selective DNA binding agents in cell-free systems. However, these rules are not fully transferrable to predicting activity in cells, tissues or animals, and additional refinements to our understanding of DNA recognition would help biomedical studies. Similar complexities are encountered when using internal β-alanines as polyamide building blocks in place of N-methylpyrrole; β-alanines were introduced in polyamide designs to maintain good hydrogen bonding registry with the target DNA, especially for long polyamides or those with several GC bp (P.B. Dervan, A.R. Urbach, Essays Contemp. Chem. (2001) 327-339). Thus, to clarify important subtleties of molecular recognition, we studied the effects of replacing a single pyrrole with β-alanine in 8-ring polyamides designed against the Ets-1 transcription factor. Replacement of a single internal N-methylpyrrole with β-alanine to generate a β/Im pairing in two 8-ring polyamides causes a decrease in DNA binding affinity by two orders of magnitude and decreases DNA binding selectivity, contrary to expectations based on the literature. Measurements were made by fluorescence spectroscopy, quantitative DNA footprinting and surface plasmon resonance, with these vastly different techniques showing excellent agreement. Furthermore, results were validated for a range of DNA substrates from small hairpins to long dsDNA sequences. Docking studies helped show that β-alanine does not make efficient hydrophobic contacts with the rest of the polyamide or nearby DNA, in contrast to pyrrole. These results help refine design principles and expectations for polyamide-DNA recognition.
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Affiliation(s)
- James K Bashkin
- Department of Chemistry & Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA.
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34
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Synthesis and DNA binding properties of 1-(3-aminopropyl)-imidazole-containing triamide f-Im∗PyIm: A novel diamino polyamide designed to target 5′-ACGCGT-3′. Bioorg Med Chem Lett 2012; 22:5898-902. [DOI: 10.1016/j.bmcl.2012.07.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/20/2012] [Indexed: 12/27/2022]
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35
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Sedláček O, Hrubý M, Studenovský M, Větvička D, Svoboda J, Kaňková D, Kovář J, Ulbrich K. Polymer conjugates of acridine-type anticancer drugs with pH-controlled activation. Bioorg Med Chem 2012; 20:4056-63. [DOI: 10.1016/j.bmc.2012.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 04/27/2012] [Accepted: 05/04/2012] [Indexed: 11/26/2022]
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36
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Inclán M, Albelda MT, Frías JC, Blasco S, Verdejo B, Serena C, Salat-Canela C, Díaz ML, García-España A, García-España E. Modulation of DNA binding by reversible metal-controlled molecular reorganizations of scorpiand-like ligands. J Am Chem Soc 2012; 134:9644-56. [PMID: 22594493 DOI: 10.1021/ja300538s] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
DNA interaction with scorpiand azamacrocycles has been achieved through modulation of their binding affinities. Studies performed with different experimental techniques provided evidence that pH or metal-driven molecular reorganizations of these ligands regulate their ability to interact with calf thymus DNA (ctDNA) through an intercalative mode. Interestingly enough, metal-driven molecular reorganizations serve to increase or decrease the biological activities of these compounds significantly.
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Affiliation(s)
- Mario Inclán
- Instituto de Ciencia Molecular, Departamento de Química Inorgánica, Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
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37
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Palau W, Di Primo C. Single-cycle kinetic analysis of ternary DNA complexes by surface plasmon resonance on a decaying surface. Biochimie 2012; 94:1891-9. [PMID: 22580385 DOI: 10.1016/j.biochi.2012.04.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 04/30/2012] [Indexed: 12/16/2022]
Abstract
Complexes involving three DNA strands were used to demonstrate that the single-cycle kinetics (SCK) method, which consists in injecting sequentially samples at increasing concentrations and until now used exclusively to investigate bimolecular complexes by surface plasmon resonance, can be extended to the kinetic analysis of ternary complexes. DNA targets, B, were designed with sequences of variable lengths on their 3' sides that recognise a surface-immobilized biotinylated DNA anchor, A. These targets displayed on their 5' sides sequences that recognise DNA oligonucleotides of variable lengths, C, namely the analytes. Combinations of B and C DNA oligonucleotides on A generated ternary complexes each composed of two Watson-Crick helices displaying different kinetic properties. The target-analyte B-C duplexes were formed by sequentially injecting three increasing concentrations of the analytes C during the dissociation phase of the target B from the anchor A. The sensorgrams for the target-analyte complexes dissociating from the functionalized surface were successfully fitted by the SCK method while the target dissociated from the anchor, i.e. on a decaying surface. Within the range of applicability of the method which is driven by the rate of dissociation of the target from the anchor, the rate and equilibrium constants characteristic of these target-analyte duplexes of the ternary complexes did not depend on how fast the targets dissociated from the immobilized DNA anchor. In addition the results agreed very well with those obtained when such duplexes were analysed directly as bimolecular complexes, i.e. when the target, modified with a biotin, was directly immobilized onto a streptavidin sensor chip surface rather than captured by an anchor. Therefore the method we named SCKODS (Single-Cycle Kinetics On a Decaying Surface) can also be used to investigate complexes formed during a dissociation phase, in a ternary complex context. The SCKODS method can be combined with the SCK one to fully characterize the two bimolecular complexes of a ternary complex.
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Affiliation(s)
- William Palau
- Univ. Bordeaux, Laboratoire ARNA, F-33000 Bordeaux, France
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38
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Ofori LO, Hoskins J, Nakamori M, Thornton CA, Miller BL. From dynamic combinatorial 'hit' to lead: in vitro and in vivo activity of compounds targeting the pathogenic RNAs that cause myotonic dystrophy. Nucleic Acids Res 2012; 40:6380-90. [PMID: 22492623 PMCID: PMC3401475 DOI: 10.1093/nar/gks298] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The myotonic dystrophies (DM) are human diseases in which the accumulation of toxic RNA (CUG or CCUG) repeats in the cell causes sequestration of splicing factors, including MBNL1, leading to clinical symptoms such as muscle wasting and myotonia. We previously used Dynamic Combinatorial Chemistry to identify the first compounds known to inhibit (CUG)-MBNL1 binding in vitro. We now report transformation of those compounds into structures with activity in vivo. Introduction of a benzo[g]quinoline substructure previously unknown in the context of RNA recognition, as well as other modifications, provided several molecules with enhanced binding properties, including compounds with strong selectivity for CUG repeats over CAG repeats or CAG–CUG duplex RNA. Compounds readily penetrate cells, and improve luciferase activity in a mouse myoblast assay in which enzyme function is coupled to a release of nuclear CUG–RNA retention. Most importantly, two compounds are able to partially restore splicing in a mouse model of DM1.
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Affiliation(s)
- Leslie O Ofori
- Department of Chemistry, University of Rochester, Rochester, NY 14642, USA
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Liu Y, Chai Y, Kumar A, Tidwell RR, Boykin DW, Wilson WD. Designed compounds for recognition of 10 base pairs of DNA with two at binding sites. J Am Chem Soc 2012; 134:5290-9. [PMID: 22369366 DOI: 10.1021/ja211628j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Short AT base pair sequences that are separated by a small number of GCs are common in eukaryotic parasite genomes. Cell-permeable compounds that bind effectively and selectively to such sequences present an attractive therapeutic approach. Compounds with linked, one or two amidine-benzimidazole-phenyl (ABP) motifs were designed, synthesized, and evaluated for binding to adjacent AT sites by biosensor-surface plasmon resonance (SPR). A surprising feature of the linked ABP motifs is that a set of six similar compounds has three different minor groove binding modes with the target sequences. Compounds with one ABP bind independently to two separated AT sites. Unexpectedly, compounds with two ABP motifs can bind strongly either as monomers or as cooperative dimers to the full site. The results are supported by mass spectrometry and circular dichroism, and models to explain the different binding modes are presented.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, United States
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40
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Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance. JOURNAL OF AMINO ACIDS 2012; 2012:816032. [PMID: 22500214 PMCID: PMC3303711 DOI: 10.1155/2012/816032] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 11/07/2011] [Indexed: 01/04/2023]
Abstract
Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR.
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41
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Zhang T, Wu Z, Du J, Hu Y, Liu L, Yang F, Jin Q. Anti-Japanese-encephalitis-viral effects of kaempferol and daidzin and their RNA-binding characteristics. PLoS One 2012; 7:e30259. [PMID: 22276167 PMCID: PMC3262791 DOI: 10.1371/journal.pone.0030259] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 12/12/2011] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND New therapeutic tools and molecular targets are needed for treatment of Japanese encephalitis virus (JEV) infections. JEV requires an α-1 translational frameshift to synthesize the NS1' protein required for viral neuroinvasiveness. Several flavonoids have been shown to possess antiviral activity in vitro against a wide spectrum of viruses. To date, the antiviral activities of flavonol kaempferol (Kae) and isoflavonoid daidzin (Dai) against JEV have not been described. METHODOLOGY/PRINCIPAL FINDINGS The 50% cytotoxic concentration (CC(50)) and 50% effective concentration (EC(50)) against JEV were investigated in BHK21 cells by MTS reduction. Activity against viral genomic RNA and proteins was measured by real-time RT-PCR and western blotting. The frameshift site RNA-binding characterization was also determined by electrospray ionization mass spectrometry, isothermal titration calorimetry and autodocking analysis. EC(50) values of Kae and Dai were 12.6 and 25.9 µM against JEV in cells pretreated before infection, whereas in cells infected before treatment, EC(50) was 21.5 and 40.4 µM, respectively. Kae exhibited more potent activity against JEV and RNA binding in cells following internalization through direct inhibition of viral replication and protein expression, indicating that its antiviral activity was principally due to direct virucidal effects. The JEV frameshift site RNA (fsRNA) was selected as a target for assaying Kae and Dai. ITC of fsRNA revealed an apparent K(b) value for Kae that was nine fold stronger than that for Dai. This binding was confirmed and localized to the RNA using ESI-MS and autodock analysis. Kae could form non-covalent complexes with fsRNA more easily than Dai could. CONCLUSIONS/SIGNIFICANCE Kae demonstrates more potent antiviral activity against JEV than does Dai. The mode of action of Kae as an anti-JEV agent seems to be related to its ability to inactivate virus by binding with JEV fsRNA.
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Affiliation(s)
- Ting Zhang
- Institute of Pathogen Biology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Zhiqiang Wu
- Institute of Pathogen Biology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Jiang Du
- Institute of Pathogen Biology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Yongfeng Hu
- Institute of Pathogen Biology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Liguo Liu
- Institute of Pathogen Biology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Fan Yang
- Institute of Pathogen Biology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- * E-mail: (FY); (QJ)
| | - Qi Jin
- Institute of Pathogen Biology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- * E-mail: (FY); (QJ)
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Hu J, Li W, Wang T, Lin Z, Jiang M, Hu F. Development of a label-free and innovative approach based on surface plasmon resonance biosensor for on-site detection of infectious bursal disease virus (IBDV). Biosens Bioelectron 2012; 31:475-9. [DOI: 10.1016/j.bios.2011.11.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/10/2011] [Accepted: 11/10/2011] [Indexed: 11/17/2022]
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43
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Satam V, Babu B, Chavda S, Savagian M, Sjoholm R, Tzou S, Ramos J, Liu Y, Kiakos K, Lin S, David Wilson W, Hartley JA, Lee M. Novel diamino imidazole and pyrrole-containing polyamides: Synthesis and DNA binding studies of mono- and diamino-phenyl-ImPy*Im polyamides designed to target 5'-ACGCGT-3'. Bioorg Med Chem 2011; 20:693-701. [PMID: 22222156 DOI: 10.1016/j.bmc.2011.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/04/2011] [Accepted: 12/06/2011] [Indexed: 12/28/2022]
Abstract
Pyrrole- and imidazole-containing polyamides are widely investigated as DNA sequence selective binding agents that have potential use as gene control agents. The key challenges that must be overcome to realize this goal is the development of polyamides with low molar mass so the molecules can readily diffuse into cells and concentrate in the nucleus. In addition, the molecules must have appreciable water solubility, bind DNA sequence specifically, and with high affinity. It is on this basis that the orthogonally positioned diamino/dicationic polyamide Ph-ImPy*Im 5 was designed to target the sequence 5'-ACGCGT-3'. Py* denotes the pyrrole unit that contains a N-substituted aminopropyl pendant group. The DNA binding properties of diamino polyamide 5 were determined using a number of techniques including CD, ΔT(M), DNase I footprinting, SPR and ITC studies. The effects of the second amino moiety in Py* on DNA binding affinity over its monoamino counterpart Ph-ImPyIm 3 were assessed by conducting DNA binding studies of 3 in parallel with 5. The results confirmed the minor groove binding and selectivity of both polyamides for the cognate sequence 5'-ACGCGT-3'. The diamino/dicationic polyamide 5 showed enhanced binding affinity and higher solubility in aqueous media over its monoamino/monocationic counterpart Ph-ImPyIm 3. The binding constant of 5, determined from SPR studies, was found to be 1.5 × 10(7)M(-1), which is ∼3 times higher than that for its monoamino analog 3 (4.8 × 10(6)M(-1)). The affinity of 5 is now approaching that of the parent compound f-ImPyIm 1 and its diamino equivalent 4. The advantages of the design of diamino polyamide 5 over 1 and 4 are its sequence specificity and the ease of synthesis compared to the N-terminus pyrrole analog 2.
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Affiliation(s)
- Vijay Satam
- Division of Natural and Applied Sciences, Department of Chemistry, Hope College, 35 East, 12th Street, Holland, MI 49423, USA
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44
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Wang S, Munde M, Wang S, Wilson WD. Minor groove to major groove, an unusual DNA sequence-dependent change in bend directionality by a distamycin dimer. Biochemistry 2011; 50:7674-83. [PMID: 21800847 DOI: 10.1021/bi201010g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA sequence-dependent conformational changes induced by the minor groove binder, distamycin, have been evaluated by polyacrylamide gel electrophoresis. The distamycin binding affinity, cooperativity, and stoichiometry with three target DNA sequences that have different sizes of alternating AT sites, ATAT, ATATA, and ATATAT, have been determined by mass spectrometry and surface plasmon resonance to help explain the conformational changes. The results show that distamycin binds strongly to and bends five or six AT base pair minor groove sites as a dimer with positive cooperativity, while it binds to ATAT as a weak, slightly anticooperative dimer. The bending direction was evaluated with an in phase A-tract reference sequence. Unlike other similar monomer minor groove binding compounds, such as netropsin, the distamycin dimer changes the directionality of the overall curvature away from the minor groove to the major groove. This distinct structural effect may allow designed distamycin derivatives to have selective therapeutic effects.
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Affiliation(s)
- Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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45
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Liu Y, Kumar A, Depauw S, Nhili R, David-Cordonnier MH, Lee MP, Ismail MA, Farahat AA, Say M, Chackal-Catoen S, Batista-Parra A, Neidle S, Boykin DW, Wilson WD. Water-mediated binding of agents that target the DNA minor groove. J Am Chem Soc 2011; 133:10171-83. [PMID: 21627167 DOI: 10.1021/ja202006u] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecule complexes with DNA that incorporate linking water molecules are rare, and the DB921-DNA complex has provided a unique and well-defined system for analysis of water-mediated binding in the context of a DNA complex. DB921 has a benzimidazole-biphenyl system with terminal amidines that results in a linear conformation that does not possess the appropriate radius of curvature to match the minor groove shape and represents a new paradigm that does not fit the classical model of minor groove interactions. To better understand the role of the bound water molecule observed in the X-ray crystal structure of the DB921 complex, synthetic modifications have been made in the DB921 structure, and the interactions of the new compounds with DNA AT sites have been evaluated with an array of methods, including DNase I footprinting, biosensor-surface plasmon resonance, isothermal titration microcalorimetry, and circular dichroism. The interaction of a key compound, which has the amidine at the phenyl shifted from the para position in DB921 to the meta position, has also been examined by X-ray crystallography. The detailed structural, thermodynamic, and kinetic results provide valuable new information for incorporation of water molecules in the design of new lead scaffolds for targeting DNA in chemical biology and therapeutic applications.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, USA
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46
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Munoz EM, Lorenzo-Abalde S, González-Fernández A, Quintela O, Lopez-Rivadulla M, Riguera R. Direct surface plasmon resonance immunosensor for in situ detection of benzoylecgonine, the major cocaine metabolite. Biosens Bioelectron 2011; 26:4423-8. [PMID: 21664118 DOI: 10.1016/j.bios.2011.04.056] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/27/2011] [Accepted: 04/28/2011] [Indexed: 12/25/2022]
Abstract
In this paper the development of the first direct surface plasmon resonance (SPR) immunoassay for the detection of benzoylecgonine (BZE) is described. Immunosensor chips consisting of a high affinity monoclonal anti-BZE-antibody (anti-BZE-Ab) immobilized at high density to a sensor chip were prepared. First, BZE detection in Hepes buffer was achieved by direct, real time monitoring of the binding between BZE in solution and the surface bound antibody. The detection protocol was based on calibration curves obtained from reaction rate data and end point data analysis of sensorgrams registered after injection of a series of known BZE concentrations over the chips. Moreover, immunosensor accuracy, reproducibility, stability and robustness were tested to demonstrate their good performance as reusable devices. The immunosensor was used for BZE detection in oral fluid (OF) showing that, within 180 s, our immunoassay detects BZE concentrations as low as 4 μg/L in filtered OF-buffer (1:4) samples. This value is remarkably lower than current cut off levels established by the Substance Abuse and Mental Health Services Administration. These results manifest the potential use of this direct SPR immunoassay for the in situ sensitive detection of recent cocaine abuse, of utility in roadside drug OF testing. Moreover, it exemplifies the high potential of direct SPR immunoassays for the rapid, sensitive detection of small molecules in contrast with the more established indirect methods.
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Affiliation(s)
- Eva M Munoz
- Department of Organic Chemistry and Centre for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, Av de las Ciencias, 15782 Santiago de Compostela, Spain
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47
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Chavda S, Liu Y, Babu B, Davis R, Sielaff A, Ruprich J, Westrate L, Tronrud C, Ferguson A, Franks A, Tzou S, Adkins C, Rice T, Mackay H, Kluza J, Tahir SA, Lin S, Kiakos K, Bruce CD, Wilson WD, Hartley JA, Lee M. Hx, a novel fluorescent, minor groove and sequence specific recognition element: design, synthesis, and DNA binding properties of p-anisylbenzimidazole-imidazole/pyrrole-containing polyamides. Biochemistry 2011; 50:3127-36. [PMID: 21388229 DOI: 10.1021/bi102028a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
With the aim of incorporating a recognition element that acts as a fluorescent probe upon binding to DNA, three novel pyrrole (P) and imidazole (I)-containing polyamides were synthesized. The compounds contain a p-anisylbenzimidazolecarboxamido (Hx) moiety attached to a PP, IP, or PI unit, giving compounds HxPP (2), HxIP (3), and HxPI (4), respectively. These fluorescent hybrids were tested against their complementary nonfluorescent, non-formamido tetraamide counterparts, namely, PPPP (5), PPIP (6), and PPPI (7) (cognate sequences 5'-AAATTT-3', 5'-ATCGAT-3', and 5'-ACATGT-3', respectively). The binding affinities for both series of polyamides for their cognate and noncognate sequences were ascertained by surface plasmon resonance (SPR) studies, which revealed that the Hx-containing polyamides gave binding constants in the 10(6) M(-1) range while little binding was observed for the noncognates. The binding data were further compared to the corresponding and previously reported formamido-triamides f-PPP (8), f-PIP (9), and f-PPI (10). DNase I footprinting studies provided additional evidence that the Hx moiety behaved similarly to two consecutive pyrroles (PP found in 5-7), which also behaved like a formamido-pyrrole (f-P) unit found in distamycin and many formamido-triamides, including 8-10. The biophysical characterization of polyamides 2-7 on their binding to the abovementioned DNA sequences was determined using thermal melts (ΔT(M)), circular dichroism (CD), and isothermal titration calorimetry (ITC) studies. Density functional calculations (B3LYP) provided a theoretical framework that explains the similarity between PP and Hx on the basis of molecular electrostatic surfaces and dipole moments. Furthermore, emission studies on polyamides 2 and 3 showed that upon excitation at 322 nm binding to their respective cognate sequences resulted in an increase in fluorescence at 370 nm. These low molecular weight polyamides show promise for use as probes for monitoring DNA recognition processes in cells.
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Affiliation(s)
- Sameer Chavda
- Division of Natural and Applied Sciences, Department of Chemistry, Hope College, Holland, Michigan 49423, United States
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48
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Hunt RA, Munde M, Kumar A, Ismail MA, Farahat AA, Arafa RK, Say M, Batista-Parra A, Tevis D, Boykin DW, Wilson WD. Induced topological changes in DNA complexes: influence of DNA sequences and small molecule structures. Nucleic Acids Res 2011; 39:4265-74. [PMID: 21266485 PMCID: PMC3105405 DOI: 10.1093/nar/gkq1362] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Heterocyclic diamidines are compounds with antiparasitic properties that target the minor groove of kinetoplast DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structures are likely to be involved. In this study, we have developed a polyacrylamide gel electrophoresis-based screening method to determine topological effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and ATATA. The AAAAA and AAATT sequences have the largest intrinsic bend, whereas the TTTAA and ATATA sequences are relatively straight. The changes caused by binding of the compounds are sequence dependent, but generally the topological effects on AAAAA and AAATT are similar as are the effects on TTTAA and ATATA. A total of 13 compounds with a variety of structural differences were evaluated for topological changes to DNA. All compounds decrease the mobility of the ATATA sequence that is consistent with decreased minor groove width and bending of the relatively straight DNA into the minor groove. Similar, but generally smaller, effects are seen with TTTAA. The intrinsically bent AAAAA and AAATT sequences, which have more narrow minor grooves, have smaller mobility changes on binding that are consistent with increased or decreased bending depending on compound structure.
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Affiliation(s)
- Rebecca A Hunt
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
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49
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Chomean S, Potipitak T, Promptmas C, Ittarat W. Quartz crystal microbalance-based biosensor for the detection of α-thalassemia 1 (SEA deletion). Clin Chem Lab Med 2011; 48:1247-54. [PMID: 20578968 DOI: 10.1515/cclm.2010.258] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND DNA piezoelectric biosensors have become a promising tool in molecular medicine since they do not require any label or staining. Here, a DNA piezoelectric biosensor based on a quartz crystal microbalance (QCM) was created to identify abnormal genes causing α-thalassemia 1 (SEA deletion). METHODS The functionalized gold electrode of the quartz crystal was coated with avidin and the biotinylated DNA probe was attached. The target gene causing α-thalassemia 1 was amplified and hybridized with the immobilized probe. DNA hybridization was indicated by changes in the quartz resonance frequencies. Diagnostic ability of the new α-thalassemia 1 biosensor was validated using both known and unknown blood samples. Specificity was tested using samples of β-thalassemia and α-thalassemia 2. Stability of the sensor was also evaluated. RESULTS The new biosensor could clearly identify α-thalassemia 1 (SEA deletion), both carrier and disease states, from the normal genotype. Identification accuracy was compatible to the standard gel electrophoresis. It was specific only to α-thalassemia 1 since no cross reaction was found with β-thalassemia and α-thalassemia 2. The sensor could be kept at room temperature up to 6 months with consistent identification accuracy. CONCLUSIONS The label free QCM based biosensor was successfully developed to diagnose an abnormal human globin gene causing α-thalassemia 1 (SEA deletion). Its accuracy, specificity and sensitivity were comparable to the standard method. Its stable diagnostic potency up to 6 months implied its field application in thalassemic control program.
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Affiliation(s)
- Sirinart Chomean
- Faculty of Medical Technology, Department of Clinical Microscopy, Mahidol University, Nakhon Pathom, Thailand
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