Contributors |
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ix | |
Preface |
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xi | |
Foreword |
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xvi | |
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Controlled Heat-Denaturation of DNA Plasmids and PCR Fragments |
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1 | (28) |
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4 | (13) |
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4 | (1) |
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Temperature-Dependence of Plasmid Denaturation |
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5 | (1) |
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Buffer-Strength Dependence of Plasmid Denaturation |
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6 | (1) |
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Time Course of Heat-Denaturation of DNA Plasmids of Varying Sizes |
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6 | (2) |
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Denaturation of Plasmids Containing a Difficult Region |
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8 | (1) |
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Amount of DNA Needed for Optimal Sequencing |
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9 | (1) |
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Renaturation Kinetics of Plasmids After Heat Denaturation |
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10 | (1) |
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Denaturation of PCR Fragments of Various Sizes and Correlation with DNA Sequencing |
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10 | (5) |
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Buffer-Strength and Temperature Dependence of PCR Fragments Denaturation |
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15 | (1) |
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Renaturation Kinetics of PCR Fragments After Heat Denaturation |
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16 | (1) |
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Benefits of Heat Denaturation |
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17 | (8) |
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25 | (4) |
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Heat Denaturation Is an Effective Step in Sequencing of Many Difficult DNA Templates |
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29 | (36) |
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31 | (1) |
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Primer on Controlled Heat Denaturation of Plasmids |
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32 | (18) |
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Examples of Sequencing of Various Difficult Templates |
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50 | (4) |
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Sequencing of GC-Rich Templates |
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50 | (1) |
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Sequencing Regions Containing Various Repeats |
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50 | (1) |
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Sequencing of Regions with Hairpin Structures |
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51 | (1) |
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Sequencing Through Long Homopolymer Stretches |
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51 | (3) |
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Amplification of Difficult Regions with Various DNA Polymerases |
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54 | (1) |
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Isolation of Difficult Templates with Various Commercial Kits: Effect on Sequence Quality |
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54 | (4) |
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The World Wide Web as a Resource for Information on Sequencing of Difficult Templates |
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58 | (2) |
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60 | (5) |
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Solutions for Sequencing Difficult Regions |
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65 | (26) |
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65 | (1) |
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66 | (1) |
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66 | (4) |
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70 | (1) |
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70 | (2) |
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70 | (1) |
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71 | (1) |
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71 | (1) |
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71 | (1) |
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Cycle Sequencing Conditions |
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71 | (1) |
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72 | (1) |
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72 | (1) |
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72 | (14) |
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Templates with GC-Rich Region |
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73 | (1) |
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Polynucleotide-Repeats: Template #143, Template #58OR, and Template #513 |
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73 | (9) |
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Homopolymer Regions: Template #773 and Others |
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82 | (4) |
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86 | (2) |
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87 | (1) |
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Blending Works for Some Templates |
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87 | (1) |
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88 | (1) |
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88 | (3) |
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Improving Sequence Results from Difficult Templates with Phi 29 DNA Polymerase and Nucleotide Analogs: the TempliPhi™ Sequence Resolver Kit |
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91 | (18) |
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94 | (1) |
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94 | (12) |
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Non-Repetitive Sequences Composed of Just Two Nucleotides |
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100 | (4) |
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Homopolymer Repeat Sequences |
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104 | (2) |
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106 | (3) |
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Sequencing Through Various Secondary Structures: Detailed Studies of pDEST Vectors and Other DNA Templates with Hairpins |
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109 | (16) |
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110 | (1) |
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110 | (11) |
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Re-Sequencing of Other pDEST Vectors |
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117 | (1) |
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Sequencing of Other Hairpin Structures |
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118 | (3) |
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121 | (4) |
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Transcriptional Sequencing as a Tool for Reading Difficult-to-Read Templates |
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125 | (16) |
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126 | (10) |
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Overview of Transcriptional Sequencing |
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127 | (1) |
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Advantages of Transcriptional Sequencing |
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128 | (3) |
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Characteristics of Modified RNAP |
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131 | (1) |
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Sequencing of Difficult-to-Read Templates by the Transcriptional Sequencing Method |
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132 | (3) |
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Multiple Displacement Amplification (MDA)-TS |
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135 | (1) |
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136 | (5) |
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Bias-Free Cloning of ``Unclonable'' DNA for Simplified Genomic Finishing |
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141 | (22) |
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143 | (1) |
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Transcription-Free Cloning with the Linear pJAZZ Vector |
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143 | (1) |
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144 | (8) |
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144 | (2) |
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Cloning Large AT-Rich DNA |
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146 | (3) |
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Cloning Large GC-Rich DNA |
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149 | (1) |
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149 | (1) |
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Efficient Library Construction and Assembly |
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149 | (1) |
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Cloning of Large PCR Products |
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149 | (1) |
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150 | (2) |
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152 | (1) |
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Random Shear BAC Library Construction |
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152 | (4) |
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Random Shearing of Undigestable Genomic DNA |
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153 | (1) |
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Cloning Large Inserts in a Random Shear BAC Library |
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153 | (2) |
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Amplification of Copy Number in the Random Shear Library |
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155 | (1) |
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156 | (7) |
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Bioinformatics Tools to Aid Sequencing of Difficult Templates |
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163 | (16) |
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166 | (1) |
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167 | (8) |
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175 | (4) |
Index |
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179 | |