Functional Nucleic Acids Detection in Food Safety: Theories and Applications

484 Pages·2016·8.65 MB·English

by  Wentao Xu (auth.)

Wentao Xu
Functional
Nucleic Acids
Detection in
Food Safety
Theories and Applications
Functional Nucleic Acids Detection in Food Safety
ThiSisaFMBlankPage
Wentao Xu
Functional Nucleic Acids
Detection in Food Safety
Theories and Applications
WentaoXu
BeijingAdvancedInnovationCenter
forFoodNutritionandHumanHealth,
CollegeofFoodScience&Nutritional
Engineering
ChinaAgriculturalUniversity
Beijing,China
BeijingLaboratoryforFoodQuality
andSafety,CollegeofFood
Science&NutritionalEngineering
ChinaAgriculturalUniversity
Beijing,China
ISBN978-981-10-1617-2 ISBN978-981-10-1618-9 (eBook)
DOI10.1007/978-981-10-1618-9
LibraryofCongressControlNumber:2016943551
©SpringerScience+BusinessMediaSingapore2016
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Preface
Food safety is usually a nonnegotiable attribute for consumers in their decision-
making process as well as for manufacturers in the global trade. It is of great
significance to detect the potential danger that may harm the quality of food to
control and regulate food safety in an official and legal way. Contributed by the
progressinanalyticalchemistryandmolecularbiology,typesofmethodsappeared
tofulfillthespecificandsensitivedetection.Theapplieddetectionmethodshaveall
beenfocusedontargetcharacteristicproperties,varyingintheirphysical,chemical,
andbiologicalactivities.Butthereexistsafactthatallthesehazardexposuresare
related to a magic molecule – nucleic acid. Nucleic acids are the most important
biological macromolecules, essential for allknown forms oflife; each is found in
abundanceinalllivingthings,wheretheyplayaroleinencoding,transmitting,and
expressing genetic information. What genetic central dogma tells us is that infor-
mationisconveyedthroughthenucleicacidsequence,ortheorderofnucleotides
withinaDNAorRNAmolecule.Ontheotherhand,single-strandedDNAcanfold
intocomplextertiarystructuresandplayanactiveroleinmolecularrecognitionand
catalysis such as mycotoxins, the whole bacteria and heavy metals, etc. Once
recognized, the complex becomes much more activated, which will be helpful
in their physical, chemiluminescence, and electrochemiluminescence detection.
Thus, it is indicated obviously that nucleic acids will be enough for the detection
ofallfoodbornepotentialhazardfactors,andresearchonnucleicacidsisbecoming
profound in food safety assurance. This book aims to offer a summarized and
comprehensive representation of nucleic acid detection methods in food safety
forprofessionalsinterestedinthisareaandthepublic.
Thisbookisdividedintotwoparts.PartI,consisting13chapters,discussesthe
basic principles of nucleic acid detection owing to various detecting demands.
Chapters 1 and 2 serve as an introduction to target nucleic acids and their
corresponding extraction methods. Chapter 3 introduces the basic mechanism of
nucleicaciddetection.Chapters4and5discussthenecessarynucleicaciddetection
compositions–standardmaterialsandendogenousgene.Chapters6,7,8,9,and10
summarize unknown gene exploration, digital PCR, quantification, and high-
v
vi Preface
throughput and isothermal detection methods. Chapters 11, 12, and 13 try to
connect aptamer, lateral strips and biosensors to detection methods. Part II is
aboutthenovelapplicationofdetectionmethodsingeneticallymodifiedorganisms,
dead–alive microorganism identification, microbial diversity, heavy metal detec-
tion,genetoxicity,andnoncodingRNAidentification.
The book was fulfilled through the joint efforts of all contributors: Chenguang
Wang, Ying Shang, Pengyu Zhu, Yuancong Xu, Nan Cheng, Longjiao Zhu,
MingzhangGuo,BoyangZhang,LiyeZhu,WenyingTian,WenjinXiang,Xingtian
Cui, Yuting Chen, Jingjing Tian, and Xiangli Shao. I am very grateful for their
suggestions and help in preparing the manuscripts. Special thanks go out to the
National Science and Technology Major Project, the Beijing New-Star Plan of
Science and Technology, and the Beijing Advanced Innovation Center for Food
NutritionandHumanHealthbecausewithouttheirsupport,somepartsofthiswork
wouldnothavebeenaccomplished.
Beijing,China WentaoXu
April2016
Contents
1 Introduction:ABriefGuidetoTargetsandStrategies
ofFunctionalNucleicAcidsDetectioninFoodSafety. . . . . . . . . . . 1
1.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 SignificanceofNucleicAcidsinFoodSafetyDetection . . . . . . 6
1.2.1 TargetsFocusedontheMicroscopicView. . . . . . . . . 7
1.2.2 TargetsFocusedontheMacroscopicView. . . . . . . . . 8
1.3 ProperandApplicableStrategiesonNucleicAcidDetection
inFoodSafety. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.4 ScopeoftheBook. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2 AdaptableMethodstoExtractNucleicAcidTargets
andEvaluateQuality. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.1 TheImportanceofNucleicAcidExtraction. . . . . . . . . . . . . . . 17
2.1.1 DNAExtraction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.1.2 RNAExtraction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2 ThePrincipleofNucleicAcidExtraction. . . . . . . . . . . . . . . . . 18
2.3 GeneralStepsofDNAExtractionMethods. . . . . . . . . . . . . . . 19
2.3.1 PreparationoftheSample.. . . . .. . . . .. . . . .. . . . .. 19
2.3.2 CellLysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.3.3 Purification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.4 TheClassificationofDNAExtractionMethod
byCellLysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.4.1 ChemicalMethods. . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.4.2 PhysicalMethods. . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.4.3 EnzymaticLysisMethods. . . .. . . . . . . .. . . . . . . .. . 23
2.5 ClassificationofDNAExtractionMethodsbySamples. . . . . . . 24
2.5.1 Plants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.5.2 Animal. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
vii
viii Contents
2.5.3 Microorganisms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.5.4 Deep-ProcessedFood. . . . . . . . . . . . . . . . . . . . . . . . . 30
2.6 DNAQuantificationTechnologies. . . . . . . . . . . . . . . . . . . . . . 30
2.6.1 AgaroseGelElectrophoresis. . . . . . . . . . . . . . . . . . . . 30
2.6.2 UltravioletSpectrophotometry. . . . . . . . . . . . . . . . . . 31
2.6.3 Fluorometry. .. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . 32
2.7 Prospects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3 BasicRulesinNucleicAcid-MediatedAmplification
andHybridizationMethodsinFoodSafetyDetection:
AReview. . . . . . . . . .. . . . . . . . . . .. . . . . . . . . .. . . . . . . . . . .. . . 37
3.1 BasicTheoryonMolecularDiagnoses. . . . . . . . . . . . . . . . . . . 37
3.1.1 Watson–CrickBase-PairingPrinciple. . . . . . . . . . . . . 38
3.1.2 DNAReplicationInVivo. . . . . . . . . . . . . . . . . . . . . . 39
3.1.3 RecognitionBetweenTargetandProbe. . . . . . . . . . . . 39
3.2 PolymeraseChainReaction(PCR).. . . . .. . . . .. . . . .. . . . .. 40
3.2.1 KeyComponentsinPCR. . . . . . . . . . . . . . . . . . . . . . 42
3.2.2 Kinetics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
3.2.3 AnalysisofPCRProducts. . . . . . . . . . . . . . . . . . . . . 45
3.2.4 PrinciplesofPrimersandProbeDesign. . . . . . . . . . . . 46
3.3 CommonPrecautionsonReactionConditioning. . . . . . . . . . . . 51
3.3.1 NestedPCR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
3.3.2 TouchdownPCR. . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.3.3 ThePCRInhibitors. . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.4 HybridizationChainReaction. . . . . . . . . . . . . . . . . . . . . . . . . 52
3.4.1 WorkingPrinciple. . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3.4.2 Real-TimeHCR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
3.4.3 DesigningPrinciple. . . . . . . . . . . . . . . . . . . . . . . . . . 54
3.5 ComparisonBetweenPCRandHCR. . . . . . . . . . . . . . . . . . . . 55
3.6 Prospect. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4 ReferenceMaterials:AGoldenCriterioninNucleicAcid
Identification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
4.1 Introduction:DefinitionsandClassificationofReference
Materials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
4.1.1 DefinitionofReferenceMaterials. . . . . . . . . . . . . . . . 64
4.1.2 InstitutionstoMakeReferenceMaterials. . . . . . . . . . . 66
4.1.3 CategoriesofReferenceMaterials. . . . . .. . . . . . . . .. 67
4.2 ProceduresfortheProductionofReferenceMaterials. . . . . . . . 68
4.2.1 EstimationoftheDemandforReferenceMaterial. . . . 68
4.2.2 PlanningtheProductionofReferenceMaterial. . . . . . 69
4.2.3 QuestandProcessingofReferenceMaterial. . . . . . . . 69
4.2.4 HomogeneityTesting. . . . . . . . . . . . . . . . . . . . . . . . . 69
4.2.5 StabilityTesting. . . .. . . .. . . .. . . .. . . .. . . .. . . .. 70
Contents ix
4.3 ReferenceMaterialattheMolecularLevel. . . . . . . . . . . . . . . . 70
4.3.1 DevelopmentandApplicationofStandardMaterial
attheMolecularLevel. . . . . . . . . . . . . . . . . . . . . . . . 71
4.3.2 ProductionofReferenceMaterialsattheMolecular
Level. .. . . . .. . . . .. . . . .. . . .. . . . .. . . . .. . . . .. 71
4.3.3 ClassificationandApplicationofReferenceMaterials
ofNucleicAcids. . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
4.4 CurrentSituationofReferenceMaterialandItsApplication
inVariousFields. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.4.1 Microorganisms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.4.2 MolecularBiology. . . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.4.3 GeneticallyModifiedOrganisms. . . . . . . . . . . . . . . . . 76
4.4.4 GeneMethylation. . . . . . . . . . . . . . . . . . . . . . . . . . . 77
4.4.5 Genetics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.4.6 Viruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.5 Prospects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
5 ReferenceGene:In-SpeciesUniversalityVersus
Between-SpeciesUniquity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
5.1 Definition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
5.2 TheClassificationsoftheReferenceGenes. . . . . . . . . . . . . . . 86
5.2.1 TheReferenceGeneontheGenome. . . . . . . . . . . . . . 86
5.2.2 TheReferenceGeneontheTranscriptome. . . . . . . . . 88
5.2.3 MicroorganismReferenceGeneIdentification. . . . . . . 91
5.3 TheUniversalEndogenousReferenceGene. . . . . . . . . . . . . . . 93
5.4 MethodsforIdentifyingtheReferenceGene. . . . . . . . . . . . . . 94
5.5 Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
5.5.1 IngredientSourceIdentification. . . . . . . . . . . . . . . . . 97
5.5.2 TheAdulterationIdentification. . . . . . . . . . . . . . . . . . 97
5.5.3 DNAQualityEvaluationinPCR. . . . . . . . . . . . . . . . 98
5.5.4 QuantificationoftheTargetMaterials
intheMixture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
5.6 Prospect. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
6 PCR-BasedTechnologiesforIdentifyingUnknown
GeneSequences. . .. . . . .. . . .. . . . .. . . .. . . .. . . . .. . . .. . . . .. 107
6.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
6.2 TraditionalGenomeWalkingMethods. . . . . . . . . . . . . . . . . . . 108
6.2.1 InversePCR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
6.2.2 ThermalAsymmetricInterlacedPCR. . . . . . . . . . . . . 109
6.2.3 Cassette-LigationPCR. . . . . . . . . . . . . . . . . . . . . . . . 110
6.3 NovelGenomeWalkingMethods. . . . . . . . . . . . . . . . . . . . . . 110
6.3.1 A-TLinkerPCR. . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
6.3.2 Loop-LinkerPCR. . . . . . . . . . . . . . . . . . . . . . . . . . . 112