1
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Pirojsirikul T, Lee VS, Nimmanpipug P. Unraveling Bacterial Single-Stranded Sequence Specificities: Insights from Molecular Dynamics and MMPBSA Analysis of Oligonucleotide Probes. Mol Biotechnol 2024; 66:582-591. [PMID: 38374320 DOI: 10.1007/s12033-024-01082-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/10/2024] [Indexed: 02/21/2024]
Abstract
We utilized molecular dynamics (MD) simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) free energy calculations to investigate the specificity of two oligonucleotide probes, namely probe B and probe D, in detecting single-stranded DNA (ssDNA) within three bacteria families: Enterobacteriaceae, Pasteurellaceae, and Vibrionaceae. Due to the limited understanding of molecular mechanisms in the previous research, we have extended the discussion to focus specifically on investigating the binding process of bacteria-probe DNA duplexes, with an emphasis on analyzing the binding free energy. The role of electrostatic contributions in the specificity between the oligonucleotide probes and the bacterial ssDNAs was investigated and found to be crucial. Our calculations yielded results that were highly consistent with the experimental data. Through our study, we have successfully exhibited the benefits of utilizing in-silico approaches as a powerful virtual-screening tool, particularly in research areas that demand a thorough comprehension of molecular interactions.
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Affiliation(s)
- Teerapong Pirojsirikul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, 90110, Thailand.
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Center of Theoretical and Computational Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Piyarat Nimmanpipug
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
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2
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Xing C, Zheng X, Zhang Q. Constructing DNA logic circuits based on the toehold preemption mechanism. RSC Adv 2021; 12:338-345. [PMID: 35424506 PMCID: PMC8978688 DOI: 10.1039/d1ra08687a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/14/2021] [Indexed: 11/21/2022] Open
Abstract
Strand displacement technology and ribozyme digestion technology have enriched the intelligent toolbox of molecular computing and provided more methods for the construction of DNA logic circuits. In recent years, DNA logic circuits have developed rapidly, and their scalability and accuracy in molecular computing and information processing have been fully demonstrated. However, existing DNA logic circuits still have some problems such as high complexity of DNA strands (number of DNA strands) hindering the expansion of practical computing tasks. In view of the above problems, we presented a toehold preemption mechanism and applied it to construct DNA logic circuits using E6-type DNAzymes, such as half adder circuit, half subtractor circuit, and 4-bit square root logic circuit. Different from the dual-track logic expressions, all the signals in the circuits of this study were monorail which substantially reduced the number of DNA strands in the DNA logic circuits. The presented preemption mechanism provides a way to simplify the implementation of large and complex DNA integrated circuits.
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Affiliation(s)
- Cuicui Xing
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education Dalian 116622 China
| | - Xuedong Zheng
- College of Computer Science, Shenyang Aerospace University Shenyang 110136 China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education Dalian 116622 China
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
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3
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Chung S, Gurudatt NG, Jeon J, Ban C, Shim YB. Fast Aptamer Generation Method Based on the Electrodynamic Microfluidic Channel and Evaluation of Aptamer Sensor Performance. Anal Chem 2020; 93:1416-1422. [PMID: 33369387 DOI: 10.1021/acs.analchem.0c03231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We demonstrate for the first time a fast aptamer generation method based on the screen-printed electrodynamic microfluidic channel device, where a specific aptamer selectively binds to a target protein on channel walls, following recovery and separation. A malaria protein as a model target, Plasmodium vivax lactate dehydrogenase (PvLDH) was covalently bonded to the conductive polymer layer formed on the carbon channel walls to react with the DNA library in a fluid. Then, the AC electric field was symmetrically applied on the channel walls for inducing the specific binding of the target protein to DNA library molecules. In this case, the partitioning efficiency between PvLDH and DNA library in the channel was attained to be 1.67 × 107 with the background of 5.56 × 10-6, which was confirmed using the quantitative polymerase chain reaction (qPCR). The selectively captured DNAs were isolated from the protein and separated in situ to give five aptamers with different sequences by one round cycle. The dissociation constants (Kd) of the selected aptamers were determined employing both electrochemical impedance spectroscopy (EIS) and the fluorescence method. The sensing performance of each aptamer was evaluated for the PvLDH detection after individual immobilization on the screen-printed array electrodes. The most sensitive aptamer revealed a detection limit of 7.8 ± 0.4 fM. The sensor reliability was evaluated by comparing it with other malaria sensors.
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Affiliation(s)
- Saeromi Chung
- Department of Chemistry and Institute of Biophysio Sensor Technology, Pusan National University, Busan 46241, Republic of Korea
| | - Nanjanagudu Ganesh Gurudatt
- Department of Chemistry and Institute of Biophysio Sensor Technology, Pusan National University, Busan 46241, Republic of Korea
| | - Jinsung Jeon
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Yoon-Bo Shim
- Department of Chemistry and Institute of Biophysio Sensor Technology, Pusan National University, Busan 46241, Republic of Korea
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4
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Liu X, Sun S, Wu Y, Zhou Y, Gu S, Yu H, Yi C, Gu M, Jiang J, Liu B, Zhang T, Gong Z. Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:112-121. [PMID: 31494982 DOI: 10.1111/tpj.14522] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/27/2019] [Accepted: 08/21/2019] [Indexed: 05/04/2023]
Abstract
Fluorescence in situ hybridization using probes based on oligonucleotides (oligo-FISH) is a useful tool for chromosome identification and karyotype analysis. Here we developed two oligo-FISH probes that allow the identification of each of the 12 pairs of chromosomes in rice (Oryza sativa). These two probes comprised 25 717 (green) and 25 215 (red) oligos (45 nucleotides), respectively, and generated 26 distinct FISH signals that can be used as a barcode to uniquely label each of the 12 pairs of rice chromosomes. Standard karyotypes of rice were established using this system on both mitotic and meiotic chromosomes. Moreover, dual-color oligo-FISH was used to characterize diverse chromosomal abnormalities. Oligo-FISH analyses using these probes in various wild Oryza species revealed that chromosomes from the AA, BB or CC genomes generated specific and intense signals similar to those in rice, while chromosomes with the EE genome generated less specific signals and the FF genome gave no signal. Together, the oligo-FISH probes we established will be a powerful tool for studying chromosome variations and evolution in the genus Oryza.
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Affiliation(s)
- Xiaoyu Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Shang Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yong Zhou
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Siwei Gu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Hengxiu Yu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Chuandeng Yi
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Minghong Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
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5
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Lee WC, Kim KB, Gurudatt N, Hussain KK, Choi CS, Park DS, Shim YB. Comparison of enzymatic and non-enzymatic glucose sensors based on hierarchical Au-Ni alloy with conductive polymer. Biosens Bioelectron 2019; 130:48-54. [DOI: 10.1016/j.bios.2019.01.028] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 01/12/2023]
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6
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Dual redox labeling of DNA as a tool for electrochemical detection of p53 protein-DNA interactions. Anal Chim Acta 2019; 1050:123-131. [DOI: 10.1016/j.aca.2018.10.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/04/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022]
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7
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Chan D, Barsan MM, Korpan Y, Brett CM. L-lactate selective impedimetric bienzymatic biosensor based on lactate dehydrogenase and pyruvate oxidase. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.02.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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8
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Chiorcea-Paquim AM, Oliveira SCB, Diculescu VC, Oliveira-Brett AM. Applications of DNA-Electrochemical Biosensors in Cancer Research. PAST, PRESENT AND FUTURE CHALLENGES OF BIOSENSORS AND BIOANALYTICAL TOOLS IN ANALYTICAL CHEMISTRY: A TRIBUTE TO PROFESSOR MARCO MASCINI 2017. [DOI: 10.1016/bs.coac.2017.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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9
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Zhang W, Wang ML, Khalili S, Cranford SW. Materiomics for Oral Disease Diagnostics and Personal Health Monitoring: Designer Biomaterials for the Next Generation Biomarkers. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:12-29. [PMID: 26760957 PMCID: PMC4739130 DOI: 10.1089/omi.2015.0144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We live in exciting times for a new generation of biomarkers being enabled by advances in the design and use of biomaterials for medical and clinical applications, from nano- to macro-materials, and protein to tissue. Key challenges arise, however, due to both scientific complexity and compatibility of the interface of biology and engineered materials. The linking of mechanisms across scales by using a materials science approach to provide structure-process-property relations characterizes the emerging field of 'materiomics,' which offers enormous promise to provide the hitherto missing tools for biomaterial development for clinical diagnostics and the next generation biomarker applications towards personal health monitoring. Put in other words, the emerging field of materiomics represents an essentially systematic approach to the investigation of biological material systems, integrating natural functions and processes with traditional materials science perspectives. Here we outline how materiomics provides a game-changing technology platform for disruptive innovation in biomaterial science to enable the design of tailored and functional biomaterials--particularly, the design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. Rigorous and complementary computational modeling and experimental techniques will provide an efficient means to develop new clinical technologies in silico, greatly accelerating the translation of materiomics-driven oral health diagnostics from concept to practice in the clinic.
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Affiliation(s)
- Wenjun Zhang
- Laboratory for Nanotechnology In Civil Engineering (NICE), Northeastern University, Boston, Massachusetts
- Interdisciplinary Engineering Program, College of Engineering, Northeastern University, Boston, Massachusetts
| | - Ming L. Wang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts
| | - Sammy Khalili
- Department of Otorhinolaryngology-Head and Neck Surgery, Aurora Medical Group, Milwaukee, Wisconsin
| | - Steven W. Cranford
- Laboratory for Nanotechnology In Civil Engineering (NICE), Northeastern University, Boston, Massachusetts
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts
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10
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Macazo F, Karpel RL, White RJ. Monitoring cooperative binding using electrochemical DNA-based sensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:868-75. [PMID: 25517392 PMCID: PMC4303326 DOI: 10.1021/la504083c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/15/2014] [Indexed: 05/20/2023]
Abstract
Electrochemical DNA-based (E-DNA) sensors are utilized to detect a variety of targets including complementary DNA, small molecules, and proteins. These sensors typically employ surface-bound single-stranded oligonucleotides that are modified with a redox-active molecule on the distal 3' terminus. Target-induced flexibility changes of the DNA probe alter the efficiency of electron transfer between the redox active methylene blue and the electrode surface, allowing for quantitative detection of target concentration. While numerous studies have utilized the specific and sensitive abilities of E-DNA sensors to quantify target concentration, no studies to date have demonstrated the ability of this class of collision-based sensors to elucidate biochemical-binding mechanisms such as cooperativity. In this study, we demonstrate that E-DNA sensors fabricated with various lengths of surface-bound oligodeoxythymidylate [(dT)n] sensing probes are able to quantitatively distinguish between cooperative and noncooperative binding of a single-stranded DNA-binding protein. Specifically, we demonstrate that oligo(dT) E-DNA sensors are able to quantitatively detect nM levels (50 nM-4 μM) of gene 32 protein (g32p). Furthermore, the sensors exhibit signal that is able to distinguish between the cooperative binding of the full-length g32p and the noncooperative binding of the core domain (*III) fragment to single-stranded DNA. Finally, we demonstrate that this binding is both probe-length- and ionic-strength-dependent. This study illustrates a new quantitative property of this powerful class of biosensor and represents a rapid and simple methodology for understanding protein-DNA binding mechanisms.
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Affiliation(s)
- Florika
C. Macazo
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Richard L. Karpel
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Ryan J. White
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
- E-mail:
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11
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Huang X, Leduc C, Ravussin Y, Li S, Davis E, Song B, Li D, Xu K, Accili D, Wang Q, Leibel R, Lin Q. A differential dielectric affinity glucose sensor. LAB ON A CHIP 2014; 14:294-301. [PMID: 24220675 PMCID: PMC3893139 DOI: 10.1039/c3lc51026c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A continuous glucose monitor with a differential dielectric sensor implanted within the subcutaneous tissue that determines the glucose concentration in the interstitial fluid is presented. The device, created using microelectromechanical systems (MEMS) technology, consists of sensing and reference modules that are identical in design and placed in close proximity. Each module contains a microchamber housing a pair of capacitive electrodes residing on the device substrate and embedded in a suspended, perforated polymer diaphragm. The microchambers, enclosed in semi-permeable membranes, are filled with either a polymer solution that has specific affinity to glucose or a glucose-insensitive reference solution. To accurately determine the glucose concentration, changes in the permittivity of the sensing and the reference solutions induced by changes in glucose concentration are measured differentially. In vitro characterization demonstrated the sensor was capable of measuring glucose concentrations from 0 to 500 mg dL(-1) with resolution and accuracy of ~1.7 μg dL(-1) and ~1.74 mg dL(-1), respectively. In addition, device drift was reduced to 1.4% (uncontrolled environment) and 11% (5 °C of temperature variation) of that from non-differential measurements, indicating significant stability improvements. Preliminary animal testing demonstrated that the differential sensor accurately tracks glucose concentration in blood. This sensor can potentially be used clinically as a subcutaneously implanted continuous monitoring device in diabetic patients.
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Affiliation(s)
- Xian Huang
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA.
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12
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Label-free detection of protein–DNA interactions using electrochemical impedance spectroscopy. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.06.063] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Babkina SS, Ulakhovich NA. Determination of Pharmaceuticals Based on Indole Alkaloids with Amperometric DNA-Sensors and Enzyme Immunoassay Test-System. ANAL LETT 2011. [DOI: 10.1080/00032711003789975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Schopf E, Liu Y, Deng JC, Yang S, Cheng G, Chen Y. tuberculosis detection via rolling circle amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2011; 3:267-273. [PMID: 32938023 DOI: 10.1039/c0ay00529k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hybridization-based assays for DNA detection often use single-stranded DNA (ssDNA) probes to capture ssDNA targets in solution. Unfortunately, these assays are often not able to detect double-stranded DNA (dsDNA). Here, we achieve highly sensitive dsDNA target detection by including short oligonucleotide sequences during denaturing and cooling. After performing an isothermal nucleic acid amplification technique (Rolling Circle Amplification, RCA), these captured dsDNA targets are labeled, allowing single amplified molecules to be imaged and counted. This detection method was first applied to the detection of PCR-generated (polymerase chain reaction) dsDNA targets, yielding a limit of detection of 4.25 fM. As an application of the developed assay, the detection of extracted Mycobacterium tuberculosis (M. tb.) genomic DNA was attempted. A M. tb.-specific target was detected with high specificity compared to similar bacteria, and a detection limit of 10 000 colony forming units (cfu) ml-1 was achieved, close to the sensitivity required for clinical diagnosis.
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Affiliation(s)
- Eric Schopf
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Yang Liu
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Jane C Deng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Siyin Yang
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Genhong Cheng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Yong Chen
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
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15
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Dual-aptamer-based delivery vehicle of doxorubicin to both PSMA (+) and PSMA (-) prostate cancers. Biomaterials 2010; 32:2124-32. [PMID: 21147500 DOI: 10.1016/j.biomaterials.2010.11.035] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 11/14/2010] [Indexed: 01/15/2023]
Abstract
We have designed a dual-aptamer complex specific to both prostate-specific membrane antigens (PSMA) (+) and (-) prostate cancer cells. In the complex, an A10 RNA aptamer targeting PSMA (+) cells and a DUP-1 peptide aptamer specific to PSMA (-) cells were conjugated through streptavidin. Doxorubicin-loaded onto the stem region of the A10 aptamer was delivered not only to PSMA (+) cells but to PSMA (-) cells, and eventually induced apoptosis in both types of prostate cancer cells. Cell death was monitored by measuring guanine concentration in cells using differential pulse voltammetry (DPV), a simple and rapid electrochemical method, and was further confirmed by directly observing cell morphologies cultured on the transparent indium tin oxide (ITO) glass electrode and checking their viabilities using a trypan blue assay. To investigate the in vivo application of the dual-aptamer system, both A10 and DUP-1 aptamers were immobilized on the surface of thermally cross-linked superparamagnetic iron oxide nanoparticles (TCL-SPION). Selective cell uptakes and effective drug delivery action of these probes were verified by Prussian blue staining and trypan blue staining, respectively.
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16
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Witte C, Lisdat F. Direct Detection of DNA and DNA-Ligand Interaction by Impedance Spectroscopy. ELECTROANAL 2010. [DOI: 10.1002/elan.201000410] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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McTiernan CD, Chahma M. Synthesis and characterization of nucleobase functionalized monothiophenes. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.08.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Min K, Song KM, Cho M, Chun YS, Shim YB, Ku JK, Ban C. Simultaneous electrochemical detection of both PSMA (+) and PSMA (-) prostate cancer cells using an RNA/peptide dual-aptamer probe. Chem Commun (Camb) 2010; 46:5566-8. [PMID: 20407731 DOI: 10.1039/c002524k] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using an RNA/peptide dual-aptamer probe, both PSMA (+) and PSMA (-) prostate cancer cells were simultaneously detected by electrochemical impedance spectroscopy. This approach can be applied as a general tool for early diagnosis of prostate cancer.
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Affiliation(s)
- Kyoungin Min
- Department of Chemistry, Pohang University of Science and Technology, San31, Hyoja-dong, Pohang, Gyungbuk, 790-784, South Korea
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19
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Jatsch A, Schillinger EK, Schmid S, Bäuerle P. Biomolecule assisted self-assembly of π-conjugated oligomers. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b926594e] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Babkina SS, Budnikov GK, Ulakhovich NA. Bioaffine methods for determining ajmaline using an amperometric DNA-sensor and an immunoenzyme spectrophotometric test system. JOURNAL OF ANALYTICAL CHEMISTRY 2009. [DOI: 10.1134/s1061934809090147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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A simple and direct electrochemical detection of interferon-gamma using its RNA and DNA aptamers. Biosens Bioelectron 2008; 23:1819-24. [PMID: 18406597 DOI: 10.1016/j.bios.2008.02.021] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 02/25/2008] [Accepted: 02/25/2008] [Indexed: 11/21/2022]
Abstract
Tuberculosis is the most frequent cause of infection-related death worldwide. We constructed a simple and direct electrochemical sensor to detect interferon (IFN)-gamma, a selective marker for tuberculosis pleurisy, using its RNA and DNA aptamers. IFN-gamma was detected by its 5'-thiol-modified aptamer probe immobilized on the gold electrode. Interaction between IFN-gamma and the aptamer was recorded using electrochemical impedance spectroscopy and quartz crystal microbalance (QCM) with high sensitivity. The RNA-aptamer-based sensor showed a low detection limit of 100 fM, and the DNA-aptamer-based sensor detected IFN-gamma to 1 pM in sodium phosphate buffer. With QCM analysis, the aptamer immobilized on the electrode and IFN-gamma bound to the aptamer probe was quantified. This QCM result shows that IFN-gamma exists in multimeric forms to interact with the aptamers, and the RNA aptamer prefers the high multimeric state of IFN-gamma. Such a preference may describe the low detection limit of the RNA aptamer shown by impedance analysis. In addition, IFN-gamma was detected to 10 pM by the DNA aptamer in fetal bovine serum, a mimicked biological system, which has similar components to pleural fluid.
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22
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Jatsch A, Kopyshev A, Mena-Osteritz E, Bäuerle P. Self-Organizing Oligothiophene−Nucleoside Conjugates: Versatile Synthesis via “Click”-Chemistry. Org Lett 2008; 10:961-4. [DOI: 10.1021/ol703090f] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anja Jatsch
- Institute of Organic Chemistry II and Advanced Materials, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Alexey Kopyshev
- Institute of Organic Chemistry II and Advanced Materials, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Elena Mena-Osteritz
- Institute of Organic Chemistry II and Advanced Materials, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Peter Bäuerle
- Institute of Organic Chemistry II and Advanced Materials, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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23
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Singh K, Rahman MA, Son JI, Kim KC, Shim YB. An amperometric immunosensor for osteoproteogerin based on gold nanoparticles deposited conducting polymer. Biosens Bioelectron 2008; 23:1595-601. [PMID: 18304799 DOI: 10.1016/j.bios.2008.01.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 12/13/2007] [Accepted: 01/16/2008] [Indexed: 11/17/2022]
Abstract
An amperometric immunosensor was fabricated for the detection of osteoproteogerin (OPG) by covalently immobilizing a monoclonal OPG antibody (anti-OPG) onto the gold nanoparticles (AuNPs) deposited functionalized conducting polymer (5,2':5',2''-terthiophene-3'-carboxylic acid). AuNPs were electrochemically deposited onto the conducting polymer using cyclic voltammetry. The particle size of deposited AuNPs was controlled by varying the scan rate and was characterized by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). The immobilization of anti-OPG was also confirmed using XPS. The principle of immunosensor was based on a competitive immunoassay between free-OPG and labeled-OPG for the active sites of anti-OPG. HRP was used as a label that electrochemically catalyzes the H(2)O(2) reduction. The catalytic reduction was monitored amperometrically at -0.4V vs. Ag/AgCl. The immunosensor showed a linear range between 2.5 and 25pg/ml and the detection limit was determined to be 2pg/ml. The proposed immunosensor was successfully applied for real human samples to detect OPG.
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Affiliation(s)
- Kanika Singh
- School of Mechanical Engineering and MEMS/Nano Technology Center, Pusan National University, Pusan 609-735, South Korea
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24
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Rahman MA, Kumar P, Park DS, Shim YB. Electrochemical Sensors Based on Organic Conjugated Polymers. SENSORS (BASEL, SWITZERLAND) 2008; 8:118-141. [PMID: 27879698 PMCID: PMC3681146 DOI: 10.3390/s8010118] [Citation(s) in RCA: 230] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 01/04/2008] [Indexed: 11/20/2022]
Abstract
Organic conjugated polymers (conducting polymers) have emerged as potentialcandidates for electrochemical sensors. Due to their straightforward preparation methods,unique properties, and stability in air, conducting polymers have been applied to energystorage, electrochemical devices, memory devices, chemical sensors, and electrocatalysts.Conducting polymers are also known to be compatible with biological molecules in aneutral aqueous solution. Thus, these are extensively used in the fabrication of accurate,fast, and inexpensive devices, such as biosensors and chemical sensors in the medicaldiagnostic laboratories. Conducting polymer-based electrochemical sensors and biosensorsplay an important role in the improvement of public health and environment because rapiddetection, high sensitivity, small size, and specificity are achievable for environmentalmonitoring and clinical diagnostics. In this review, we summarized the recent advances inconducting polymer-based electrochemical sensors, which covers chemical sensors(potentiometric, voltammetric, amperometric) and biosensors (enzyme based biosensors,immunosensors, DNA sensors).
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Affiliation(s)
- Md Aminur Rahman
- Department of Chemistry and Center for Innovative Bio.Physio Sensor Technology, Pusan National University, Keumjeong-ku, Busan 609-735, South Korea.
| | - Pankaj Kumar
- Department of Chemistry and Center for Innovative Bio.Physio Sensor Technology, Pusan National University, Keumjeong-ku, Busan 609-735, South Korea.
| | - Deog-Su Park
- Department of Chemistry and Center for Innovative Bio.Physio Sensor Technology, Pusan National University, Keumjeong-ku, Busan 609-735, South Korea.
| | - Yoon-Bo Shim
- Department of Chemistry and Center for Innovative Bio.Physio Sensor Technology, Pusan National University, Keumjeong-ku, Busan 609-735, South Korea.
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25
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Pan Q, Zhang R, Bai Y, He N, Lu Z. An electrochemical approach for detection of specific DNA-binding protein by gold nanoparticle-catalyzed silver enhancement. Anal Biochem 2007; 375:179-86. [PMID: 18164677 DOI: 10.1016/j.ab.2007.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Revised: 11/23/2007] [Accepted: 12/03/2007] [Indexed: 11/25/2022]
Abstract
Interaction between transcription factor and sequence-specific DNA plays an important role in regulation of gene transcription in biological systems. As electrochemical intercalators, gold (Au) nanoparticles show high catalysis activity and compatibility for detection of biological molecules. In this article, we report an electrochemical approach for sequence-specific DNA-binding transcription factor detection by Au nanoparticle-catalyzed silver (Ag) enhancement at interface between electrodes and electrolyte solutions. Here unimolecular hairpin oligonucleotides were self-assembled onto Au electrode surface and their elongation on Au electrode surface was carried out to form double-stranded oligonucleotides with transcription factor NF-kappaB (nuclear factor-kappa B) binding sites. Au nanoparticle-catalyzed Ag deposition was detected by anodic stripping voltammetry (ASV) for NF-kappaB binding. It was found that this method for the detection of sequence-specific DNA-binding protein showed pronounced specificity and that the detection limit was as low as 0.1 pM. The findings indicated that our method can have applications in transcription regulation, operator site recognition, and functional gene inspection.
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Affiliation(s)
- Qin Pan
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
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26
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Ramsey JE, Daugherty MA, Kelm RJ. Hydrodynamic studies on the quaternary structure of recombinant mouse Purbeta. J Biol Chem 2006; 282:1552-60. [PMID: 17121857 DOI: 10.1074/jbc.m609356200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Purbeta is a gene regulatory factor belonging to a family of highly conserved nucleic acid-binding proteins related by their ability to preferentially bind single-stranded DNA or RNA sequences rich in purine nucleotides. In conjunction with Puralpha, Purbeta has been implicated in transcriptional and translational repression of genes encoding contractile proteins found in the heart and vasculature. Although several models of sequence-specific DNA recognition, strand separation, and activator inhibition by oligomeric Puralpha and Purbeta have been proposed, it is currently unclear whether protein-protein interaction is a prerequisite to, or a consequence of nucleic acid binding. In this study, a recombinant protein purification scheme was devised to yield homogenous mouse Purbeta devoid of nucleic acid. Recombinant Purbeta was then subjected to light scattering and analytical ultracentrifugation analyses to assess the size, shape, and oligomeric state of the purified protein in solution. Results of laser light scattering and sedimentation velocity experiments indicated that Purbeta reversibly self-associates in the absence of nucleic acid. Both approaches independently showed that the hydrodynamic shape of the Purbeta homodimer is markedly asymmetric and non-spherical. Sedimentation velocity analyses indicated that dimeric Purbeta has a sedimentation coefficient of 3.96 Svedberg, a frictional coefficient ratio (f/f(0)) of 1.60, and a hydrodynamic radius of 4.43 nm. These values were consistent with those determined by independent dynamic light scattering studies. Sedimentation equilibrium analyses confirmed that Purbeta self-associates in a reversible monomer-dimer equilibrium characterized by a K(d) = 1.13 +/- 0.27 microm.
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Affiliation(s)
- Jon E Ramsey
- Department of Biochemistry and Medicine, Cardiovascular Research Institute, University of Vermont College of Medicine, Burlington, Vermont 05405, USA
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27
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Malhotra BD, Chaubey A, Singh SP. Prospects of conducting polymers in biosensors. Anal Chim Acta 2006; 578:59-74. [PMID: 17723695 DOI: 10.1016/j.aca.2006.04.055] [Citation(s) in RCA: 246] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2006] [Revised: 04/17/2006] [Accepted: 04/20/2006] [Indexed: 10/24/2022]
Abstract
Applications of conducting polymers to biosensors have recently aroused much interest. This is because these molecular electronic materials offer control of different parameters such as polymer layer thickness, electrical properties and bio-reagent loading, etc. Moreover, conducting polymer based biosensors are likely to cater to the pressing requirements such as biocompatibility, possibility of in vivo sensing, continuous monitoring of drugs or metabolites, multi-parametric assays, miniaturization and high information density. This paper deals with the emerging trends in conducting polymer based biosensors during the last about 5 years.
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Affiliation(s)
- Bansi D Malhotra
- Biomolecular Electronics and Conducting Polymer Research Group, National Physical Laboratory, Dr. K.S. Krishnan Marg, New Delhi 110012, India.
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28
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Babkina SS, Budnikov GK. Electrochemical biosensors based on nucleic acids and their use in bioaffinity assays for determining DNA and and its effectors. JOURNAL OF ANALYTICAL CHEMISTRY 2006. [DOI: 10.1134/s1061934806080028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Cho M, Lee S, Han SY, Park JY, Rahman MA, Shim YB, Ban C. Electrochemical detection of mismatched DNA using a MutS probe. Nucleic Acids Res 2006; 34:e75. [PMID: 16772400 PMCID: PMC1483224 DOI: 10.1093/nar/gkl364] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A direct and label-free electrochemical biosensor for the detection of the protein–mismatched DNA interaction was designed using immobilized N-terminal histidine tagged Escherichia coli. MutS on a Ni-NTA coated Au electrode. General electrochemical methods, cyclic voltammetry (CV), electrochemical quartz crystal microbalance (EQCM) and impedance spectroscopy, were used to ascertain the binding affinity of mismatched DNAs to the MutS probe. The direct results of CV and impedance clearly reveal that the interaction of MutS with the CC heteroduplex was much stronger than that with AT homoduplex, which was not differentiated in previous results (GT > CT > CC ≈ AT) of a gel mobility shift assay. The EQCM technique was also able to quantitatively analyze MutS affinity to heteroduplexes.
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Affiliation(s)
| | | | | | | | - Md Aminur Rahman
- Department of Chemistry, Pusan National UniversityBusan, 609-735, South Korea
| | - Yoon-Bo Shim
- Department of Chemistry, Pusan National UniversityBusan, 609-735, South Korea
- To whom correspondence should be addressed. Tel: +82 54 279 2127; Fax: +82 54 279 3399;
| | - Changill Ban
- To whom correspondence should be addressed. Tel: +82 54 279 2127; Fax: +82 54 279 3399;
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30
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Shiddiky MJA, Park DS, Shim YB. Detection of polymerase chain reaction fragments using a conducting polymer-modified screen-printed electrode in a microfluidic device. Electrophoresis 2006; 26:4656-63. [PMID: 16283692 DOI: 10.1002/elps.200500447] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A simple and fast method for electrochemical detection of amplified fragments by PCR was successfully developed using CE in a microfluidic device with a modified screen-printed carbon electrode (SPCE). The surfaces of the SPCE were modified with poly-5,2'-5',2''-terthiophene-3'-carboxylic acid, which improves the analysis performance by lowering the detection potential, enhancing the S/N characteristics, and avoiding electrode poisoning. DNA fragments amplified by PCR were separated within 210 s in a 75.5 mm-long coated-separation channel at a separation field strength of -200 V/cm. To minimize the sample adsorption into the inner surface of the capillary wall, which disturbs the separation, a dynamically coated capillary with an acrylamide solution was used. Furthermore, the analysis procedure was simplified and rendered reproducible by using 0.50% w/v hydroxyethylcellulose as a separation matrix in a coated channel. The reproducibility of the analysis employing the coated channel yielded RSD of 4.3% for the peak areas and 1.4% for the migration times in eight repetitive measurements at a modified electrode, compared with 21.3 and 9.4% for a bare electrode. The sensitivity of the assay was 18.74 pAs/(pg/microL) with a detection limit of 584.31 +/- 1.3 fg/microL.
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Affiliation(s)
- Muhammad J A Shiddiky
- Department of Chemistry and Center for Innovative BioPhysio Sensor Technology, Pusan National University, Keumjeong-ku, Busan, South Korea
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31
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Knapp AM, Ramsey JE, Wang SX, Godburn KE, Strauch AR, Kelm RJ. Nucleoprotein interactions governing cell type-dependent repression of the mouse smooth muscle alpha-actin promoter by single-stranded DNA-binding proteins Pur alpha and Pur beta. J Biol Chem 2006; 281:7907-18. [PMID: 16436378 DOI: 10.1074/jbc.m509682200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pur alpha and Pur beta are structurally related single-stranded DNA/RNA-binding proteins implicated in the control of cell growth and differentiation. The goal of this study was to determine whether Pur alpha and Pur beta function in a redundant, distinct, or collaborative manner to suppress smooth muscle alpha-actin gene expression in cell types relevant to wound repair and vascular remodeling. RNA interference-mediated loss-of-function analyses revealed that, although Pur beta was the dominant repressor, the combined action of endogenous Pur alpha and Pur beta was necessary to fully repress the full-length smooth muscle alpha-actin promoter in cultured fibroblasts but to a lesser extent in vascular smooth muscle cells. The activity of a minimal core enhancer containing a truncated 5' Pur repressor binding site was unaffected by knockdown of Pur alpha and/or Pur beta in fibroblasts. Conversely, gain-of-function studies indicated that Pur alpha or Pur beta could each independently repress core smooth muscle alpha-actin enhancer activity albeit in a cell type-dependent fashion. Biochemical analyses indicated that purified recombinant Pur alpha and Pur beta were essentially identical in terms of their binding affinity and specificity for GGN repeat-containing strands of several cis-elements comprising the core enhancer. However, Pur alpha and Pur beta exhibited more distinctive protein interaction profiles when evaluated for binding to enhancer-associated transcription factors in extracts from fibroblasts and vascular smooth muscle cells. These findings support the hypothesis that Pur alpha and Pur beta repress smooth muscle alpha-actin gene transcription by means of DNA strand-selective cis-element binding and cell type-dependent protein-protein interactions.
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MESH Headings
- Actins/metabolism
- Animals
- Binding, Competitive
- Biotinylation
- Blotting, Western
- DNA/chemistry
- DNA, Single-Stranded/chemistry
- DNA-Binding Proteins/chemistry
- Dose-Response Relationship, Drug
- Enhancer Elements, Genetic
- Enzyme-Linked Immunosorbent Assay
- Epitopes/chemistry
- Fibroblasts/metabolism
- Genes, Reporter
- Genetic Vectors
- Mice
- Mice, Inbred C57BL
- Myocytes, Smooth Muscle/metabolism
- Nerve Tissue Proteins/chemistry
- Nucleoproteins/chemistry
- Plasmids/metabolism
- Promoter Regions, Genetic
- Protein Binding
- RNA/chemistry
- RNA Interference
- Transcription Factors/chemistry
- Transcription, Genetic
- Transgenes
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Affiliation(s)
- Anna M Knapp
- Department of Biochemistry, Cardiovascular Research Institute, University of Vermont College of Medicine, Burlington, Vermont 05405, USA
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32
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Cha SK. Detection of Guanine Based DNA and its Damage with Electrodes Incorporating a Polymeric film of [Ru(v-bpy)3]2+. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2005. [DOI: 10.5012/jkcs.2005.49.4.343] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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van den Heuvel RHH, Gato S, Versluis C, Gerbaux P, Kleanthous C, Heck AJR. Real-time monitoring of enzymatic DNA hydrolysis by electrospray ionization mass spectrometry. Nucleic Acids Res 2005; 33:e96. [PMID: 15956101 PMCID: PMC1150282 DOI: 10.1093/nar/gni099] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A fast and direct method for the monitoring of enzymatic DNA hydrolysis was developed using electrospray ionization mass spectrometry. We incorporated the use of a robotic chip-based electrospray ionization source for increased reproducibility and throughput. The mass spectrometry method allows the detection of DNA fragments and intact non-covalent protein–DNA complexes in a single experiment. We used the method to monitor in real-time single-stranded (ss) DNA hydrolysis by colicin E9 DNase and to characterize transient non-covalent E9 DNase–DNA complexes present during the hydrolysis reaction. The mass spectra showed that E9 DNase interacts with ssDNA in the absence of a divalent metal ion, but is strictly dependent on Ni2+ or Co2+ for ssDNA hydrolysis. We demonstrated that the sequence selectivity of E9 DNase is dependent on the ratio protein:ssDNA or the ssDNA concentration and that only 3′-hydroxy and 5′-phosphate termini are produced. It was also shown that the homologous E7 DNase is reactive with Zn2+ as transition metal ion and that this DNase displays a different sequence selectivity. The method described is of general use to analyze the reactivity and specificity of nucleases.
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Affiliation(s)
- Robert H H van den Heuvel
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
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