Electrochemistry of Nucleic Acids

809 Pages·2007·18.46 MB·English

PERSPECTIVES IN
BIOANALYSIS
VOLUME 1
i
This page intentionally left blank
ii
PERSPECTIVES IN BIOANALYSIS
ELECTROCHEMISTRY OF NUCLEIC ACIDS
AND PROTEINS – TOWARDS
ELECTROCHEMICAL SENSORS
FOR GENOMICS AND PROTEOMICS
EDITORS
EMIL PALECˇEK F. SCHELLER J. WANG
INSTITUTEOFBIOPHYSICS UNIVERSITATPOTSDAM, CENTERFORBIOELECTRONICS
ACADEMYOFSCIENCES ANALYTISCHEBIOCHEMIE ANDBIOSENSORS
OFTHECZECHREPUBLIC KARL-LIEBKNECHTSTR.,24–25 BIODESIGNINSTITUTE
KRALOVOPOLSKA135 HAUS25,B2.13–14 DEPARTMENTSOFCHEMICAL
61265BRNO 14475GOLM &MATERIALSENGINEERING
CZECHREPUBLIC GERMANY ANDCHEMISTRY
ARIZONASTATEUNIVERSITY
1001S.MCALLISTERAVE
P.O.BOX875801TEMPE
AZ85287-5801,USA
VOLUME 1
Amsterdam–Boston–Heidelberg–London–NewYork–Oxford
Paris–SanDiego–SanFrancisco–Singapore–Sydney–Tokyo
iii
ELSEVIERB.V. ELSEVIERInc. ELSEVIERLtd ELSEVIERLtd
Radarweg29 525BStreet,Suite1900 TheBoulevard,LangfordLane 84TheobaldsRoad
P.O.Box211,1000AEAmsterdam SanDiego,CA92101-4495 Kidlington,OxfordOX51GB LondonWC1X8RR
TheNetherlands USA UK UK
r2005ElsevierB.V.Allrightsreserved.
ThisworkisprotectedundercopyrightbyElsevierB.V.,andthefollowingtermsandconditionsapplytoitsuse:
Photocopying
Singlephotocopies ofsinglechapters maybemadeforpersonal useasallowed bynationalcopyright laws.
PermissionofthePublisherandpaymentofafeeisrequiredforallotherphotocopying,includingmultipleor
systematic copying, copying for advertising or promotional purposes, resale, and all forms of document
delivery.Specialratesareavailableforeducationalinstitutionsthatwishtomakephotocopiesfornon-profit
educationalclassroomuse.
Permissions may be sought directly from Elsevier’s Rights Department in Oxford, UK: phone (+44) 1865
843830,fax[phone],e-mail:[email protected]
theElsevierhomepage(http://www.elsevier.com/locate/permissions).
IntheUSA,usersmayclearpermissionsandmakepaymentsthroughtheCopyrightClearanceCenter,Inc.,222
RosewoodDrive,Danvers,MA01923,USA;phone:[phone],fax:[phone],andinthe
UKthroughtheCopyrightLicensingAgencyRapidClearanceService(CLARCS),90TottenhamCourtRoad,
LondonW1P0LP,UK;phone:[phone];fax:[phone].Othercountriesmayhavealocal
reprographicrightsagencyforpayments.
DerivativeWorks
Tablesofcontentsmaybereproducedforinternalcirculation,butpermissionofthePublisherisrequiredfor
externalresaleordistributionofsuchmaterial.PermissionofthePublisherisrequiredforallotherderivative
works,includingcompilationsandtranslations.
ElectronicStorageorUsage
Permission of the Publisher is required to store or use electronically any material contained in this work,
includinganychapterorpartofachapter.
Exceptasoutlinedabove,nopartofthisworkmaybereproduced,storedinaretrievalsystemortransmittedin
anyformorbyanymeans,electronic,mechanical,photocopying,recordingorotherwise,withoutpriorwritten
permissionofthePublisher.
Addresspermissionsrequeststo:Elsevier’sRightsDepartment,atthefaxande-mailaddressesnotedabove.
Notice
NoresponsibilityisassumedbythePublisherforanyinjuryand/ordamagetopersonsorpropertyasamatter
of products liability, negligence or otherwise, or from any use or operation of any methods, products,
instructionsorideascontainedinthematerialherein.Becauseofrapidadvancesinthemedicalsciences,in
particular,independentverificationofdiagnosesanddrugdosagesshouldbemade.
Firstedition2005
LibraryofCongressCataloginginPublicationData
AcatalogrecordisavailablefromtheLibraryofCongress.
BritishLibraryCataloguinginPublicationData
AcataloguerecordisavailablefromtheBritishLibrary.
ISBN-10: 0-444-52150-X
ISBN-13: 978-0-444-52150-7
ISSN: 1871-0069
∞ The paper used in this publication meets the requirements of ANSI/NISO Z39.48-1992 (Permanence of
Paper).PrintedinTheNetherlands.
Working together to grow
libraries in developing countries
www.elsevier.com | www.bookaid.org | www.sabre.org
iv
Contents
Contributors xi
Preface xv
Chapter 1 Polarography of DNA. Retrospective View
Emil Palecˇek
1. Introduction 1
2. Retrospective view 5
3. Oscillographic polarography at controlled A.C. 8
4. Electrogenerated products 9
5. Nu¨rnberg’s cyclic voltammetry with HMDE 10
6. Summary and conclusion 11
List of abbreviations 12
Acknowledgments 12
References 12
Chapter 2 Electrochemical Properties of Nucleic Acid Components
Vladimı´r Vetterl and Stanislav Hasonˇ
1. Introduction 18
2. Adsorption and two-dimensional condensation 18
3. Electroreduction and electrooxidation of nucleic acid components 51
4. Concluding remarks 57
List of abbreviations 58
Acknowledgments 60
References 60
Chapter 3 Electrochemistry of Nucleic Acids
Emil Palecˇek and Frantisˇek Jelen
1. Introduction 74
2. Electrochemical methods and electrodes 77
3. Adsorption of nucleic acids 80
4. Reduction and oxidation of nucleic acids at electrodes 86
5. Changes in DNA conformation at surfaces 104
6. Electrochemical principles in NA biosensors 121
7. Electrochemical DNA biosensors: Future prospects 149
8. Summary and conclusion 150
List of abbreviations 152
Acknowledgments 153
References 153
v
vi Contents
Chapter 4 Electrochemical Nucleic Acid Biosensors
Joseph Wang
1. Introduction 175
2. Electrochemical biosensing of DNA hybridization 177
3. Conclusions and outlook 189
Acknowledgment 190
References 190
Chapter 5 Amplified Electrochemical and Photoelectrochemical Analysis of
DNA
Eugenii Katz, Bilha Willner and Itamar Willner
1. Introduction 195
2. Enzyme-amplified electrochemical analysis of DNA 202
3. Amplified electrochemical detection of DNA using nucleic acid-
functionalized metallic or semiconductor nanoparticles 211
4. Nano- and micro-objects as carriers for the amplified electrochemical
detection of DNA 219
5. Analysis of DNA by direct conductivity measurements 227
6. Amplified sensing of DNA in the presence of magnetic particles 230
7. Photoelectrochemical detection of DNA 233
8. Conclusions and perspectives 239
Acknowledgments 241
References 241
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
2. Principle and instrumentation of electrical detection 248
3. Low-density electrical DNA arrays 251
4. Integrated CMOS DNA arrays 256
5. Electrical label-free detection of DNA arrays 261
6. Electrical protein microarrays 264
7. Electrical hapten microarrays 267
List of abbreviations 271
References 272
Chapter 7 Carbon Electrodes in DNA Hybridisation Research
G. Marrazza, F. Lucarelli and M. Mascini
1. DNA probe immobilisation 280
2. Hybridisation reaction 283
3. Labelling and electrochemical detection 284
4. Conclusions 293
List of abbreviations 293
References 294
Contents vii
Chapter 8 Conducting Polymers for DNA Sensors and DNA Chips: from
Fabrication to Molecular Detection
Pascal Mailley, Andre´ Roget and Thierry Livache
1. Introduction 297
2. ECP-based genosensors: Design and fabrication 298
3. DNA hybridisation detection at ECP–DNA interfaces 310
4. Conclusions 324
List of abbreviations 325
References 325
Chapter 9 Control of Chloride Ion Exchange by DNA Hybridization at
Polypyrrole Electrode
Temitope Aiyejorun, Liz Thompson, Janusz Kowalik, Mira Josowicz and
Jirˇı´ Janata
1. Introduction 331
2. Principle of operation 333
3. Procedures 335
4. Overview of selectivity studies 336
5. Time versus detection limit 337
6. Summary 340
Acknowledgments 341
References 342
Chapter 10 Threading Intercalators as Redox Indicators
Shigeori Takenaka
1. Introduction 345
2. What is a threading intercalator 346
3. Ferrocenylnaphthalene diimide derivatives as a threading intercalator 347
4. Immobilization of a thiolated oligonucleotide on the gold electrode 350
5. DNA sensor based on ferrocenylnaphthalene diimide as an
electrochemical hybridization indicator 352
6. SNP detection with a ferrocenylnaphthalene diimide-based DNA sensor 354
7. Mediated current in DNA detection 359
8. Electrochemical gene detection based on supramolecular complex
formation 360
9. DNA chips based on ferrocenylnaphthalene diimide 362
10. Conclusion 363
List of abbreviations 364
Acknowledgments 364
References 365
Chapter 11 Nanoparticle-Based Electrochemical DNA Detection
Joseph Wang
1. Introduction 369
2. Nanoparticle-based bioelectronic detection of DNA 371
viii Contents
3. Conclusions 381
Acknowledgments 382
References 382
Chapter 12 Detecting DNA Damage with Electrodes
Miroslav Fojta
1. Introduction 386
2. Relations between DNA damage and the DNA electrochemical behavior 389
3. Electrochemical sensors for DNA damage 394
4. Electrochemically controlled DNA damage 405
5. Non-covalent DNA interactions with genotoxic substances 407
6. Detection of mutations in DNA sequences 411
7. Applications 413
8. Conclusions 415
List of abbreviations 416
Acknowledgments 417
References 418
Chapter 13 Sensors for Genotoxicity and Oxidized DNA
James F. Rusling
1. Introduction 433
2. Constructing ultrathin sensor films 434
3. Voltammetric sensors for screening toxicity 438
4. Sensors for oxidized DNA 444
5. Summary and outlook for the future 448
Acknowledgments 448
References 449
Chapter 14 Electrochemical Immunosensors on the Route toProteomicChips
Axel Warsinke, Walter Sto¨cklein, Eik Leupold, Edith Micheel and
Frieder W. Scheller
1. Introduction 451
2. From immunoassays to immunosensors 452
3. Electronic protein chips 471
4. Summary and conclusion 475
List of abbreviations 476
Acknowledgments 477
References 477
Contents ix
Chapter 15 Self-Assembly of Biomolecules on Electrode Surfaces; Oligonuc-
leotides, 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. Theory and experiment of scanning tunneling microscopy 487
3. From mononucleotides to oligonucleotides 492
4. Amino acids and protein monolayers 498
5. Concluding remarks 509
List of abbreviations 511
Acknowledgments 511
References 511
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
2. Haem enzymes 525
3. Copper redox proteins and enzymes 551
Acknowledgments 575
References 575
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
2. ET pathways in recognition of DNA hybridisation 629
3. Conclusion and outlook 636
List of abbreviations 637
References 637
Chapter 18 Catalytic Hydrogen Evolution at Mercury Electrodes from
Solutions of Peptides and Proteins
Michael Heyrovsky´
1. Catalytic reactions in electrochemistry 657
2. Catalytic hydrogen evolution at electrodes 658
3. Catalysis by peptides and proteins 668
4. Summary and conclusions 679
List of abbreviations 680
References 680