Scribd Logo
Upload

Welcome to Scribd!

  • 22 views

    Index 1999 Molecular-Biology-Techniques

    Uploaded by

    ANA
    This document contains an index of terms related to molecular biology techniques. It includes terms such as: - Agarose gel electrophoresis - Cesium chloride-ethidium bromide density gradient centrifugation - DNA sequencing - Enzyme-linked immunosorbent assay - Northern blot analysis - Polymerase chain reaction - Restriction fragment length polymorphism analysis - Southern blot analysis The index provides page numbers for where these techniques are discussed in detail in another document.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content

    You might also like

    Index 1999 Molecular-Biology-Techniques

    Uploaded by

    ANA
    22 views6 pages
    This document contains an index of terms related to molecular biology techniques. It includes terms such as: - Agarose gel electrophoresis - Cesium chloride-ethidium bromide density gradient centrifugation - DNA sequencing - Enzyme-linked immunosorbent assay - Northern blot analysis - Polymerase chain reaction - Restriction fragment length polymorphism analysis - Southern blot analysis The index provides page numbers for where these techniques are discussed in detail in another document.

    Original Description:

    Original Title

    Index_1999_Molecular-Biology-Techniques

    Copyright

    © © All Rights Reserved

    Available Formats

    PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    Report this Document
    This document contains an index of terms related to molecular biology techniques. It includes terms such as: - Agarose gel electrophoresis - Cesium chloride-ethidium bromide density gradient centrifugation - DNA sequencing - Enzyme-linked immunosorbent assay - Northern blot analysis - Polymerase chain reaction - Restriction fragment length polymorphism analysis - Southern blot analysis The index provides page numbers for where these techniques are discussed in detail in another document.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    Download as pdf or txt
    22 views6 pages

    Index 1999 Molecular-Biology-Techniques

    Uploaded by

    ANA
    This document contains an index of terms related to molecular biology techniques. It includes terms such as: - Agarose gel electrophoresis - Cesium chloride-ethidium bromide density gradient centrifugation - DNA sequencing - Enzyme-linked immunosorbent assay - Northern blot analysis - Polymerase chain reaction - Restriction fragment length polymorphism analysis - Southern blot analysis The index provides page numbers for where these techniques are discussed in detail in another document.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    Download as pdf or txt
    of 6

    Index

    A DEPC, see Diethylpyrocarbonate


    Dideoxy sequencing, see DNA
    Acrylamide, safety precautions, 82,147 sequencing
    Agarose gel electrophoresis, see also Diethylpyrocarbonate
    Northern blot analysis; Southern ribonuclease elimination,
    blot analysis 192-193
    digested pGEX2 plasmid safety precautions, 193
    purification, 39-42 DNA sequencing
    polymerase chain reaction products, automated sequencing, 144,155,
    30-31, 64-66 162
    pUC119 phagemid vector confirmation of oligonucleotide-
    purification, 111 directed mutagenesis, 5,144
    dideoxy sequencing
    principle, 144
    reaction mixtures, 152-153,161
    BLAST, gene homology searching, solution preparation, 153
    157-158 templates and primers, 151
    homology searching with BLAST,
    157-158
    polyacrylamide gel electrophoresis
    Cesium chloride-ethidium bromide autoradiography, 149
    density gradient centrifugation gel preparation, 147-148
    band identification, 25, 63 loading, 148
    cell growth, 20-22 running conditions, 148, 161
    centrifugation and extraction, 22-23, solution preparation, 149
    25 radiation safety, 145, 147
    principle, 19-20
    ribonuclease treatment in plasmid
    preparation, 21-22
    solution preparation, 24 ELISA, see Enzyme-linked
    immunosorbent assay
    D Enzyme-linked immunosorbent assay,
    quantitative analysis, 91
    Daily schedule, course synopsis, 9-14 Ethidium bromide, see also Cesium
    Density gradient centrifugation, s e e chloride-ethidium bromide
    Cesium chloride-ethidium density gradient centrifugation
    bromide density gradient safety precautions, 7, 21
    229
    230 INDEX

    Northern blot analysis


    applications,192
    Fusion protein, see VirD2, glutathione rbsS transcripts
    $-transferase fusion protein agarose-formaldehyde gel
    electrophoresis,199-201,215
    G denaturation and blottingof RNA,
    203-204
    13-Galactosidase hybridizationand washing,
    filterassay in yeast two-hybrid 211-212
    system, 218-219,225-226 overview, 5-6, 192
    v/rD2 cloning into pUC119 phagemid probe preparationby nick
    vector,screening,105-106 translation,207-209
    Genomic D N A ribonuclease eliminationwith
    preparation from Agrobacterium diethylpyrocarbonate,
    tumefaciens, 165-167 192-193
    restriction digestion, 169 R N A preparationfrom tobacco
    Glutathione S-transferase, see VirD2, leaves,195-197
    glutathione S-transferase fusion
    protein O

    H Oligonucleotide-directedmutagenesis
    overview of uraciltemplate method,
    Hybridization,see Northern blot 4-5,100-102
    analysis;Southern blot analysis screening,103
    virD2 deletionmutation
    annealing reaction,129-130, 141
    background, 100-102
    Ligation cloning into pUC119 phagemid
    pGEX2 vector,45-46 vector
    pUCII9 phagemid vector,113-114 DNA purification from agarose
    gels, 111
    M ~-galactosidase screening,
    105-106
    Melting temperature, DNA, 64 ligation of restriction fragment
    and vector, 113-114
    N plasmid preparation and
    restriction analysis, 117
    Nick translation, probe preparation restriction digests, 106, 109
    Northern blot analysis, 207-209 target sequence orientation,
    Southern blot analysis 106-107
    labeling, 179 DNA sequencing confirmation, 5,
    principle, 17g 144
    purification and quantitation, oligonucleotide phosphorylation,
    180-181 125-126
    reaction conditions, 180 plasmid preparation, small-scale,
    solution preparation, 181-182 137-138
    INDEX 231

    primer extension reaction, autoradiography, 149


    133-134 gel preparation, 147-148
    restrictionanalysis in mutant loading, 148
    confirmation, 138-139 running conditions, 148, 161
    single-strandedtemplate solution preparation, 149
    preparation restriction fragment analysis, 139
    cellgrowth and infection, Polymerase chain reaction
    120-121 agarose gel electrophoresisof
    overview, 119 products, 30-31, 64-66
    phage harvesting and D N A amplificationreaction,29-30
    extraction,121-122 checklist,29, 32
    phage titer,119 contamination, 28-29
    solution preparation, 122-123 ligationof product to pGEX2 vector,
    transformation of Escherichia co]i, 45-46
    137 melting temperature of DNA, 64
    principle, 27-28
    restriction digestion of products, 37,
    67
    PCR, see Polyrnerase chain reaction solution preparation, 31
    Phenol, bufferequilibration,119,165, Power supply, safety precautions, 7
    195 Protein-protein interactions, s e e Yeast
    Phenylmethylsulfonyl fluoride,safety two-hybrid system
    precautions, 76
    Plasmid
    alkaline lysispreparation, 55-57
    purificationby cesium chloride- Radioisotopes, safety precautions, 7,
    ethidium bromide density 145,179,207
    gradient centrifugation r b s S transcripts, Northern blot analysis
    cell growth, 20-22 agarose-formaldehyde gel
    centrifugationand extraction, electrophoresis, 199-201,215
    22-23, 25 denaturation and blotting of RNA,
    principle, 19-20 203-204
    ribonuclease treatment, 21-22 hybridization and washing, 211-212
    solution preparation, 24 overview, 5-6, 192
    restrictionanalysis,59-61, 68,117, probe preparation by nick
    138-139 translation, 207-209
    restriction digestion, 36-37, 66 ribonuclease elimination with
    types for fusion protein construction, diethylpyrocarbonate, 192-193
    2O R N A preparation from tobacco
    yeast two-hybrid system, 219 leaves, 195-197
    PMSF, see Phenylmethylsulfonyl Restrictiondigestion
    fluoride cohesive end joiningin cloning, 35
    Polyacrylarnide gel electrophoresis, see genomic DNA, 169
    also Sodium dodecylsulfate- pGEX2 plasmid, 36-37
    polyacrylamide gel electrophoresis polymerase chain reaction products,
    DNA sequencing 37
    232 INDEX

    Restriction digestion (continued) loading, 83-84


    restriction analysis of plasmids, principle, 81
    59-61, 68, 117,138-139 protein detection, overview of
    Restriction fragment length methods, 81-82
    polymorphism, Southern blot running conditions, 83
    analysis of virD2 silver staining, 87-89
    agarose gel electrophoresis, 171-172, solution preparation, 85
    189 Southern blot analysis, restriction
    denaturation and blotting of gel, fragment length polymorphism
    175-177,189 analysis of virD2
    genomic DNA preparation from agarose gel electrophoresis, 171-172,
    Agrobacterium tumefaciens, 189
    165-167 denaturation and blotting of gel,
    hybridization and washing, 185-187,190 175-177, 189
    overview, 5,164 genomic DNA preparation from
    probe preparation by nick translation Agrobacterium tumefaciens,
    labeling, 179 165-167
    principle, 179 hybridization and washing,
    purification and quantitation, 180-181 185-187,190
    reaction conditions, 180 overview, 5, 164
    solution preparation, 181-182 probe preparation by nick translation
    restriction digestion of genomic labeling, 179
    DNA, 169 principle, 179
    RFLP, see Restriction fragment length purification and quantitation,
    polymorphism 180-181
    RNase reaction conditions, 180
    contamination avoidance, 21,119 solution preparation, 181-182
    diethylpyrocarbonate elimination, restriction digestion of genomic
    192-193 DNA, 169
    plasmid preparation treatment, 22
    RuBisCO gene, see rbsS

    Transformation
    Escherichia coli
    Safety precautions, overview, 7-8 fusion protein vector, 49-52,
    SDS-PAGE, see Sodium dodecylsul- 68
    fate-polyacrylamide gel oligonucleotide-directed
    electrophoresis mutagenesis, 137
    Sequencing, see DNA sequencing pUC119 phagemid vector, 117
    Sodium dodecylsulfate- yeast, 221-223
    polyacrylamide gel
    electrophoresis, see also Western V'
    blot analysis
    casting of gel, 82-83 virD2
    gel polymerization, 81 function of virulence genes, 2
    INDEX 233

    fusion to glutathione S-transferase polymerase chain reaction


    gene products, 37, 67
    fusion plasmid transformation of Escherichia coil,
    preparation by alkaline lysis, 49-52, 68
    55-57 oligonucleotide-directed
    restriction analysis, 59-61, 68 mutagenesis, deletion mutation
    overview, 3-4, 18 production
    plasmid purification by cesium annealing reaction, 129-130,
    chloride-ethidium bromide 141
    density gradient background, 100-102
    centrifugation cloning into pUC119 phagemid
    band identification, 25, 63 vector
    cell growth, 20-22 DNA purification from agarose
    centrifugation and extraction, gels, 111
    22-23, 25 ~-galactosidase screening,
    principle, 19-20 105-106
    ribonuclease treatment, ligation of restriction fragment
    21-22 and vector, 113-114
    solution preparation, 24 plasmid preparation and
    polymerase chain reaction for restriction analysis, 117
    restriction site flanking restriction digests, 106,109
    agarose gel electrophoresis of target sequence orientation,
    products, 30-31, 64-66 106-107
    amplification reaction, 29-30 DNA sequencing confirmation, 5,
    checklist, 29, 32 144
    contamination, 28-29 oligonucleotide phosphorylation,
    ligation of product to pGEX2 125-126
    vector, 45-46 plasmid preparation, small-scale,
    melting temperature of DNA, 137-138
    64 primer extension reaction,
    principle, 27-28 133-134
    solution preparation, 31 restriction analysis in mutant
    protein preparation, see VirD2, confirmation, 138-139
    glutathione $-transferase single-stranded template
    fusion protein preparation
    purification of digested pGEX2 cell growth and infection,
    plasmid 120-121
    agarose gel electrophoresis and overview, 119
    band recovery, 39-41 phage harvesting and DNA
    glass milk purification extraction, 121-122
    technique, 41-42 phage titer, 119
    restriction digestion solution preparation,
    cohesive end joining in cloning, 122-123
    35 transformation of Escherichia coil,
    pGEX2 plasmid, 36-37, 66 137
    234 INDEX

    virD2 (continued) principle, 81


    restriction fragment length protein detection, overview of
    polymorphism, Southern blot methods, 81-82
    analysis running conditions, 83
    agarose gel electrophoresis, silver staining, 87-89
    171-172,189 solution preparation, 85
    denaturation and blotting of gel, solubility, 72
    175-177,189 vector construction, see virD2
    genomic DNA preparation from Western blot analysis
    Agrobacterium tumefaciens, antibodies, 91-92
    165-167 band identification, 97-98
    hybridization and washing, blot transfer, 92-93
    185-187,190 membranes, 92
    overview, 5,164 principle, 91
    probe preparation by nick solution preparation, 94
    translation staining and washing, 93-94
    labeling, 179 VirE1, see Yeast two-hybrid system
    principle, 179 VirE2, see Yeast two-hybrid system
    purification and quantitation,
    180-181
    W
    reaction conditions, 180
    solution preparation, 181-182
    Western blot analysis
    restriction digestion of genomic
    DNA, 169 antibodies, 91-92
    VirD2, glutathione S-transferase fusion band identification, 97-98
    protein blot transfer, 92-93
    expression and purification in membranes, 92
    Escherichia coil
    principle, 91
    cell growth and lysis, 7 6 - 7 7 solution preparation, 94
    glutathione affinity purification, staining and washing, 93-94
    77
    solution preparation, 77-78 Y
    strains, 75- 76, 97
    promoter for expression, 72 Yeast two-hybrid system
    protease degradation, 72 applications, 218
    sodium dodecylsulfate- principle, 6, 218
    polyacrylarnide gel VirE1-VirE2 interactions
    electrophoresis ~-galactosidase filter assay,
    casting of gel, 82-83 218-219, 2 2 5 - 2 2 6
    gel polymerization, 81 plasmids, 219
    loading, 83-84 transformation of yeast, 2 2 1 - 2 2 3

    You might also like