1
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Hu Z, Ye W, Zhang Z, Xie T, Yuan W, Wu T. Sensitive detection of abasic sites in double-stranded DNA based on the selective reaction of enzymes. Anal Chim Acta 2022; 1223:340220. [DOI: 10.1016/j.aca.2022.340220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/28/2022]
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2
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Nano A, Furst AL, Hill MG, Barton JK. DNA Electrochemistry: Charge-Transport Pathways through DNA Films on Gold. J Am Chem Soc 2021; 143:11631-11640. [PMID: 34309382 PMCID: PMC9285625 DOI: 10.1021/jacs.1c04713] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
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Over the past 25
years, collective evidence has demonstrated that
the DNA base-pair stack serves as a medium for charge transport chemistry
in solution and on DNA-modified gold surfaces. Since this charge transport
depends sensitively upon the integrity of the DNA base pair stack,
perturbations in base stacking, as may occur with DNA base mismatches,
lesions, and protein binding, interrupt DNA charge transport (DNA
CT). This sensitivity has led to the development of powerful DNA electrochemical
sensors. Given the utility of DNA electrochemistry for sensing and
in response to recent literature, we describe critical protocols and
characterizations necessary for performing DNA-mediated electrochemistry.
We demonstrate DNA electrochemistry with a fully AT DNA sequence using
a thiolated preformed DNA duplex and distinguish this DNA-mediated
chemistry from that of electrochemistry of largely single-stranded
DNA adsorbed to the surface. We also demonstrate the dependence of
DNA CT on a fully stacked duplex. An increase in the percentage of
mismatches within the DNA monolayer leads to a linear decrease in
current flow for a DNA-bound intercalator, where the reaction is DNA-mediated;
in contrast, for ruthenium hexammine, which binds electrostatically
to DNA and the redox chemistry is not DNA-mediated, there is no effect
on current flow with mismatches. We find that, with DNA as a well
hybridized duplex, upon assembly, a DNA-mediated pathway facilitates
the electron transfer between a well coupled redox probe and the gold
surface. Overall, this report highlights critical points to be emphasized
when utilizing DNA electrochemistry and offers explanations and controls
for analyzing confounding results.
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Affiliation(s)
- Adela Nano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael G Hill
- Department of Chemistry, Occidental College, Los Angeles, California 90041, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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3
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Hong SW, Lee SY, Hwang GT. Fluorene‐Labeled 2'‐Deoxyuridine as an Environmentally Sensitive Probe for Detection of an Abasic Site. ChemistrySelect 2020. [DOI: 10.1002/slct.202003432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Seung Woo Hong
- Department of Chemistry and Green-Nano Materials Research Center Kyungpook National University Daegu 41566 Republic of Korea
| | - So Young Lee
- Department of Chemistry and Green-Nano Materials Research Center Kyungpook National University Daegu 41566 Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center Kyungpook National University Daegu 41566 Republic of Korea
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4
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Reprint of "Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces". J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Dauphin-Ducharme P, Arroyo-Currás N, Plaxco KW. High-Precision Electrochemical Measurements of the Guanine-, Mismatch-, and Length-Dependence of Electron Transfer from Electrode-Bound DNA Are Consistent with a Contact-Mediated Mechanism. J Am Chem Soc 2019; 141:1304-1311. [PMID: 30605323 DOI: 10.1021/jacs.8b11341] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Despite 25 years' effort, serious questions remain regarding the mechanism(s) underlying electron transfer through (or from) electrode-bound double-stranded DNA. In part this is because a control experiment regarding the putatively critical role of guanine bases in the most widely proposed transport mechanism (hopping from guanine to guanine through the π-stack) appears to be lacking from the prior literature. In response, we have employed chronoamperometry, which allows for high-precision determination of electron transfer rates, to characterize transfer to a redox reporter appended onto electrode-bound DNA duplexes. Specifically, we have measured the effects of guanines and base mismatches on the electron transfer rate associated with such constructs. Upon doing so, we find that, counter to prior reports, the transfer rate is, to within relatively tight experimental confidence intervals, unaffected by either. Parallel studies of the dependence of the electron transfer rate on the length of the DNA suggest that transfer from this system obeys a "collision" mechanism in which the redox reporter physically contacts the electrode surface prior to the exchange of electrons.
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Affiliation(s)
- Philippe Dauphin-Ducharme
- Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States
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7
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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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8
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Corbella M, Voityuk AA, Curutchet C. How abasic sites impact hole transfer dynamics in GC-rich DNA sequences. Phys Chem Chem Phys 2018; 20:23123-23131. [DOI: 10.1039/c8cp03572e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hole transfer dynamics through GC-rich DNA duplexes containing abasic sites is strongly modulated by the nature of the unpaired nucleobase.
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Affiliation(s)
- Marina Corbella
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC-UB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Alexander A. Voityuk
- Institució Catalana de Recerca i Estudis Avançats (ICREA)
- 08010 Barcelona
- Spain
- Institut de Química Computacional i Catàlisi and Departament de Química
- Universitat de Girona
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC-UB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
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9
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Varmira K, Saed-Mocheshi M, Jalalvand AR. Electrochemical sensing and bio-sensing of bisphenol A and detection of its damage to DNA: A comprehensive review. SENSING AND BIO-SENSING RESEARCH 2017. [DOI: 10.1016/j.sbsr.2017.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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10
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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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11
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Wong JR, Shao F. Hole Transport in A-form DNA/RNA Hybrid Duplexes. Sci Rep 2017; 7:40293. [PMID: 28084308 PMCID: PMC5233965 DOI: 10.1038/srep40293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/01/2016] [Indexed: 01/28/2023] Open
Abstract
DNA/RNA hybrid duplexes are prevalent in many cellular functions and are an attractive target form for electrochemical biosensing and electric nanodevice. However the electronic conductivities of DNA/RNA hybrid duplex remain relatively unexplored and limited further technological applications. Here cyclopropyl-modified deoxyribose- and ribose-adenosines were developed to explore hole transport (HT) in both DNA duplex and DNA/RNA hybrids by probing the transient hole occupancies on adenine tracts. HT yields through both B-form and A-form double helixes displayed similar shallow distance dependence, although the HT yields of DNA/RNA hybrid duplexes were lower than those of DNA duplexes. The lack of oscillatory periods and direction dependence in HT through both helixes implied efficient hole propagation can be achieved via the hole delocalization and coherent HT over adenine tracts, regardless of the structural variations.
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Affiliation(s)
- Jiun Ru Wong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)
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12
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Fojta M, Daňhel A, Havran L, Vyskočil V. Recent progress in electrochemical sensors and assays for DNA damage and repair. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.11.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Condie AG, Yan Y, Gerson SL, Wang Y. A Fluorescent Probe to Measure DNA Damage and Repair. PLoS One 2015; 10:e0131330. [PMID: 26309022 PMCID: PMC4550365 DOI: 10.1371/journal.pone.0131330] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/31/2015] [Indexed: 12/15/2022] Open
Abstract
DNA damage and repair is a fundamental process that plays an important role in cancer treatment. Base excision repair (BER) is a major repair pathway that often leads to drug resistance in DNA-targeted cancer chemotherapy. In order to measure BER, we have developed a near infrared (NIR) fluorescent probe. This probe binds to a key intermediate, termed apurinic/apyrimidinic (AP) site, in the BER pathway where DNA damage and repair occurs. We have developed an assay to show the efficacy of the probe binding to AP sites and have shown that it can distinguish AP sites in DNA extract from chemotherapy treated cells. This probe has potential application in monitoring patient response to chemotherapy and evaluating new drugs in development.
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Affiliation(s)
- Allison G Condie
- Department of Radiology, Chemistry, and Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Yan Yan
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, United States of America
| | - Stanton L Gerson
- Department of Hematology and Oncology, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States of America
| | - Yanming Wang
- Department of Radiology, Chemistry, and Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, United States of America
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14
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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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15
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Hansen AG, Salvatore P, Karlsen KK, Nichols RJ, Wengel J, Ulstrup J. Electrochemistry and in situ scanning tunnelling microscopy of pure and redox-marked DNA- and UNA-based oligonucleotides on Au(111)-electrode surfaces. Phys Chem Chem Phys 2013; 15:776-86. [PMID: 23073185 DOI: 10.1039/c2cp42351k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied adsorption and electrochemical electron transfer of several 13- and 15-base DNA and UNA (unlocked nucleic acids) oligonucleotides (ONs) linked to Au(111)-electrode surfaces via a 5'-C6-SH group using cyclic voltammetry (CV) and scanning tunnelling microscopy in aqueous buffer under electrochemical potential control (in situ STM). 2,2',6',2''-Terpyridine (terpy) onto which the transition metal ions Fe(2+/3+), Os(2+/3+) and Ru(2+/3+) could be coordinated after UNA monolayer formation was attached to UNA via a flexible linker. The metal centres offer CV probes and in situ STM contrast markers, and the flexible UNA/linker a potential binder for intercalation. CV of pure and mercaptohexanol diluted ON monolayers displayed reductive desorption signals but also, presumably capacitive, signals at higher potentials. Distinct voltammetric signals arise on metal binding. Those from Ru-binding are by far the strongest and in accord with multiple site Ru-attachment. In situ STM disclosed molecular scale features in varying coverage on addition of the metal ions. The Ru-derivatives showed a bias voltage dependent broad maximum in the tunnelling current-overpotential correlation which could be correlated with theoretical frames for condensed matter conductivity of redox molecules. Together the data suggest that Ru-units are bound to both terpy and the UNA-DNA backbone.
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Affiliation(s)
- Allan G Hansen
- Department of Chemistry, Building 207, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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16
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Wu F, Sun Y, Shao Y, Xu S, Liu G, Peng J, Liu L. DNA abasic site-selective enhancement of sanguinarine fluorescence with a large emission shift. PLoS One 2012. [PMID: 23185252 PMCID: PMC3502418 DOI: 10.1371/journal.pone.0048251] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Small molecules that can specifically bind to a DNA abasic site (AP site) have received much attention due to their importance in DNA lesion identification, drug discovery, and sensor design. Herein, the AP site binding behavior of sanguinarine (SG), a natural alkaloid, was investigated. In aqueous solution, SG has a short-wavelength alkanolamine emission band and a long-wavelength iminium emission band. At pH 8.3, SG experiences a fluorescence quenching for both bands upon binding to fully matched DNAs without the AP site, while the presence of the AP site induces a strong SG binding and the observed fluorescence enhancement for the iminium band are highly dependent on the nucleobases flanking the AP site, while the alkanolamine band is always quenched. The bases opposite the AP site also exert some modifications on the SG's emission behavior. It was found that the observed quenching for DNAs with Gs and Cs flanking the AP site is most likely caused by electron transfer between the AP site-bound excited-state SG and the nearby Gs. However, the flanking As and Ts that are not easily oxidized favor the enhanced emission. This AP site-selective enhancement of SG fluorescence accompanies a band conversion in the dominate emission from the alkanolamine to iminium band thus with a large emission shift of about 170 nm. Absorption spectra, steady-state and transient-state fluorescence, DNA melting, and electrolyte experiments confirm that the AP site binding of SG occurs and the stacking interaction with the nearby base pairs is likely to prevent the converted SG iminium form from contacting with water that is thus emissive when the AP site neighbors are bases other than guanines. We expect that this fluorophore would be developed as a promising AP site binder having a large emission shift.
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Affiliation(s)
- Fei Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Yanwei Sun
- Chuyang Honors College, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
- * E-mail:
| | - Shujuan Xu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Guiying Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Jian Peng
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Lingling Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
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17
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Salvatore P, Karlsen KK, Hansen AG, Zhang J, Nichols RJ, Ulstrup J. Polycation induced potential dependent structural transitions of oligonucleotide monolayers on Au(111)-surfaces. J Am Chem Soc 2012; 134:19092-8. [PMID: 23098321 DOI: 10.1021/ja306877s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have studied self-assembled molecular monolayers (SAMs) of several 3'-C3-SH conjugated single-strand (ss) and double-strand (ds) 20-base oligonucleotides (ONs) immobilized on single-crystal, atomically planar Au(111)-electrode surfaces in the presence of the triply positively charged base spermidine (Spd). This cation binds strongly to the polyanionic ON backbone and stabilizes the ds-form relative to the ss-form. A combination of chemical ON synthesis, melting temperature measurements, cyclic voltammetry (CV), and in situ scanning tunneling microscopy (STM) in aqueous biological buffer under electrochemical potential control was used. Spd binding was found to increase notably the ds-ON melting temperature. CV displays capacitive features associated with ss- and ds-ON. A robust capacitive peak around -0.35 V versus saturated calomel electrode (SCE), specific to ds-ON and highly sensitive to base pair mismatches, was consistently observed. The peak is likely to be caused by surface structural reorganization around the peak potential and located close to reported peak potentials of several DNA intercalating or covalently tethered redox molecules reported as probes for long-range electron transfer.
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Affiliation(s)
- Princia Salvatore
- Department of Chemistry, Building 207, and Nano•DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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18
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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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19
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Electrochemical detection of DNA hybridization using metallacarborane unit. Bioelectrochemistry 2012; 87:78-83. [DOI: 10.1016/j.bioelechem.2011.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 08/26/2011] [Accepted: 10/28/2011] [Indexed: 11/17/2022]
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20
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Lee SH, Wang S, Kool ET. Templated chemistry for monitoring damage and repair directly in duplex DNA. Chem Commun (Camb) 2012; 48:8069-71. [PMID: 22782065 DOI: 10.1039/c2cc34060g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report the fluorogenic detection of the product of base excision repair (an abasic site) in a specific sequence of duplex DNA. This is achieved by DNA-templated chemistry, employing triple helix-forming probes that contain unnatural nucleobases designed to selectively recognize the site of a missing base. Light-up signals of up to 36-fold were documented, and probes could be used to monitor enzymatic removal of a damaged base.
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Affiliation(s)
- Seoung Ho Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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21
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Hvastkovs EG, Schenkman JB, Rusling JF. Metabolic toxicity screening using electrochemiluminescence arrays coupled with enzyme-DNA biocolloid reactors and liquid chromatography-mass spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2012; 5:79-105. [PMID: 22482786 PMCID: PMC3399491 DOI: 10.1146/annurev.anchem.111808.073659] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
New chemicals or drugs must be guaranteed safe before they can be marketed. Despite widespread use of bioassay panels for toxicity prediction, products that are toxic to a subset of the population often are not identified until clinical trials. This article reviews new array methodologies based on enzyme/DNA films that form and identify DNA-reactive metabolites that are indicators of potentially genotoxic species. This molecularly based methodology is designed in a rapid screening array that utilizes electrochemiluminescence (ECL) to detect metabolite-DNA reactions, as well as biocolloid reactors that provide the DNA adducts and metabolites for liquid chromatography-mass spectrometry (LC-MS) analysis. ECL arrays provide rapid toxicity screening, and the biocolloid reactor LC-MS approach provides a valuable follow-up on structure, identification, and formation rates of DNA adducts for toxicity hits from the ECL array screening. Specific examples using this strategy are discussed. Integration of high-throughput versions of these toxicity-screening methods with existing drug toxicity bioassays should allow for better human toxicity prediction as well as more informed decision making regarding new chemical and drug candidates.
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Affiliation(s)
- Eli G. Hvastkovs
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858;
| | - John B. Schenkman
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 06269;
| | - James F. Rusling
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 06269;
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269;
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22
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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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23
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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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24
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Mehrgardi MA, Ahangar LE. Silver nanoparticles as redox reporters for the amplified electrochemical detection of the single base mismatches. Biosens Bioelectron 2011; 26:4308-13. [DOI: 10.1016/j.bios.2011.04.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/09/2011] [Accepted: 04/11/2011] [Indexed: 10/18/2022]
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25
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Romano CA, Sontz PA, Barton JK. Mutants of the base excision repair glycosylase, endonuclease III: DNA charge transport as a first step in lesion detection. Biochemistry 2011; 50:6133-45. [PMID: 21651304 DOI: 10.1021/bi2003179] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Endonuclease III (EndoIII) is a base excision repair glycosylase that targets damaged pyrimidines and contains a [4Fe-4S] cluster. We have proposed a model where BER proteins that contain redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in the detection of DNA lesions. Here, several mutants of EndoIII were prepared to probe their efficiency of DNA/protein charge transport. Cyclic voltammetry experiments on DNA-modified electrodes show that aromatic residues F30, Y55, Y75, and Y82 help mediate charge transport between DNA and the [4Fe-4S] cluster. On the basis of circular dichroism studies to measure protein stability, mutations at residues W178 and Y185 are found to destabilize the protein; these residues may function to protect the [4Fe-4S] cluster. Atomic force microscopy studies furthermore reveal a correlation in the ability of mutants to carry out protein/DNA CT and their ability to relocalize onto DNA strands containing a single base mismatch; EndoIII mutants that are defective in carrying out DNA/protein CT do not redistribute onto mismatch-containing strands, consistent with our model. These results demonstrate a link between the ability of the repair protein to carry out DNA CT and its ability to relocalize near lesions, thus pointing to DNA CT as a key first step in the detection of base damage in the genome.
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Affiliation(s)
- Christine A Romano
- Division of Chemistry and Chemical Engineering, California Institute of Technolog, Pasadena, California 91125, USA
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Nasirizadeh N, Zare HR, Pournaghi-Azar MH, Hejazi MS. Introduction of hematoxylin as an electroactive label for DNA biosensors and its employment in detection of target DNA sequence and single-base mismatch in human papilloma virus corresponding to oligonucleotide. Biosens Bioelectron 2010; 26:2638-44. [PMID: 21146975 DOI: 10.1016/j.bios.2010.11.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Accepted: 11/17/2010] [Indexed: 01/21/2023]
Abstract
For the detection of DNA hybridization, a new electrochemical biosensor was developed on the basis of the interaction of hematoxylin with 20-mer deoxyoligonucleotides (from human papilloma virus, HPV). The study was performed based on the interaction of hematoxylin with an alkanethiol DNA probe self-assembled gold electrode (ss-DNA/AuE) and its hybridization form (ds-DNA/AuE). The optimum conditions were found for the immobilization of HPV probe on the gold electrode (AuE) surface and its hybridization with the target DNA. Electrochemical detection of the self-assembled DNA and the hybridization process were performed by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) over the potential range where the accumulated hematoxylin at the modified electrode was electroactive. Observing a remarkable difference between the voltammetric signals of the hematoxylin obtained from different hybridization samples (non-complementary, mismatch and complementary DNAs), we confirmed the potential of the developed biosensor in detecting and discriminating the target complementary DNA from non-complementary and mismatch oligonucleotides. Under optimum conditions, the electrochemical signal had a linear relationship with the concentration of the target DNA ranging from 12.5 nM to 350.0 nM, and the detection limit was 3.8 nM.
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Affiliation(s)
- Navid Nasirizadeh
- Department of Chemistry, Yazd University, P.O. Box 89195-741, Yazd, Iran
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Jakobsen U, Shelke SA, Vogel S, Sigurdsson ST. Site-directed spin-labeling of nucleic acids by click chemistry: detection of abasic sites in duplex DNA by EPR spectroscopy. J Am Chem Soc 2010; 132:10424-8. [PMID: 20617829 DOI: 10.1021/ja102797k] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This paper describes a spin label that can detect and identify local structural deformations in duplex DNA, in particular abasic sites. The spin label was incorporated into DNA by a new postsynthetic approach using click-chemistry on a solid support, which simplified both the synthesis and purification of the spin-labeled oligonucleotides. A nitroxide-functionalized azide, prepared by a short synthetic route, was reacted with an oligomer containing 5-ethynyl-2'-dU. The conjugation proceeded in quantitative yield and resulted in a fairly rigid linker between the modified nucleotide and the nitroxide spin label. The spin label was used to detect, for the first time, abasic sites in duplex DNA by X-band CW-EPR spectroscopy and give information about other structural deformations as well as local conformational changes in DNA. For example, reduced mobility of the spin label in a mismatched pair with T was consistent with the spin label displacing the T from the duplex. Addition of mercury(II) to this mispair resulted in a substantial increase in the motion of the spin label, consistent with formation of a metallopair between the T and the spin-labeled base that results in movement of the spin label out of the duplex and toward the solution. Thus, reposition of the spin label, when acting as a mercury(II)-controlled mechanical lever, can be readily detected by EPR spectroscopy. The ease of incorporation and properties of the new spin label make it attractive for EPR studies of nucleic acids and other macromolecules.
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Affiliation(s)
- Ulla Jakobsen
- Department of Physics and Chemistry, University of Southern Denmark, Nucleic Acid Center Campusvej 55, 5230 Odense, Denmark
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Slinker JD, Muren NB, Gorodetsky AA, Barton JK. Multiplexed DNA-modified electrodes. J Am Chem Soc 2010; 132:2769-74. [PMID: 20131780 DOI: 10.1021/ja909915m] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 microm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format.
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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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Affiliation(s)
- Joseph C. Genereux
- 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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Hvastkovs EG, Buttry DA. Recent advances in electrochemical DNA hybridization sensors. Analyst 2010; 135:1817-29. [DOI: 10.1039/c0an00113a] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dahlmann HA, Vaidyanathan VG, Sturla SJ. Investigating the biochemical impact of DNA damage with structure-based probes: abasic sites, photodimers, alkylation adducts, and oxidative lesions. Biochemistry 2009; 48:9347-59. [PMID: 19757831 PMCID: PMC2789562 DOI: 10.1021/bi901059k] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA sustains a wide variety of damage, such as the formation of abasic sites, pyrimidine dimers, alkylation adducts, or oxidative lesions, upon exposure to UV radiation, alkylating agents, or oxidative conditions. Since these forms of damage may be acutely toxic or mutagenic and potentially carcinogenic, it is of interest to gain insight into how their structures impact biochemical processing of DNA, such as synthesis, transcription, and repair. Lesion-specific molecular probes have been used to study polymerase-mediated translesion DNA synthesis of abasic sites and TT dimers, while other probes have been developed for specifically investigating the alkylation adduct O(6)-Bn-G and the oxidative lesion 8-oxo-G. In this review, recent examples of lesion-specific molecular probes are surveyed; their specificities of incorporation opposite target lesions compared to unmodified nucleotides are discussed, and limitations of their applications under physiologically relevant conditions are assessed.
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Affiliation(s)
| | | | - Shana J. Sturla
- To whom correspondence should be addressed: ; Phone: 612-626-0496; Fax: 612-624-0139
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Chapter 6 Application of New Methods for Detection of DNA Damage and Repair. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 277:217-51. [DOI: 10.1016/s1937-6448(09)77006-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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