9780444521507

Electrochemistry of Nucleic Acids and Proteins

by ; ;
  • ISBN13:

    9780444521507

  • ISBN10:

    044452150X

  • Format: Hardcover
  • Copyright: 2006-01-20
  • Publisher: Elsevier Science
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Summary

"This book is concerned with the electron transfer between electrodes on one hand and DNA, RNA and proteins on the other hand and with the use of electrochemistry and electrochemical sensors in DNA and protein analyses. Electrochemical bioassays involve newly emerging fields of genomic, proteomics, biomedicine and biotechnology. DNA and protein chips with electrochemical detection represent new tools of science, medicine and other areas of practical life in this century."--BOOK JACKET.

Table of Contents

Contributors xi
Preface xv
Chapter 1 Polarography of DNA. Retrospective View
Emil Palecek
1. Introduction
1(4)
1.1. Early studies
3(2)
2. Retrospective view
5(3)
2.1. Conditions for polarographic analysis of native and denatured DNAs
6(1)
2.2. Different polarographic methods and mercury electrodes
7(1)
2.3. DNA surface denaturation
7(1)
3. Oscillographic polarography at controlled A.C.
8(1)
4. Electrogenerated products
9(1)
5. Nürnberg's cyclic voltammetry with HMDE
10(1)
6. Summary and conclusion
11(1)
List of abbreviations
12(1)
Acknowledgments
12(1)
References
12(6)
Chapter 2 Electrochemical Properties of Nucleic Acid Components
Vladimir Vetterl and Stanislav Hason
1. Introduction
18(1)
2. Adsorption and two-dimensional condensation
18(33)
2.1. Mercury electrodes
18(5)
2.2. Mercury film electrodes based on the graphite substrates
23(10)
2.2.1. Optical roughness and surface morphology of the mercury-modified graphite surfaces
23(3)
2.2.2. Phase transitions in adsorbed nucleic acid nucleoside layers at Hg- modified graphite electrodes: perimental aspects
26(2)
2.2.3. Adsorption and kinetics of phase transitions of adenosine at the mercury-modified graphite surfaces
28(3)
2.2.4. Adsorption and kinetics of phase transitions of cytidine at the mercury- modified graphite surfaces
31(2)
2.3. Solid amalgam-alloy electrodes
33(3)
2.3.1. Optical roughness and surface morphology of the solid amalgam-alloy surfaces
34(1)
2.3.2. Adsorption of adenosine at the different solid amalgam-alloy electrodes
34(2)
2.4. Solid metal electrodes
36(10)
2.4.1. Gold electrodes
36(5)
2.4.2. Silver electrodes
41(3)
2.4.3. Copper electrodes
44(1)
2.4.4. Bismuth electrodes
45(1)
2.5. Semiconductor electrodes
46(2)
2.5.1. Single-crystal n-CdSe
46(1)
2.5.2. Silicon
46(1)
2.5.3. Gallium arsenide
47(1)
2.6. Minerals, soils and resins
48(1)
2.7. Adsorption of base and/or nucleosides mixtures
49(2)
2.7.1. Adsorption at Hg electrode
49(1)
2.7.2. Adsorption at Au(1 1 1)
50(1)
2.8. Adsorption of bases at Hg from non-aqueous solvents
51(1)
3. Electroreduction and electrooxidation of nucleic acid components
51(6)
3.1. Electroreduction at mercury electrode
51(2)
3.1.1. Determination of picogram quantities of DNA by stripping transfer voltammetry
53(1)
3.2. Electrooxidation at carbon electrodes
53(3)
3.3. Electrooxidation at diamond electrode
56(1)
3.4. Effect of uracil adsorption on the oxygen reduction at platinum electrode
56(1)
3.5. Sparingly soluble compounds at the mercury electrode
57(1)
4. Concluding remarks
57(1)
List of abbreviations
58(2)
Acknowledgments
60(1)
References
60(14)
Chapter 3 Electrochemistry of Nucleic Acids
Emil Palecek and Frantisek Jelen
1. Introduction
74(3)
2. Electrochemical methods and electrodes
77(3)
2.1. Methods
77(1)
2.1.1. Elimination voltammetry with linear scan (EVLS)
77(1)
2.2. Electrodes
78(8)
2.2.1. Solid amalgam electrodes
79(1)
3. Adsorption of nucleic acids
80(6)
4. Reduction and oxidation of nucleic acids at electrodes
86(18)
4.1. Oxidation
87(3)
4.1.1. Solid electrodes
87(2)
4.1.2. Mercury electrodes
89(1)
4.2. Reduction
90(14)
4.2.1. Reduction of ss nucleic acids
91(13)
5. Changes in DNA conformation at surfaces
104(17)
5.1. History
104(1)
5.2. Effects of electrochemical methods and types of mercury electrodes
104(2)
5.2.1. Methods working with large voltage excursions during the DME drop lifetime or with stationary electrodes
105(1)
5.3. Changes in DNA conformation at mercury surfaces as detected by conventional polarographic and voltammetric methods
106(8)
5.3.1. Conditions not involving ionization of DNA bases
107(5)
5.3.2. Conditions involving ionization of bases
112(2)
5.4. Carbon electrodes
114(1)
5.5. Changes in DNA structure at DNA-modified electrodes
114(6)
5.5.1. Mercury electrodes
115(2)
5.5.2. DNA-modified platinum and gold electrodes
117(3)
5.5.3. Other methods and surfaces
120(1)
5.6. Concluding remarks
120(1)
6. Electrochemical principles in NA biosensors
121(28)
6.1. DNA hybridization and detection at the same surface
122(6)
6.1.1. Immobilization of DNA at electrode surfaces
123(1)
6.1.2. Blocking and interfacing the electrode (transducer) surface
124(4)
6.2. DNA hybridization and detection at two different surfaces
128(4)
6.2.1. Length determination of long repetitive sequences
131(1)
6.3. Electroactive markers covalently bound to DNA
132(5)
6.3.1. Osmium labels
134(2)
6.3.2. Ferrocene and other labels
136(1)
6.4. Electrocatalytic oxidation of DNA
137(4)
6.5. DNA conductivity in DNA sensors
141(4)
6.5.1. DNA conductivity
141(1)
6.5.2. Charge transfer in DNA sensors
142(3)
6.6. Changes in DNA structure signaling DNA hybridization
145(4)
7. Electrochemical DNA biosensors: Future prospects
149(1)
8. Summary and conclusion
150(2)
List of abbreviations
152(1)
Acknowledgments
153(1)
References
153(22)
Chapter 4 Electrochemical Nucleic Acid Biosensors
Joseph Wang
1. Introduction
175(2)
2. Electrochemical biosensing of DNA hybridization
177(12)
2.1. Surface immobilization
177(2)
2.2. The hybridization event
179(1)
2.3. Electrochemical transduction of DNA hybridization
180(76)
2.3.1. Indicator-based detection
181(2)
2.3.2. Use of enzyme labels for detecting DNA hybridization
183(1)
2.3.3. Use of nanoparticle tracers
184(1)
2.3.4. Label-free electrochemical biosensing of DNA hybridization
185(3)
2.3.5. Other attractive routes and amplification schemes
188(1)
3. Conclusions and outlook
189(1)
Acknowledgment
190(1)
References
190(5)
Chapter 5 Amplified Electrochemical and Photoelectrochemical Analysis of DNA
Eugenii Katz, Bilha Willner and Itamar Willner
1. Introduction
195(7)
2. Enzyme-amplified electrochemical analysis of DNA
202(9)
3. Amplified electrochemical detection of DNA using nucleic acid- functionalized metallic or semiconductor nanoparticles
211(8)
4. Nano- and micro-objects as carriers for the amplified electrochemical detection of DNA
219(8)
5. Analysis of DNA by direct conductivity measurements
227(3)
6. Amplified sensing of DNA in the presence of magnetic particles
230(3)
7. Photoelectrochemical detection of DNA
233(6)
8. Conclusions and perspectives
239(2)
Acknowledgments
241(1)
References
241(6)
Chapter 6 Fully Electrical Microarrays
R. Hintsche, B. Elsholz, G. Piechotta, R. Woerl, C.G.J. Schabmueller, J. Albers, V. Dharuman, E. Nebling, A. Hanisch, L. Blohm, F. Hofmann, B. Holzapfl, A. Frey, C. Paulus, M. Schienle and R. Thewes
1. Introduction
247(1)
2. Principle and instrumentation of electrical detection
248(3)
3. Low-density electrical DNA arrays
251(5)
4. Integrated CMOS DNA arrays
256(5)
4.1. Extended CMOS processing
257(3)
4.2. Circuit design issues and system integration
260(1)
5. Electrical label-free detection of DNA arrays
261(3)
6. Electrical protein microarrays
264(3)
7. Electrical hapten microarrays
267(4)
List of abbreviations
271(1)
References
272(8)
Chapter 7 Carbon Electrodes in DNA Hybridisation Research
G. Marrazza, F. Lucarelli and M. Mascini
1. DNA probe immobilisation
280(3)
1.1. Adsorption at fixed potential
280(1)
1.2. Avidin—biotin system
280(1)
1.3. Covalent immobilisation by carbodiimide
281(2)
2. Hybridisation reaction
283(1)
3. Labelling and electrochemical detection
284(9)
3.1. Electroactive intercalative compounds/groove binders
284(3)
3.2. Indicator-free approach
287(2)
3.3. Enzyme labels for hybridisation detection
289(3)
3.4. Biomagnetic assays
292(1)
4. Conclusions
293(1)
List of abbreviations
293(1)
References
294(3)
Chapter 8 Conducting Polymers for DNA Sensors and DNA Chips: from Fabrication to Molecular Detection
Pascal Mailley, André Roget and Thierry Livache
1. Introduction
297(1)
2. ECP-based genosensors: Design and fabrication
298(12)
2.1. How to interface ECPs and DNA
298(6)
2.1.1. The polyelectrolyte approach
298(3)
2.1.2. DNA immobilisation through chemical or biochemical complexation
301(1)
2.1.3. Covalent coupling of DNA and ECPs
301(3)
2.2. How to process ECPs for DNA array fabrication
304(6)
2.2.1. ECP modification of microelectrode arrays
306(1)
2.2.2. ECP modification of homogeneous conducting substrates
307(3)
3. DNA hybridisation detection at ECP–DNA interfaces
310(14)
3.1. DNA hybridisation transduction at passive ECP interfaces
310(6)
3.1.1. Label-based detection
310(4)
3.1.2. Label-free hybridisation detection
314(2)
3.2. ECP-based transduction
316(19)
3.2.1. ECP-based homogeneous phase bioassays
317(1)
3.2.2. DNA sensors based on ECP supports
318(6)
4. Conclusions
324(1)
List of abbreviations
325(1)
References
325(6)
Chapter 9 Control of Chloride Ion Exchange by DNA Hybridization at Polypyrrole Electrode
Temitope Aiyejorun, Liz Thompson, Janusz Kowalik, Mira Josowicz and Jiri Janata
1. Introduction
331(2)
2. Principle of operation
333(2)
3. Procedures
335(1)
3.1. Preparation of the generic probe
335(1)
3.2. Probe characterization
335(1)
3.3. Hybridization detection
336(1)
4. Overview of selectivity studies
336(1)
5. Time versus detection limit
337(3)
6. Summary
340(1)
Acknowledgments
341(1)
References
342(3)
Chapter 10 Threading Intercalators as Redox Indicators
Shigeori Takenaka
1. Introduction
345(1)
2. What is a threading intercalator
346(1)
3. Ferrocenylnaphthalene diimide derivatives as a threading intercalator
347(3)
4. Immobilization of a thiolated oligonucleotide on the gold electrode
350(2)
5. DNA sensor based on ferrocenylnaphthalene diimide as an electrochemical hybridization indicator
352(2)
6. SNP detection with a ferrocenylnaphthalene diimide-based DNA sensor
354(5)
7. Mediated current in DNA detection
359(1)
8. Electrochemical gene detection based on supramolecular complex formation
360(2)
9. DNA chips based on ferrocenylnaphthalene diimide
362(1)
10. Conclusion
363(1)
List of abbreviations
364(1)
Acknowledgments
364(1)
References
365(4)
Chapter 11 Nanop article-Based Electrochemical DNA Detection
Joseph Wang
1. Introduction
369(2)
1.1. Particle-based assays
369(1)
1.2. Nanoparticle-based optical DNA assays
370(1)
2. Nanoparticle-based bioelectronic detection of DNA
371(10)
2.1. Why electrical detection?
371(1)
2.2. Nanoparticle-based electrochemical hybridization assays
371(1)
2.3. Gold and silver metal tags for electrical DNA detection
372(3)
2.4. Use of magnetic beads
375(1)
2.5. Inorganic colloids tracers: Toward electrical coding
376(3)
2.6. Ultrasensitive particle-based assays based multiple amplification avenues
379(2)
3. Conclusions
381(1)
Acknowledgments
382(1)
References
382(4)
Chapter 12 Detecting DNA Damage with Electrodes
Miroslav Fojta
1. Introduction
386(3)
1.1. DNA damage and repair
386(1)
1.2. Current methods in DNA damage analysis
387(2)
2. Relations between DNA damage and the DNA electrochemical behavior
389(5)
2.1. Polarographic and voltammetric techniques in studies of DNA damage
391(3)
3. Electrochemical sensors for DNA damage
394(11)
3.1. DNA-modified electrodes
394(1)
3.2. Detection of DNA strand breaks
395(5)
3.2.1. Mercury and solid amalgam electrodes
396(3)
3.2.2. Other electrodes
399(1)
3.3. Detection of damage to DNA bases
400(5)
3.3.1. Guanine redox signals
401(2)
3.3.2. Specific signals of modified DNA bases and base adducts
403(1)
3.3.3. DNA conformation changes due to base modifications
404(1)
3.3.4. Use of DNA repair enzymes in electrochemical detection of damage to DNA bases
405(1)
4. Electrochemically controlled DNA damage
405(2)
4.1. In situ electrochemical analysis of DNA damage at electrodes
406(1)
5. Non-covalent DNA interactions with genotoxic substances
407(4)
5.1. Studies of DNA–binder interactions in solution
407(2)
5.2. DNA-modified electrodes as sensors for non-covalently binding substances
409(1)
5.3. Changes of DNA interfacial behavior upon interactions with non-covalent binders
410(1)
6. Detection of mutations in DNA sequences
411(2)
6.1. Utilization of reduced stability of mismatched DNA duplexes
411(1)
6.2. Techniques based on specific structural features of the base mismatches
411(1)
6.3. Primer extension-based techniques
412(1)
6.4. Trinucleotide repeat expansions
412(1)
7. Applications
413(2)
7.1. DNA–drug interactions
413(1)
7.2. Toxicity and antioxidant capacity testing
414(1)
7.3. Environmental analysis
415(1)
8. Conclusions
415(1)
List of abbreviations
416(1)
Acknowledgments
417(1)
References
418(15)
Chapter 13 Sensors for Genotoxicity and Oxidized DNA
James F. Rusling
1. Introduction
433(1)
2. Constructing ultrathin sensor films
434(4)
3. Voltammetric sensors for screening toxicity
438(6)
3.1. Sensors without enzymes
438(3)
3.2. Sensors providing bioactivation
441(2)
3.3. Electrochemiluminescence (ECL) detection
443(1)
4. Sensors for oxidized DNA
444(4)
4.1. Voltammetric sensors
444(2)
4.2. ECL sensors
446(2)
5. Summary and outlook for the future
448(1)
Acknowledgments
448(1)
References
449(2)
Chapter 14 Electrochemical Immunosensors on the Route to Proteomic Chips
Axel Warsinke, Walter Stöcklein, Eik Leupold, Edith Micheel and Frieder W. Scheller
1. Introduction
451(1)
2. From immunoassays to immunosensors
452(19)
2.1. Coupling of binding assays with electrochemical indication
452(3)
2.1.1. Antibodies : The recognition elements of immunoassays
452(2)
2.1.2. Electrochemical indication
454(1)
2.2. Electrochemical immunoassays
455(8)
2.2.1. Enzyme-labeled electrochemical immunoassays
455(3)
2.2.2. Redox-labeled immunoassays
458(5)
2.3. Electrochemical immunosensors
463(24)
2.3.1. Enzyme immunosensors
464(3)
2.3.2. Redox-labeled immunosensors
467(2)
2.3.3. Label-free immunosensors
469(2)
3. Electronic protein chips
471(4)
4. Summary and conclusion
475(1)
List of abbreviations
476(1)
Acknowledgments
477(1)
References
477(8)
Chapter 15 Self-Assembly of Biomolecules on Electrode Surfaces; Oligonucleotides, Amino Acids, and Proteins toward the Single-Molecule Level
Hainer Wackerbarth, Jingdong Zhang, Mikala Grubb, Allan Glargaard Hansen, Bee Lean Ooi, Hans Erik Mølager Christensen and Jens Ulstrup
1. Introduction
485(2)
2. Theory and experiment of scanning tunneling microscopy
487(5)
2.1. Molecular conductivity and mechanisms of the in situ STM process
487(3)
2.2. Properties of the Au(1 1 1) surface
490(2)
3. From mononucleotides to oligonucleotides
492(6)
3.1. Self-assembly on Au(1 1 1)
492(6)
4. Amino acids and protein monolayers
498(11)
4.1. Network-like clusters in cysteine adlayers on Au(1 1 1)
498(5)
4.2. Assembling of the iron-sulfur protein pyrococcus furiosus ferredoxin on thiolate-modified Au(1 1 1) surfaces
503(4)
4.3. An alternative strategy for intelligent materials — artifical proteins
507(2)
5. Concluding remarks
509(2)
List of abbreviations
511(1)
Acknowledgments
511(1)
References
511(6)
Chapter 16 Direct Electrochemistry of Proteins and Enzymes
Elena E. Ferapontova, Sergey Shleev, Tautgirdas Ruzgas, Leonard Stoica, Andreas Christenson, Jan Tkac, Alexander I. Yaropolov and Lo Gorton
1. Introduction
517(8)
2. Haem enzymes
525(26)
2.1. Monocofactor-containing proteins
527(12)
2.1.1. Microperoxidase
527(1)
2.1.2. Cytochrome c
528(2)
2.1.3. Peroxidase and catalase
530(9)
2.2. Multi-cofactor-containing enzymes
539(12)
2.2.1. Cellobiose dehydrogenase
543(3)
2.2.2. Sulphite oxidase
546(2)
2.2.3. Fructose dehydrogenase
548(1)
2.2.4. Theophylline oxidase
549(2)
3. Copper redox proteins and enzymes
551(24)
3.1. T1 copper redox protein — azurin
554(2)
3.2. T2 copper enzyme — galactose oxidase
556(2)
3.3. T3 copper enzyme — tyrosinase
558(4)
3.4. "Blue" multi-copper oxidases
562(37)
3.4.1. Ascorbate oxidase
562(2)
3.4.2. Bilirubin oxidase
564(2)
3.4.3. Ceruloplasmin
566(2)
3.4.4. Laccase
568(6)
3.4.5. Additional enzymes
574(1)
Acknowledgments
575(1)
References
575(24)
Chapter 17 Amperometric Enzyme Sensors based on Direct and Mediated Electron Transfer
Sabine Borgmann, Gerhard Hartwich, Albert Schulte and Wolfgang Schuhmann
1. Electron-transfer pathways between redox proteins and electrode surfaces
599(30)
1.1. Introduction
599(3)
1.2. Marcus-theory of electron transfer
602(2)
1.3. Structural and ET properties of redox proteins
604(3)
1.3.1. Small redox proteins
605(1)
1.3.2. Redox proteins with tightly bound cofactors inside the protein shell
606(1)
1.3.3. Multi-cofactors redox proteins
606(1)
1.4. Immobilisation of proteins on electrode surfaces
607(7)
1.5. Design of ET pathways
614(10)
1.6. Optimisation of sensor architectures
624(4)
1.7. Enzyme microstructures
628(1)
2. ET pathways in recognition of DNA hybridisation
629(7)
2.1. Affinity-based recognition of dsDNA
632(1)
2.1.1. Detection of dsDNA via intercalators
632(1)
2.1.2. Detection of dsDNA via signalling ODNs
632(1)
2.2. Amplified recognition of DNA hybridisation
633(25)
2.2.1. Enzyme-amplified recognition of dsDNA
633(1)
2.2.2. Chemical amplification for recognition of dsDNA
634(2)
2.2.3. Bioelectronic hybrid devices for recognising DNA hybridisation
636(1)
3. Conclusion and outlook
636(1)
List of abbreviations
637(1)
References
637(20)
Chapter 18 Catalytic Hydrogen Evolution at Mercury Electrodes from Solutions of Peptides and Proteins
Michael Heyrovský
1. Catalytic reactions in electrochemistry
657(1)
2. Catalytic hydrogen evolution at electrodes
658(10)
2.1. Definition
658(1)
2.2. Non-catalytic hydrogen evolution at mercury electrodes
659(1)
2.3. The catalysts
660(4)
2.4. Mechanism of catalysis
664(2)
2.5. Electrochemical techniques
666(2)
3. Catalysis by peptides and proteins
668(11)
3.1. Introduction
668(2)
3.2. Catalytically active groups
670(1)
3.3. Brdicka reaction
670(4)
3.4. Peptides
674(2)
3.5. Proteins
676(3)
3.6. Changes of proteins
679(1)
4. Summary and conclusions
679(1)
List of abbreviations
680(1)
References
680(10)
Chapter 19 Electroactivity of Proteins: Possibilities in Biomedicine and Proteomics
Emil Palecek
1. Introduction
690(4)
1.1. History
691(1)
1.2. Protein adsorption and immobilization
691(3)
1.2.1. Modified electrode surfaces
692(1)
1.2.2. Bare electrodes
693(1)
2. Electroactivity of peptides at carbon and mercury electrodes
694(7)
2.1. Electrooxidation at carbon electrodes
694(1)
2.2. Electroactivity of peptides at mercury electrodes
695(6)
2.2.1. Peak H
696(5)
3. Electroactivity of proteins
701(15)
3.1. Electroactivity of avidin and streptavidin
701(7)
3.1.1. Avidin–biotin binding
704(3)
3.1.2. Interfacial behavior of avidin and avidin–biotin
707(1)
3.1.3. Concluding remarks
708(1)
3.2. Native, mutant and denatured proteins
708(7)
3.2.1. Changes in protein catalytic responses due to single amino acid exchange
709(3)
3.2.2. Denatured proteins
712(3)
3.3. Voltammetric and polarographic signals of some proteins in presence of guanidine
715(1)
4. Redox states of peptides and proteins
716(2)
4.1. Electroreduction of disulfide bonds
716(1)
4.2. Electrochemical analysis of reduced peptides and proteins
717(1)
5. Aggregation of proteins
718(7)
5.1. Parkinson's disease (PD)
719(1)
5.2. α-Synuclein (ASyn)
719(6)
5.2.1. Electrochemical analysis of α-synuclein
720(2)
5.2.2. Aggregation of α-synuclein
722(1)
5.2.3. Hydrogen evolution catalyzed by α-synuclein at mercury electrodes
723(2)
6. Signals of thiolated oligodeoxynucleotides in cobalt-containing solutions
725(1)
6.1. Thioalkanes and thiolated ODNs at gold and mercury electrodes
725(1)
6.2. Thiolated ODNs in cobalt-containing solutions
725(1)
7. DNA–protein interactions
726(6)
7.1. Electrochemical analysis of DNA–protein interactions
728(4)
7.1.1. Single-surface techniques
729(2)
7.1.2. Double-surface techniques
731(1)
8. Introduction of electroactive markers to probe the protein structure
732(4)
8.1. Concluding remarks
736(1)
9. Summary and conclusion
736(3)
List of abbreviations
739(1)
Acknowledgments
740(1)
References
740(15)
Chapter 20 Polarography of Proteins: A History
Petr Zuman and Emil Palecek
1. Introduction
755(1)
2. Electrochemistry of proteins
756(9)
2.1. Early history
756(3)
2.2. Catalytic hydrogen evolution at mercury electrodes
759(5)
2.2.1. Analysis of proteins
759(1)
2.2.2. Denaturation of proteins
759(2)
2.2.3. Cancer research
761(1)
2.2.4. Proteolysis and immunochemistry
762(1)
2.2.5. Adsorption of proteins
763(1)
2.3. Voltammetry at solid electrodes
764(1)
3. Summary and conclusions
765(1)
Acknowledgments
765(1)
References
765(8)
Index 773

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