1
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Wettasinghe AP, Seifi MO, Bravo M, Adams AC, Patel A, Lou M, Kahanda D, Peng H, Stelling AL, Fan L, Slinker JD. Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair. Protein Sci 2023; 32:e4815. [PMID: 37874269 PMCID: PMC10659936 DOI: 10.1002/pro.4815] [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: 07/22/2023] [Revised: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
DNA helicase activity is essential for the vital DNA metabolic processes of recombination, replication, transcription, translation, and repair. Recently, an unexpected, rapid exponential ATP-stimulated DNA unwinding rate was observed from an Archaeoglobus fulgidus helicase (AfXPB) as compared to the slower conventional helicases from Sulfolobus tokodaii, StXPB1 and StXPB2. This unusual rapid activity suggests a "molecular wrench" mechanism arising from the torque applied by AfXPB on the duplex structure in transitioning from open to closed conformations. However, much remains to be understood. Here, we investigate the concentration dependence of DNA helicase binding and ATP-stimulated kinetics of StXPB2 and AfXPB, as well as their binding and activity in Bax1 complexes, via an electrochemical assay with redox-active DNA monolayers. StXPB2 ATP-stimulated activity is concentration-independent from 8 to 200 nM. Unexpectedly, AfXPB activity is concentration-dependent in this range, with exponential rate constants varying from seconds at concentrations greater than 20 nM to thousands of seconds at lower concentrations. At 20 nM, rapid exponential signal decay ensues, linearly reverses, and resumes with a slower exponential decay. This change in AfXPB activity as a function of its concentration is rationalized as the crossover between the fast molecular wrench and slower conventional helicase modes. AfXPB-Bax1 inhibits rapid activity, whereas the StXPB2-Bax1 complex induces rapid kinetics at higher concentrations. This activity is rationalized with the crystal structures of these complexes. These findings illuminate the different physical models governing molecular wrench activity for improved biological insight into a key factor in DNA repair.
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Affiliation(s)
| | - Melodee O. Seifi
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Marco Bravo
- Department of BiochemistryUniversity of CaliforniaRiversideCaliforniaUSA
| | - Austen C. Adams
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Aman Patel
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Monica Lou
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Dimithree Kahanda
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Hao‐Che Peng
- Department of ChemistryThe University of Texas at DallasRichardsonTexasUSA
| | | | - Li Fan
- Department of ChemistryThe University of Texas at DallasRichardsonTexasUSA
| | - Jason D. Slinker
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
- Department of ChemistryThe University of Texas at DallasRichardsonTexasUSA
- Department of Materials Science and EngineeringThe University of Texas at DallasRichardsonTexasUSA
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2
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Sankar K, Baer R, Grazon C, Sabatelle RC, Lecommandoux S, Klapperich CM, Galagan JE, Grinstaff MW. An Allosteric Transcription Factor DNA-Binding Electrochemical Biosensor for Progesterone. ACS Sens 2022; 7:1132-1137. [PMID: 35412319 PMCID: PMC9985479 DOI: 10.1021/acssensors.2c00133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe an electrochemical strategy to transduce allosteric transcription factor (aTF) binding affinity to sense steroid hormones. Our approach utilizes square wave voltammetry to monitor changes in current output as a progesterone (PRG)-specific aTF (SRTF1) unbinds from the cognate DNA sequence in the presence of PRG. The sensor detects PRG in artificial urine samples with sufficient sensitivity suitable for clinical applications. Our results highlight the capability of using aTFs as the biorecognition elements to develop electrochemical point-of-care biosensors for the detection of small-molecule biomarkers and analytes.
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Affiliation(s)
- Karthika Sankar
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA
| | - R Baer
- Department of Microbiology, Boston University, Boston, MA 02215, USA
| | - Chloé Grazon
- Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France.,University Bordeaux, Institut des Sciences Moléculaires (CNRS UMR 5255), 33405 Talence, France
| | - Robert C. Sabatelle
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Catherine M. Klapperich
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James E. Galagan
- Department of Microbiology, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Corresponding Author James E. Galagan; , Mark W. Grinstaff;
| | - Mark W. Grinstaff
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.,Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Corresponding Author James E. Galagan; , Mark W. Grinstaff;
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3
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Pourmadadi M, Ahmadi MJ, Dinani HS, Ajalli N, Dorkoosh F. Theranostic applications of stimulus-responsive systems based on Fe2O3. Pharm Nanotechnol 2022; 10:90-112. [PMID: 35142274 DOI: 10.2174/2211738510666220210105113] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/18/2021] [Accepted: 11/26/2021] [Indexed: 11/22/2022]
Abstract
According to the interaction of nanoparticles with biological systems, enthusiasm for nanotechnology in biomedical applications has been developed in the past decades. Fe2O3 nanoparticles, as the most stable iron oxide, have special merits that make them useful widely for detecting diseases, therapy, drug delivery, and monitoring the therapeutic process. This review presents the fabrication methods of Fe2O3-based materials and their photocatalytic and magnetic properties. Then, we highlight the application of Fe2O3-based nanoparticles in diagnosis and imaging, different therapy methods, and finally, stimulus-responsive systems, such as pH-responsive, magnetic-responsive, redox-responsive, and enzyme-responsive, with an emphasis on cancer treatment. In addition, the potential of Fe2O3 to combine diagnosis and therapy within a single particle called theranostic agent will be discussed.
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Affiliation(s)
- Mehrab Pourmadadi
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Mohammad Javad Ahmadi
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | | | - Narges Ajalli
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Farid Dorkoosh
- Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
- Medical Biomaterial Research Center (MBR), Tehran University of Medical Science, Tehran, Iran
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4
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Wettasinghe AP, Singh N, Starcher CL, DiTusa CC, Ishak-Boushaki Z, Kahanda D, McMullen R, Motea EA, Slinker JD. Detecting Attomolar DNA-Damaging Anticancer Drug Activity in Cell Lysates with Electrochemical DNA Devices. ACS Sens 2021; 6:2622-2629. [PMID: 34156840 DOI: 10.1021/acssensors.1c00365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Here, we utilize electrochemical DNA devices to quantify and understand the cancer-specific DNA-damaging activity of an emerging drug in cellular lysates at femtomolar and attomolar concentrations. Isobutyl-deoxynyboquinone (IB-DNQ), a potent and tumor-selective NAD(P)H quinone oxidoreductase 1 (NQO1) bioactivatable drug, was prepared and biochemically verified in cancer cells highly expressing NQO1 (NQO1+) and knockdowns with low NQO1 expression (NQO1-) by Western blot, NQO1 activity analysis, survival assays, oxygen consumption rate, extracellular acidification rate, and peroxide production. Lysates from these cells and the IB-DNQ drug were then introduced to a chip system bearing an array of DNA-modified electrodes, and their DNA-damaging activity was quantified by changes in DNA-mediated electrochemistry arising from base-excision repair. Device-level controls of NQO1 activity and kinetic analysis were used to verify and further understand the IB-DNQ activity. A 380 aM IB-DNQ limit of detection and a 1.3 fM midpoint of damage were observed in NQO1+ lysates, both metrics 2 orders of magnitude lower than NQO1- lysates, indicating the high IB-DNQ potency and selectivity for NQO1+ cancers. The device-level damage midpoint concentration in NQO1+ lysates was over 8 orders of magnitude lower than cell survival benchmarks, likely due to poor IB-DNQ cellular uptake, demonstrating that these devices can identify promising drugs requiring improved cell permeability. Ultimately, these results indicate the noteworthy potency and selectivity of IB-DNQ and the high sensitivity and precision of electrochemical DNA devices to analyze agents/drugs involved in DNA-damaging chemotherapies.
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Affiliation(s)
- Ashan P. Wettasinghe
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Naveen Singh
- Department of Biochemistry and Molecular Biology, Simon Comprehensive Cancer Center, Indiana University School of Medicine, 980 W. Walnut Street, Walther Hall R3 C551, Indianapolis, Indiana 46202, United States
| | - Colton L. Starcher
- Department of Biochemistry and Molecular Biology, Simon Comprehensive Cancer Center, Indiana University School of Medicine, 980 W. Walnut Street, Walther Hall R3 C551, Indianapolis, Indiana 46202, United States
| | - Chloe C. DiTusa
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Zakari Ishak-Boushaki
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Dimithree Kahanda
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
- Department of Physics, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Reema McMullen
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Edward A. Motea
- Department of Biochemistry and Molecular Biology, Simon Comprehensive Cancer Center, Indiana University School of Medicine, 980 W. Walnut Street, Walther Hall R3 C551, Indianapolis, Indiana 46202, United States
| | - Jason D. Slinker
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
- Department of Materials Science and Engineering, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
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5
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Li D, Li Y, Luo F, Qiu B, Lin Z. Ultrasensitive Homogeneous Electrochemiluminescence Biosensor for a Transcription Factor Based on Target-Modulated Proximity Hybridization and Exonuclease III-Powered Recycling Amplification. Anal Chem 2020; 92:12686-12692. [DOI: 10.1021/acs.analchem.0c03086] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Dan Li
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Ya Li
- Department of Ultrasound, Fourth People’s Hospital of Taizhou City, Jianshu, 225300, China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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6
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Cyclic enzymatic amplification method for highly sensitive detection of nuclear factor-kappa B. Anal Chim Acta 2019; 1068:80-86. [DOI: 10.1016/j.aca.2019.03.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/11/2022]
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7
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Han X, Yu Z, Li F, Shi W, Fu C, Yan H, Zhang G. Two kanamycin electrochemical aptamer-based sensors using different signal transduction mechanisms: A comparison of electrochemical behavior and sensing performance. Bioelectrochemistry 2019; 129:270-277. [PMID: 31254804 DOI: 10.1016/j.bioelechem.2019.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/16/2019] [Accepted: 06/16/2019] [Indexed: 12/15/2022]
Abstract
Two typical kanamycin-A (KAN-A) electrochemical aptamer-based sensors employing different signal transduction mechanisms were deliberately designed and constructed with a similar structure. One sensor (sensor-1) was based on the classical probe conformation changing mode (PCCM) with a methylene blue (MB) label used as an electrochemical tag; the other sensor (sensor-2) used the target-induced signal probe shifting (TISPS) method with a free MB label in the assay solution. The difference in signal transduction mechanisms resulted in big differences in basic electrochemical behavior and comprehensive sensing performance. The results show that both sensor types exhibit different electrochemical behavior in square wave voltammetry, cyclic voltammetry, and in sensitivity, with detection limits of 3.0 nM for sensor-1 and 60.0 pM for sensor-2 in buffer. When validated for practical and quantitative detection of tap water and milk samples, both sensing methods performed well with detection limits of <260 nM and measurement times of <40 min. In addition, accuracy was good with mean recoveries of 72.3-92.6% and precision was acceptable with a relative standard deviation (RSD) of ≤14.2%. The basis for the similarities and differences in performance is also presented.
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Affiliation(s)
- Xianda Han
- School of Materials Science and Engineering, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China; Post-Doctoral Research Center, Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
| | - Zhigang Yu
- School of Materials Science and Engineering, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China; Post-Doctoral Research Center, Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China.
| | - Fengqin Li
- Post-Doctoral Research Center, Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
| | - Wenbing Shi
- Post-Doctoral Research Center, Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
| | - Cuicui Fu
- Post-Doctoral Research Center, Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
| | - Hong Yan
- School of Materials Science and Engineering, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China
| | - Guiling Zhang
- School of Materials Science and Engineering, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China.
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8
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Zhao H, Ye D, Mao X, Li F, Xu J, Li M, Zuo X. Stepping gating of ion channels on nanoelectrode via DNA hybridization for label-free DNA detection. Biosens Bioelectron 2019; 133:141-146. [PMID: 30925363 DOI: 10.1016/j.bios.2019.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/10/2019] [Accepted: 03/17/2019] [Indexed: 12/21/2022]
Abstract
Natural ion channels on cell membrane can gate the transport of ions and molecules by the conformational alteration of transmembrane proteins to regulate the normal physiological activities of cells. Inspired by the similarity of the conformation change under specific stimuli, here we introduce an ion channel gating model on a single nanoelectrode by anchoring DNA-gated switches on the very nanotip of gold nanoelectrode to mimic the response-to-stimulus behaviors of ion channels on bio-membranes. The surface-tethered DNA ion channels can be switched on by the Watson-Crick base pairing, which can alter the conformation of the tethered DNA from lying state to upright state. And these conformational alterations of the anchored DNA switches can effectively gate the transport of potassium ferricyanide onto the electrode interface. By continuously initiating the gates with DNA of different concentrations, we achieved the stepping gating of ion channels on a single nanoelectrode. Further, we demonstrated that the ion gating system on nanoelectrode showed excellent sensing performance. For example, the response kinetic was very fast with the signal saturation time of ~1 min, the reproducibility of the OFF/ON switch was robust enough to sustain for two cycles, and simultaneously, the specificity was high enough to distinguish complementary DNA and noncomplementary DNA. When used for label-free DNA detection, the limit of detection can be as low as 10 pM. This study provides a promising avenue to achieve label free and real-time detection of multiple biomolecules.
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Affiliation(s)
- Haipei Zhao
- NEST Lab, Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China; Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dekai Ye
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jiaqiang Xu
- NEST Lab, Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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9
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Kahanda D, Singh N, Boothman DA, Slinker JD. Following anticancer drug activity in cell lysates with DNA devices. Biosens Bioelectron 2018; 119:1-9. [PMID: 30098460 PMCID: PMC6217983 DOI: 10.1016/j.bios.2018.07.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/20/2018] [Accepted: 07/28/2018] [Indexed: 11/19/2022]
Abstract
There is a great need to track the selectivity of anticancer drug activity and to understand the mechanisms of associated biological activity. Here we focus our studies on the specific NQO1 bioactivatable drug, ß-lapachone, which is in several Phase I clinical trials to treat human non-small cell lung, pancreatic and breast cancers. Multi-electrode chips with electrochemically-active DNA monolayers are used to track anticancer drug activity in cellular lysates and correlate cell death activity with DNA damage. Cells were prepared from the triple-negative breast cancer (TNBC) cell line, MDA-MB-231 (231) to be proficient or deficient in expression of the NAD(P)H:quinone oxidoreductase 1 (NQO1) enzyme, which is overexpressed in most solid cancers and lacking in control healthy cells. Cells were lysed and added to chips, and the impact of β-lapachone (β-lap), an NQO1-dependent DNA-damaging drug, was tracked with DNA electrochemical signal changes arising from drug-induced DNA damage. Electrochemical DNA devices showed a 3.7-fold difference in the electrochemical responses in NQO1+ over NQO1- cell lysates, as well as 10-20-fold selectivity to catalase and dicoumarol controls that deactivate DNA damaging pathways. Concentration-dependence studies revealed that 1.4 µM β-lap correlated with the onset of cell death from viability assays and the midpoint of DNA damage on the chip, and 2.5 µM β-lap correlated with the midpoint of cell death and the saturation of DNA damage on the chip. Results indicate that these devices could inform therapeutic decisions for cancer treatment.
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Affiliation(s)
- Dimithree Kahanda
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, TX 75080, USA
| | - Naveen Singh
- Department of Biochemistry and Molecular Biology, Simon Cancer Center, Indiana University, 980 W. Walnut Street, Walther Hall R3 C524, Indianapolis, IN 46202, USA
| | - David A Boothman
- Department of Biochemistry and Molecular Biology, Simon Cancer Center, Indiana University, 980 W. Walnut Street, Walther Hall R3 C524, Indianapolis, IN 46202, USA
| | - Jason D Slinker
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, TX 75080, USA.
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10
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Abstract
DNA charge transport chemistry involves the migration of charge over long molecular distances through the aromatic base pair stack within the DNA helix. This migration depends upon the intimate coupling of bases stacked one with another, and hence any perturbation in that stacking, through base modifications or protein binding, can be sensed electrically. In this review, we describe the many ways DNA charge transport chemistry has been utilized to sense changes in DNA, including the presence of lesions, mismatches, DNA-binding proteins, protein activity, and even reactions under weak magnetic fields. Charge transport chemistry is remarkable in its ability to sense the integrity of DNA.
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Affiliation(s)
- Theodore J. Zwang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Edmund C. M. Tse
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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11
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Kahanda D, DuPrez KT, Hilario E, McWilliams MA, Wohlgamuth CH, Fan L, Slinker JD. Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA. Anal Chem 2018; 90:2178-2185. [PMID: 29285929 PMCID: PMC5957534 DOI: 10.1021/acs.analchem.7b04515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Much remains to be understood about the kinetics and thermodynamics of DNA helicase binding and activity. Here, we utilize probe-modified DNA monolayers on multiplexed gold electrodes as a sensitive recognition element and morphologically responsive transducer of helicase-DNA interactions. The electrochemical signals from these devices are highly sensitive to structural distortion of the DNA produced by the helicases. We used this DNA electrochemistry to distinguish the details of the DNA interactions of three distinct XPB helicases, which belong to the superfamily-2 of helicases. Clear changes in DNA melting temperature and duplex stability were observed upon helicase binding, shifts that could not be observed with conventional UV-visible absorption measurements. Binding dissociation constants were estimated in the range from 10 to 50 nM and correlated with observations of activity. ATP-stimulated DNA unwinding activity was also followed, revealing exponential time scales and distinct time constants associated with conventional and molecular wrench modes of operation further confirmed by crystal structures. These devices thus provide a sensitive measure of the structural thermodynamics and kinetics of helicase-DNA interactions.
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Affiliation(s)
- Dimithree Kahanda
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, PHY 36, Richardson, Texas 75080, United States
| | - Kevin T. DuPrez
- Department of Biochemistry, University of California, 900 University Avenue, Riverside, California 92521, United States
| | - Eduardo Hilario
- Department of Biochemistry, University of California, 900 University Avenue, Riverside, California 92521, United States
| | - Marc A. McWilliams
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, PHY 36, Richardson, Texas 75080, United States
| | - Chris H. Wohlgamuth
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, PHY 36, Richardson, Texas 75080, United States
| | - Li Fan
- Department of Biochemistry, University of California, 900 University Avenue, Riverside, California 92521, United States
| | - Jason D. Slinker
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, PHY 36, Richardson, Texas 75080, United States
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12
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Abstract
A DNA electrochemistry platform has been developed to probe proteins bound to DNA electrically. Here gold electrodes are modified with thiol-modified DNA, and DNA charge transport chemistry is used to probe DNA binding and enzymatic reaction both with redox-silent and redox-active proteins. For redox-active proteins, the electrochemistry permits the determination of redox potentials in the DNA-bound form, where comparisons to DNA-free potentials can be made using graphite electrodes without DNA modification. Importantly, electrochemistry on the DNA-modified electrodes facilitates reaction under aqueous, physiological conditions with a sensitive electrical measurement of binding and activity.
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Affiliation(s)
| | | | - Yingxin Deng
- California Institute of Technology, Pasadena, CA, United States
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13
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Arnold AR, Grodick MA, Barton JK. DNA Charge Transport: from Chemical Principles to the Cell. Cell Chem Biol 2016; 23:183-197. [PMID: 26933744 DOI: 10.1016/j.chembiol.2015.11.010] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/18/2015] [Accepted: 11/18/2015] [Indexed: 11/30/2022]
Abstract
The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology.
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Affiliation(s)
- Anna R Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael A Grodick
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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14
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Abstract
Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.
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Affiliation(s)
- Elizabeth O’Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Rebekah M.B. Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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15
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Ma ZY, Ruan YF, Xu F, Zhao WW, Xu JJ, Chen HY. Protein Binding Bends the Gold Nanoparticle Capped DNA Sequence: Toward Novel Energy-Transfer-Based Photoelectrochemical Protein Detection. Anal Chem 2016; 88:3864-71. [DOI: 10.1021/acs.analchem.6b00012] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zheng-Yuan Ma
- State Key
Laboratory of Analytical
Chemistry for Life Science and Collaborative Innovation Center of
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yi-Fan Ruan
- State Key
Laboratory of Analytical
Chemistry for Life Science and Collaborative Innovation Center of
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Fei Xu
- State Key
Laboratory of Analytical
Chemistry for Life Science and Collaborative Innovation Center of
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei-Wei Zhao
- State Key
Laboratory of Analytical
Chemistry for Life Science and Collaborative Innovation Center of
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key
Laboratory of Analytical
Chemistry for Life Science and Collaborative Innovation Center of
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key
Laboratory of Analytical
Chemistry for Life Science and Collaborative Innovation Center of
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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16
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Kahanda D, Chakrabarti G, Mcwilliams MA, Boothman DA, Slinker JD. Using DNA devices to track anticancer drug activity. Biosens Bioelectron 2016; 80:647-653. [PMID: 26901461 DOI: 10.1016/j.bios.2016.02.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/05/2016] [Accepted: 02/09/2016] [Indexed: 01/13/2023]
Abstract
It is beneficial to develop systems that reproduce complex reactions of biological systems while maintaining control over specific factors involved in such processes. We demonstrated a DNA device for following the repair of DNA damage produced by a redox-cycling anticancer drug, beta-lapachone (β-lap). These chips supported ß-lap-induced biological redox cycle and tracked subsequent DNA damage repair activity with redox-modified DNA monolayers on gold. We observed drug-specific changes in square wave voltammetry from these chips at therapeutic ß-lap concentrations of high statistical significance over drug-free control. We also demonstrated a high correlation of this change with the specific ß-lap-induced redox cycle using rational controls. The concentration dependence of ß-lap revealed significant signal changes at levels of high clinical significance as well as sensitivity to sub-lethal levels of ß-lap. Catalase, an enzyme decomposing peroxide, was found to suppress DNA damage at a NQO1/catalase ratio found in healthy cells, but was clearly overcome at a higher NQO1/catalase ratio consistent with cancer cells. We found that it was necessary to reproduce key features of the cellular environment to observe this activity. Thus, this chip-based platform enabled tracking of ß-lap-induced DNA damage repair when biological criteria were met, providing a unique synthetic platform for uncovering activity normally confined to inside cells.
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Affiliation(s)
- Dimithree Kahanda
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, TX 75080, United States
| | - Gaurab Chakrabarti
- Departments of Pharmacology, Oncology and Radiation Oncology, Laboratory of Molecular Stress Responses and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, ND2.210K 601 Forest Park Drive, Dallas, TX 75390-8807, United States
| | - Marc A Mcwilliams
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, TX 75080, United States
| | - David A Boothman
- Departments of Pharmacology, Oncology and Radiation Oncology, Laboratory of Molecular Stress Responses and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, ND2.210K 601 Forest Park Drive, Dallas, TX 75390-8807, United States
| | - Jason D Slinker
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, TX 75080, United States.
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17
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McWilliams MA, Bhui R, Taylor DW, Slinker JD. The Electronic Influence of Abasic Sites in DNA. J Am Chem Soc 2015; 137:11150-5. [DOI: 10.1021/jacs.5b06604] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marc A. McWilliams
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, Texas 75080, United States
| | - Rita Bhui
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, Texas 75080, United States
| | - David W. Taylor
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, Texas 75080, United States
| | - Jason D. Slinker
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, Texas 75080, United States
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18
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Pérez WI, Soto Y, Ramirez-Vick JE, Meléndez E. Nanostructured gold dsDNA sensor for early detection of breast cancer by beta protein 1 (BP 1). J Electroanal Chem (Lausanne) 2015; 751:49-56. [PMID: 26161048 DOI: 10.1016/j.jelechem.2015.05.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Beta protein 1 (BP1) is a homeobox protein expressed in 80% of breast cancer cells in either estrogen receptor (ER) positive or ER negative breast cancer. However, it is barely detectable in normal breast tissues. In this project we present an electrochemical DNA nanostructured gold biosensor for detection of BP1. The gold sensor is first electrochemically nanostructured in 0.5 M sulfuric acid to reach superior conductivity, larger surface area, and higher stability. Nanostructured gold surface was characterized by atomic force microscopy (AFM) and scanning electron microscopy (SEM). The nanostructured gold sensor is then modified with double-stranded (ds) DNA mapping the genomic sequence that contains the binding site for BP1. A redox-active probe (methylene blue) was intercalated in dsDNA to monitor the binding event of BP1. A linear correlation of the electrochemical response by concentration of BP1 was obtained (R2 = 0.998) with a limit of detection of 1.2 nM. This nanostructured gold dsDNA sensor is shown to be sensitive, selective, stable, and reusable allowing for its potential clinical use.
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Affiliation(s)
- Wanda I Pérez
- Department of Chemistry, University of Puerto Rico, PO Box 9019 Mayagüez, PR 00681
| | - Yarelys Soto
- Industrial Biotechnology Program, University of Puerto Rico, PO Box 9019 Mayagüez, PR 00681
| | - Jaime E Ramirez-Vick
- Engineering Science and Materials Department, University of Puerto Rico, PO Box 9019 Mayagüez, PR 00681
| | - Enrique Meléndez
- Department of Chemistry, University of Puerto Rico, PO Box 9019 Mayagüez, PR 00681
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19
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Khoshfetrat SM, Ranjbari M, Shayan M, Mehrgardi MA, Kiani A. Wireless Electrochemiluminescence Bipolar Electrode Array for Visualized Genotyping of Single Nucleotide Polymorphism. Anal Chem 2015; 87:8123-31. [DOI: 10.1021/acs.analchem.5b02515] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Mitra Ranjbari
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Mohsen Shayan
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | | | - Abolfazl Kiani
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
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20
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Furst AL, Hill MG, Barton JK. A Multiplexed, Two-Electrode Platform for Biosensing Based on DNA-Mediated Charge Transport. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6554-6562. [PMID: 26042916 PMCID: PMC4587567 DOI: 10.1021/acs.langmuir.5b00829] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We have developed a thin layer, multiplexed biosensing platform that features two working-electrode arrays for detecting small molecules, nucleic acid sequences, and DNA-binding proteins. DNA duplexes are patterned onto the primary electrode array, while a secondary electrode array is used both to initiate DNA monolayer formation and for electrochemical readout via DNA-mediated charge transport (DNA CT) chemistry. Electrochemical reduction of Cu(phendione)2(2+) (phendione is 1,10-phenanthroline-5,6-dione) at the secondary electrodes induces covalent attachment via click chemistry of ethynyl-labeled DNA probe duplexes onto the primary electrodes that have been treated with azide-terminated alkylthiols. Electrochemical impedance spectroscopy and cyclic voltammetry confirm that catalyst activation at the secondary electrode is essential to maintain the integrity of the DNA monolayer. Electrochemical readout of DNA CT processes that occur at the primary electrode is accomplished also at the secondary electrode. The two-electrode system enables the platform to function as a collector-generator using either ferrocyanide or ferricyanide as mediators with methylene blue and DNA charge transport. Electrochemical measurements at the secondary electrode eliminate the need for large background corrections. The resulting sensitivity of this platform enables the reliable and simultaneous detection of femtomoles of the transcription factors TATA-binding protein and CopG on a single multiplexed device.
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Affiliation(s)
- Ariel L. Furst
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Michael G. Hill
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
- Department of Chemistry and Chemical Biology, Occidental College, Los Angeles, CA 90041
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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21
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Liu N, Yang Z, Lou X, Wei B, Zhang J, Gao P, Hou R, Xia F. Nanopore-based DNA-probe sequence-evolution method unveiling characteristics of protein-DNA binding phenomena in a nanoscale confined space. Anal Chem 2015; 87:4037-41. [PMID: 25751160 DOI: 10.1021/acs.analchem.5b00375] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Almost all of the important functions of DNA are realized by proteins which interact with specific DNA, which actually happens in a limited space. However, most of the studies about the protein-DNA binding are in an unconfined space. Here, we propose a new method, nanopore-based DNA-probe sequence-evolution (NDPSE), which includes up to 6 different DNA-probe systems successively designed in a nanoscale confined space which unveil the more realistic characteristics of protein-DNA binding phenomena. There are several features; for example, first, the edge-hindrance and core-hindrance contribute differently for the binding events, and second, there is an equilibrium between protein-DNA binding and DNA-DNA hybridization.
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Affiliation(s)
- Nannan Liu
- §Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China
| | - Zekun Yang
- §Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China
| | - Xiaoding Lou
- §Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China
| | - Benmei Wei
- §Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China
| | - Juntao Zhang
- §Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China
| | - Pengcheng Gao
- §Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China
| | - Ruizuo Hou
- §Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China
| | - Fan Xia
- §Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China.,‡National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology (HUST), Wuhan, Hubei 430074, P. R. China
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22
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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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23
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Khoshfetrat SM, Mehrgardi MA. Amplified electrochemical genotyping of single-nucleotide polymorphisms using a graphene–gold nanoparticles modified glassy carbon platform. RSC Adv 2015. [DOI: 10.1039/c5ra03794h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A triple signal amplification strategy for the single nucleotide polymorphisms (SNPs) genotyping is reported using the graphene–gold nanoparticles (GR–AuNPs) as a sensitive platform and monobase-modified silver and gold nanoparticles (M-NPs).
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24
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Ma ZY, Ruan YF, Zhang N, Zhao WW, Xu JJ, Chen HY. A new visible-light-driven photoelectrochemical biosensor for probing DNA–protein interactions. Chem Commun (Camb) 2015; 51:8381-4. [DOI: 10.1039/c5cc01832c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A novel photoelectrochemical approach was achieved for the detection of a DNA binding protein via the protein–DNA interaction.
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Affiliation(s)
- Zheng-Yuan Ma
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Yi-Fan Ruan
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Nan Zhang
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
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25
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26
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Ordinario DD, Burke AM, Phan L, Jocson JM, Wang H, Dickson MN, Gorodetsky AA. Sequence specific detection of restriction enzymes at DNA-modified carbon nanotube field effect transistors. Anal Chem 2014; 86:8628-33. [PMID: 25137193 DOI: 10.1021/ac501441d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein-DNA interactions play a central role in many cellular processes, and their misregulation has been implicated in a number of human diseases. Thus, there is a pressing need for the development of analytical strategies for interrogating the binding of proteins to DNA. Herein, we report the electrical monitoring of a prototypical DNA-binding protein, the PvuII restriction enzyme, at microfluidic-encapsulated, DNA-modified carbon nanotube field effect transistors. Our integrated platform enables the sensitive, sequence specific detection of PvuII at concentrations as low as 0.5 pM in a volume of 0.025 μL (corresponding to ~7500 proteins). These figures of merit compare favorably to state of the art values reported for alternative fluorescent and electrical assays. The overall detection strategy represents a step toward the massively parallel electrical monitoring, identification, and quantification of protein-DNA interactions at arrayed nanoscale devices.
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Affiliation(s)
- David D Ordinario
- Department of Chemical Engineering and Materials Science, University of California, Irvine , Irvine, California 92697, United States
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27
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Zhang Y, Liu F, Nie J, Jiang F, Zhou C, Yang J, Fan J, Li J. An electrochemical sensing platform based on local repression of electrolyte diffusion for single-step, reagentless, sensitive detection of a sequence-specific DNA-binding protein. Analyst 2014; 139:2193-8. [PMID: 24647581 DOI: 10.1039/c4an00096j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we report for the first time an electrochemical biosensor for single-step, reagentless, and picomolar detection of a sequence-specific DNA-binding protein using a double-stranded, electrode-bound DNA probe terminally modified with a redox active label close to the electrode surface. This new methodology is based upon local repression of electrolyte diffusion associated with protein-DNA binding that leads to reduction of the electrochemical response of the label. In the proof-of-concept study, the resulting electrochemical biosensor was quantitatively sensitive to the concentrations of the TATA binding protein (TBP, a model analyte) ranging from 40 pM to 25.4 nM with an estimated detection limit of ∼10.6 pM (∼80 to 400-fold improvement on the detection limit over previous electrochemical analytical systems).
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Affiliation(s)
- Yun Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China.
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28
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Sensitive and selective real-time electrochemical monitoring of DNA repair. Biosens Bioelectron 2014; 54:541-6. [DOI: 10.1016/j.bios.2013.11.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/24/2013] [Accepted: 11/10/2013] [Indexed: 11/23/2022]
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29
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Williams K, Kim CS, Kim JR, Levicky R. Multimodal electrochemical sensing of transcription factor–operator complexes. Analyst 2014; 139:1463-71. [DOI: 10.1039/c3an02128a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Changes in diffusive movements, surface potential, and interfacial impedance of DNA monolayers are combined to analyze binding of unlabeled transcription factors.
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Affiliation(s)
- Keeshan Williams
- Department of Chemical & Biomolecular Engineering
- Polytechnic Institute of New York University
- Brooklyn, USA
| | - Chung-Sei Kim
- Department of Chemical & Biomolecular Engineering
- Polytechnic Institute of New York University
- Brooklyn, USA
| | - Jin Ryoun Kim
- Department of Chemical & Biomolecular Engineering
- Polytechnic Institute of New York University
- Brooklyn, USA
| | - Rastislav Levicky
- Department of Chemical & Biomolecular Engineering
- Polytechnic Institute of New York University
- Brooklyn, USA
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30
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Furst AL, Hill MG, Barton JK. DNA-modified electrodes fabricated using copper-free click chemistry for enhanced protein detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:16141-9. [PMID: 24328347 PMCID: PMC3947573 DOI: 10.1021/la403262v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A method of DNA monolayer formation has been developed using copper-free click chemistry that yields enhanced surface homogeneity and enables variation in the amount of DNA assembled; extremely low-density DNA monolayers, with as little as 5% of the monolayer being DNA, have been formed. These DNA-modified electrodes (DMEs) were characterized visually, with AFM, and electrochemically, and were found to facilitate DNA-mediated reduction of a distally bound redox probe. These low-density monolayers were found to be more homogeneous than traditional thiol-modified DNA monolayers, with greater helix accessibility through an increased surface area-to-volume ratio. Protein binding efficiency of the transcriptional activator TATA-binding protein (TBP) was also investigated on these surfaces and compared to that on DNA monolayers formed with standard thiol-modified DNA. Our low-density monolayers were found to be extremely sensitive to TBP binding, with a signal decrease in excess of 75% for 150 nM protein. This protein was detectable at 4 nM, on the order of its dissociation constant, with our low-density monolayers. The improved DNA helix accessibility and sensitivity of our low-density DNA monolayers to TBP binding reflects the general utility of this method of DNA monolayer formation for DNA-based electrochemical sensor development.
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Affiliation(s)
- Ariel L. Furst
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Michael G. Hill
- Department of Chemistry and Chemical Biology, Occidental College, Los Angeles, CA 90041
| | - Jacqueline K. Barton
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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31
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Furst A, Landefeld S, Hill MG, Barton JK. Electrochemical patterning and detection of DNA arrays on a two-electrode platform. J Am Chem Soc 2013; 135:19099-102. [PMID: 24328227 DOI: 10.1021/ja410902j] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a novel method of DNA array formation that is electrochemically formed and addressed with a two-electrode platform. Electrochemical activation of a copper catalyst, patterned with one electrode, enables precise placement of multiple sequences of DNA onto a second electrode surface. The two-electrode patterning and detection platform allows for both spatial resolution of the patterned DNA array and optimization of detection through DNA-mediated charge transport with electrocatalysis. This two-electrode platform has been used to form arrays that enable differentiation between well-matched and mismatched sequences, the detection of TATA-binding protein, and sequence-selective DNA hybridization.
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Affiliation(s)
- Ariel Furst
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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32
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Wohlgamuth CH, McWilliams MA, Slinker JD. DNA as a molecular wire: distance and sequence dependence. Anal Chem 2013; 85:8634-40. [PMID: 23964773 DOI: 10.1021/ac401229q] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functional nanowires and nanoelectronics are sought for their use in next generation integrated circuits, but several challenges limit the use of most nanoscale devices on large scales. DNA has great potential for use as a molecular wire due to high yield synthesis, near-unity purification, and nanoscale self-organization. Nonetheless, a thorough understanding of ground state DNA charge transport (CT) in electronic configurations under biologically relevant conditions, where the fully base-paired, double-helical structure is preserved, is lacking. Here, we explore the fundamentals of CT through double-stranded DNA monolayers on gold by assessing 17 base pair bridges at discrete points with a redox active probe conjugated to a modified thymine. This assessment is performed under temperature-controlled and biologically relevant conditions with cyclic and square wave voltammetry, and redox peaks are analyzed to assess transfer rate and yield. We demonstrate that the yield of transport is strongly tied to the stability of the duplex, linearly correlating with the melting temperature. Transfer rate is found to be temperature-activated and to follow an inverse distance dependence, consistent with a hopping mechanism of transport. These results establish the governing factors of charge transfer speed and throughput in DNA molecular wires for device configurations, guiding subsequent application for nanoscale electronics.
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Affiliation(s)
- Chris H Wohlgamuth
- Department of Physics, The University of Texas at Dallas , 800 W. Campbell Rd., EC 36, Richardson, Texas 75080, United States
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33
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Liu X, Ouyang L, Cai X, Huang Y, Feng X, Fan Q, Huang W. An ultrasensitive label-free biosensor for assaying of sequence-specific DNA-binding protein based on amplifying fluorescent conjugated polymer. Biosens Bioelectron 2013; 41:218-24. [DOI: 10.1016/j.bios.2012.08.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 08/08/2012] [Accepted: 08/09/2012] [Indexed: 11/15/2022]
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34
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Wang J, Zhao WW, Zhou H, Xu JJ, Chen HY. Amplified electrochemiluminescence detection of DNA-binding protein based on the synergy effect of electron and energy transfer between CdS nanocrystals and gold nanoparticles. Biosens Bioelectron 2013; 41:615-20. [DOI: 10.1016/j.bios.2012.09.041] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 10/27/2022]
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35
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Wohlgamuth CH, McWilliams MA, Slinker JD. Temperature dependence of electrochemical DNA charge transport: influence of a mismatch. Anal Chem 2013; 85:1462-7. [PMID: 23252597 DOI: 10.1021/ac302508f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charge transfer through DNA is of interest as DNA is both the quintessential biomolecule of all living organisms and a self-organizing element in bioelectronic circuits and sensing applications. Here, we report the temperature-dependent properties of DNA charge transport in an electronically relevant arrangement of DNA monolayers on gold under biologically relevant conditions, and we track the effects of incorporating a CA single base pair mismatch. Charge transfer (CT) through double stranded, 17mer monolayers was monitored by following the yield of electrochemical reduction of a Nile blue redox probe conjugated to a modified thymine. Analysis with cyclic voltammetry and square wave voltammetry shows that DNA CT increases significantly with temperature, indicative of more DNA bridges becoming active for transport. The mismatch was found to attenuate DNA CT at lower temperatures, but the effect of the mismatch diminished as temperature was increased. Voltammograms were analyzed to extract the electron transfer rate k(0), the electron transfer coefficient α, and the redox-active surface coverage Γ*. Arrhenius behavior was observed, with activation energies of 100 meV for electron transfer through well-matched DNA. Single CA mismatches increased the activation energy by 60 meV. These results have clear implications for sensing applications and are evaluated with respect to the prominent models of DNA CT.
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Affiliation(s)
- Chris H Wohlgamuth
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
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36
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Muren NB, Olmon ED, Barton JK. Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport. Phys Chem Chem Phys 2012; 14:13754-71. [PMID: 22850865 PMCID: PMC3478128 DOI: 10.1039/c2cp41602f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics.
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Affiliation(s)
- Natalie B. Muren
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Eric D. Olmon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA
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37
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Ahangar LE, Mehrgardi MA. Nanoporous gold electrode as a platform for the construction of an electrochemical DNA hybridization biosensor. Biosens Bioelectron 2012; 38:252-7. [PMID: 22727625 DOI: 10.1016/j.bios.2012.05.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/30/2022]
Abstract
The application of a nanoporous gold electrode (NPGE) in the fabrication of an electrochemical sensing system for the detection of single base mismatches (SBMs) using ferrocene-modified DNA probe has been investigated in the present manuscript. Ferrocene carboxylic acid is covalently attached to the amino-modified probe using EDC/NHS chemistry. By covalent attachment of the redox reporter molecules on the top of DNA, the direct oxidation of the ferrocene on the electrode surface is avoided. On the other hand, the electrochemical signals are amplified by anodizing the electrode surface and converting it to nanoporous form. By improving the sensitivity of the biosensor, the different SBMs including the thermodynamically stable G-A and G-T mismatches, can be easily distinguished. In this research, NPGE was prepared by anodization and chemical reduction of Au surface and used for signal amplification. Nanoporous electrode enhances the sensitivity of DNA biosensor and makes it capable to detect complementary target DNA in sub-nanomole scales.
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Affiliation(s)
- Laleh Enayati Ahangar
- Department of Chemistry, Faculty of Science, University of Isfahan, Isfahan 81746-73441, Iran
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38
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Wang J, Zhao WW, Li XR, Xu JJ, Chen HY. Potassium-doped graphene enhanced electrochemiluminescence of SiO(2)@CdS nanocomposites for sensitive detection of TATA-binding protein. Chem Commun (Camb) 2012; 48:6429. [PMID: 22618486 DOI: 10.1039/c2cc32767h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Based on the amplified signal from SiO(2)@CdS nanocomposites integrated with K-doped graphene, a new electrochemiluminescence biosensor was developed for the successful detection of transcription factor TATA-binding protein (TBP).
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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39
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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40
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Bonham AJ, Hsieh K, Ferguson BS, Vallée-Bélisle A, Ricci F, Soh HT, Plaxco KW. Quantification of transcription factor binding in cell extracts using an electrochemical, structure-switching biosensor. J Am Chem Soc 2012; 134:3346-8. [PMID: 22313286 DOI: 10.1021/ja2115663] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transcription factor expression levels, which sensitively reflect cellular development and disease state, are typically monitored via cumbersome, reagent-intensive assays that require relatively large quantities of cells. Here, we demonstrate a simple, quantitative approach to their detection based on a simple, electrochemical sensing platform. This sensor sensitively and quantitatively detects its target transcription factor in complex media (e.g., 250 μg/mL crude nuclear extracts) in a convenient, low-reagent process requiring only 10 μL of sample. Our approach thus appears a promising means of monitoring transcription factor levels.
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Affiliation(s)
- Andrew J Bonham
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, USA
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41
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Liu X, Ouyang L, Huang Y, Feng X, Fan Q, Huang W. Highly sensitive detection of DNA-binding proteins based on a cationic conjugated polymer via a target-mediated fluorescence resonance energy transfer (TMFRET) strategy. Polym Chem 2012. [DOI: 10.1039/c2py00499b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Ahangar LE, Mehrgardi MA. 3,4-Diaminobenzoic acid (DABA) as a redox label for electrochemical detection of single base mismatches. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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43
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Kurakin A. The self-organizing fractal theory as a universal discovery method: the phenomenon of life. Theor Biol Med Model 2011; 8:4. [PMID: 21447162 PMCID: PMC3080324 DOI: 10.1186/1742-4682-8-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 03/29/2011] [Indexed: 12/15/2022] Open
Abstract
A universal discovery method potentially applicable to all disciplines studying organizational phenomena has been developed. This method takes advantage of a new form of global symmetry, namely, scale-invariance of self-organizational dynamics of energy/matter at all levels of organizational hierarchy, from elementary particles through cells and organisms to the Universe as a whole. The method is based on an alternative conceptualization of physical reality postulating that the energy/matter comprising the Universe is far from equilibrium, that it exists as a flow, and that it develops via self-organization in accordance with the empirical laws of nonequilibrium thermodynamics. It is postulated that the energy/matter flowing through and comprising the Universe evolves as a multiscale, self-similar structure-process, i.e., as a self-organizing fractal. This means that certain organizational structures and processes are scale-invariant and are reproduced at all levels of the organizational hierarchy. Being a form of symmetry, scale-invariance naturally lends itself to a new discovery method that allows for the deduction of missing information by comparing scale-invariant organizational patterns across different levels of the organizational hierarchy.An application of the new discovery method to life sciences reveals that moving electrons represent a keystone physical force (flux) that powers, animates, informs, and binds all living structures-processes into a planetary-wide, multiscale system of electron flow/circulation, and that all living organisms and their larger-scale organizations emerge to function as electron transport networks that are supported by and, at the same time, support the flow of electrons down the Earth's redox gradient maintained along the core-mantle-crust-ocean-atmosphere axis of the planet. The presented findings lead to a radically new perspective on the nature and origin of life, suggesting that living matter is an organizational state/phase of nonliving matter and a natural consequence of the evolution and self-organization of nonliving matter.The presented paradigm opens doors for explosive advances in many disciplines, by uniting them within a single conceptual framework and providing a discovery method that allows for the systematic generation of knowledge through comparison and complementation of empirical data across different sciences and disciplines.
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Affiliation(s)
- Alexei Kurakin
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA.
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44
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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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45
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Slinker JD, Muren NB, Renfrew SE, Barton JK. DNA charge transport over 34 nm. Nat Chem 2011; 3:228-33. [PMID: 21336329 DOI: 10.1038/nchem.982] [Citation(s) in RCA: 270] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 12/17/2010] [Indexed: 12/12/2022]
Abstract
Molecular wires show promise in nanoscale electronics, but the synthesis of uniform, long conductive molecules is a significant challenge. Deoxyribonucleic acid (DNA) of precise length, by contrast, is synthesized easily, but its conductivity over the distances required for nanoscale devices has not been explored. Here we demonstrate DNA charge transport (CT) over 34 nm in 100-mer monolayers on gold. Multiplexed gold electrodes modified with 100-mer DNA yield sizable electrochemical signals from a distal, covalent Nile Blue redox probe. Significant signal attenuation upon incorporation of a single base-pair mismatch demonstrates that CT is DNA-mediated. Efficient cleavage of these 100-mers by a restriction enzyme indicates that the DNA adopts a native conformation accessible to protein binding. Similar electron-transfer rates measured through 100-mer and 17-mer monolayers are consistent with rate-limiting electron tunnelling through the saturated carbon linker. This DNA-mediated CT distance of 34 nm surpasses that of most reports of molecular wires.
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Affiliation(s)
- Jason D Slinker
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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46
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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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47
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Yin BC, Wu D, Ye BC. Sensitive DNA-Based Electrochemical Strategy for Trace Bleomycin Detection. Anal Chem 2010; 82:8272-7. [DOI: 10.1021/ac101761q] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin-Cheng Yin
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Di Wu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
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48
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Electrochemical probe for the monitoring of DNA–protein interactions. Biosens Bioelectron 2010; 25:2598-602. [DOI: 10.1016/j.bios.2010.04.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/02/2010] [Accepted: 04/18/2010] [Indexed: 11/22/2022]
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49
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Kucherak OA, Oncul S, Darwich Z, Yushchenko DA, Arntz Y, Didier P, Mély Y, Klymchenko AS. Switchable nile red-based probe for cholesterol and lipid order at the outer leaflet of biomembranes. J Am Chem Soc 2010; 132:4907-16. [PMID: 20225874 DOI: 10.1021/ja100351w] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cholesterol and sphingomyelin form together a highly ordered membrane phase, which is believed to play important biological functions in plasma membranes of mammalian cells. Since sphingomyelin is present mainly at the outer leaflet of cell membranes, monitoring its lipid order requires molecular probes capable to bind specifically at this leaflet and exhibit negligibly slow flip-flop. In the present work, such a probe was developed by modifying the solvatochromic fluorescent dye Nile Red with an amphiphilic anchor group. To evaluate the flip-flop of the obtained probe (NR12S), we developed a methodology of reversible redox switching of its fluorescence at one leaflet using sodium dithionite. This method shows that NR12S, in contrast to parent Nile Red, binds exclusively the outer membrane leaflet of model lipid vesicles and living cells with negligible flip-flop in the time scale of hours. Moreover, the emission maximum of NR12S in model vesicles exhibits a significant blue shift in liquid ordered phase (sphingomyelin-cholesterol) as compared to liquid disordered phase (unsaturated phospholipids). As a consequence, these two phases could be clearly distinguished in NR12S-stained giant vesicles by fluorescence microscopy imaging of intensity ratio between the blue and red parts of the probe emission spectrum. Being added to living cells, NR12S binds predominantly, if not exclusively, their plasma membranes and shows an emission spectrum intermediate between those in liquid ordered and disordered phases of model membranes. Importantly, the emission color of NR12S correlates well with the cholesterol content in cell membranes, which allows monitoring the cholesterol depletion process with methyl-beta-cyclodextrin by fluorescence spectroscopy and microscopy. The attractive photophysical and switching properties of NR12S, together with its selective outer leaflet staining and sensitivity to cholesterol and lipid order, make it a new powerful tool for studying model and cell membranes.
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Affiliation(s)
- Oleksandr A Kucherak
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401 Illkirch Cedex, France
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50
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Ou LJ, Jin PY, Chu X, Jiang JH, Yu RQ. Sensitive and Visual Detection of Sequence-Specific DNA-Binding Protein via a Gold Nanoparticle-Based Colorimetric Biosensor. Anal Chem 2010; 82:6015-24. [DOI: 10.1021/ac100907g] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Li-Juan Ou
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Pei-Yan Jin
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
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