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Analysis of Genes and Genomes Richard J. Reece UniversityofManchester,UK John Wiley & Sons, Ltd Analysis of Genes and Genomes Analysis of Genes and Genomes Richard J. Reece UniversityofManchester,UK John Wiley & Sons, Ltd Copyright2004 JohnWiley&SonsLtd,TheAtrium,SouthernGate,Chichester, WestSussexPO198SQ,England Telephone(+44)1243779777 Email(forordersandcustomerserviceenquiries):[email protected] VisitourHomePageonwww.wileyeurope.comorwww.wiley.com AllRightsReserved.Nopartofthispublicationmaybereproduced,storedinaretrievalsystemor transmittedinanyformorbyanymeans,electronic,mechanical,photocopying,recording,scanning orotherwise,exceptunderthetermsoftheCopyright,DesignsandPatentsAct1988orunderthe termsofalicenceissuedbytheCopyrightLicensingAgencyLtd,90TottenhamCourtRoad,London W1T4LP,UK,withoutthepermissioninwritingofthePublisher.RequeststothePublishershould beaddressedtothePermissionsDepartment,JohnWiley&SonsLtd,TheAtrium,SouthernGate, Chichester,WestSussexPO198SQ,England,[email protected],orfaxedto (+44)1243770620. Thispublicationisdesignedtoprovideaccurateandauthoritativeinformationinregardtothe subjectmattercovered.ItissoldontheunderstandingthatthePublisherisnotengagedinrendering professionalservices.Ifprofessionaladviceorotherexpertassistanceisrequired,theservicesofa competentprofessionalshouldbesought. OtherWileyEditorialOffices JohnWiley&SonsInc.,111RiverStreet,Hoboken,NJ07030,USA Jossey-Bass,989MarketStreet,SanFrancisco,CA94103-1741,USA Wiley-VCHVerlagGmbH,Boschstr.12,D-69469Weinheim,Germany JohnWiley&SonsAustraliaLtd,33ParkRoad,Milton,Queensland4064,Australia JohnWiley&Sons(Asia)PteLtd,2ClementiLoop#02-01,JinXingDistripark,Singapore129809 JohnWiley&SonsCanadaLtd,22WorcesterRoad,Etobicoke,Ontario,CanadaM9W1L1 Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappears inprintmaynotbeavailableinelectronicbooks. LibraryofCongressCataloging-in-PublicationData Reece,RichardJ. Analysisofgenes&genomes/RichardJ.Reece. p.;cm. Includesbibliographicalreferencesandindex. ISBN0-470-84379-9(cloth:alk.paper)–ISBN0-470-84380-2(paper:alk.paper) 1.Moleculargenetics–Research–Methodology. 2.Geneticengineering–Research–Methodology. [DNLM:1.GeneticTechniques. 2.DNA–analysis. 3.Genome.QZ52R322a2003] I.Title:Analysisofgenesandgenomes.II.Title. QH442.R4452003 572.8(cid:1)6–dc21 2003012937 BritishLibraryCataloguinginPublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary ISBN0-470-84379-9(HB) 0-470-84380-2(PB) Typesetin11/14ptSabonbyLaserwordsPrivateLimited,Chennai,India PrintedandboundinItalybyContiTipocolorSpA,Florence Thisbookisprintedonacid-freepaperresponsiblymanufacturedfromsustainableforestry inwhichatleasttwotreesareplantedforeachoneusedforpaperproduction. For Judith Contents Preface xiii Acknowledgements xv Abbreviationsand acronyms xvii 1 DNA: Structureand function 1 1.1 Nucleicacid isthe material of heredity 2 1.2 Structureof nucleicacids 7 1.3 Thedoublehelix 11 1.3.1 The antiparallelhelix 12 1.3.2 Base pairs and stacking 14 1.3.3 Gaining access to informationwith thedouble helix withoutbreakingit apart 16 1.3.4 Hydrogen bonding 17 1.4 Reversible denaturingof DNA 18 1.5 Structureof DNA in thecell 21 1.6 Theeukaryoticnucleosome 24 1.7 Thereplicationof DNA 28 1.8 DNA polymerases 31 1.9 Thereplicationprocess 33 1.10 Recombination 37 1.11 Genes and genomes 39 1.12 Genes withina genome 40 1.13 Transcription 43 1.13.1 Transcriptionin prokaryotes 43 1.13.2 Transcriptionin eukaryotes 46 1.14 RNA processing 54 1.14.1 RNA splicing 55 1.14.2 Alternative splicing 58 1.15 Translation 59 2 Basic techniquesin gene analysis 65 2.1 Restrictionenzymes 66 2.1.1 Types of restriction–modificationsystem 70 2.1.2 Other modificationsystems 72