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DNA Sequencing III: Dealing With Difficult Templates: Dealing with Difficult Templates [Kietas viršelis]

  • Formatas: Hardback, 184 pages, weight: 397 g
  • Išleidimo metai: 18-Apr-2008
  • Leidėjas: Jones and Bartlett Publishers, Inc
  • ISBN-10: 076374297X
  • ISBN-13: 9780763742973
Kitos knygos pagal šią temą:
  • Formatas: Hardback, 184 pages, weight: 397 g
  • Išleidimo metai: 18-Apr-2008
  • Leidėjas: Jones and Bartlett Publishers, Inc
  • ISBN-10: 076374297X
  • ISBN-13: 9780763742973
Kitos knygos pagal šią temą:
Sanger sequencing chemistry is already considered a mature technology, having produced complete sequencing of hundreds of microbial species and many higher organisms. Other technologies may be appearing on the horizon, but many researchers have neither the need nor the resources to make use of them at present. This collection is likely to make new technologies even less attractive in comparison to the Sanger method as contributors explain techniques researchers can use in the five to eight percent of cases in which the template proves to be difficult. The eight papers here cover controlled heat denaturation of DNA plasmids and PCR fragments, heat denaturation in sequence of difficult DNA templates, solutions for sequencing difficult regions, improving sequencing results with a commercially available sequence resolver kit, sequencing through secondary structures, transcriptional sequencing as a tool for reading, bas-free cloning of "unclonable" DNA for simplified genomic finishing, and bioinformatics tools to aid sequencing. Annotation ©2008 Book News, Inc., Portland, OR (booknews.com)
Contributors ix
Preface xi
Foreword xvi
Controlled Heat-Denaturation of DNA Plasmids and PCR Fragments
1(28)
Jan Kieleczawa
Experimental Design
4(13)
DNA Sequencing
4(1)
Temperature-Dependence of Plasmid Denaturation
5(1)
Buffer-Strength Dependence of Plasmid Denaturation
6(1)
Time Course of Heat-Denaturation of DNA Plasmids of Varying Sizes
6(2)
Denaturation of Plasmids Containing a Difficult Region
8(1)
Amount of DNA Needed for Optimal Sequencing
9(1)
Renaturation Kinetics of Plasmids After Heat Denaturation
10(1)
Denaturation of PCR Fragments of Various Sizes and Correlation with DNA Sequencing
10(5)
Buffer-Strength and Temperature Dependence of PCR Fragments Denaturation
15(1)
Renaturation Kinetics of PCR Fragments After Heat Denaturation
16(1)
Benefits of Heat Denaturation
17(8)
Conclusions
25(4)
Heat Denaturation Is an Effective Step in Sequencing of Many Difficult DNA Templates
29(36)
Jan Kieleczawa
Materials and Methods
31(1)
Primer on Controlled Heat Denaturation of Plasmids
32(18)
Examples of Sequencing of Various Difficult Templates
50(4)
Sequencing of GC-Rich Templates
50(1)
Sequencing Regions Containing Various Repeats
50(1)
Sequencing of Regions with Hairpin Structures
51(1)
Sequencing Through Long Homopolymer Stretches
51(3)
Amplification of Difficult Regions with Various DNA Polymerases
54(1)
Isolation of Difficult Templates with Various Commercial Kits: Effect on Sequence Quality
54(4)
The World Wide Web as a Resource for Information on Sequencing of Difficult Templates
58(2)
Summary
60(5)
Solutions for Sequencing Difficult Regions
65(26)
Alicia Yang
GC-Rich Regions
65(1)
Polynucleotide Repeats
66(1)
Homopolymer Regions
66(4)
Solutions
70(1)
Materials and Methods
70(2)
Formulations
70(1)
Blending
71(1)
Dilutions
71(1)
Templates
71(1)
Cycle Sequencing Conditions
71(1)
Electrophoresis
72(1)
Analysis Methods
72(1)
Results
72(14)
Templates with GC-Rich Region
73(1)
Polynucleotide-Repeats: Template #143, Template #58OR, and Template #513
73(9)
Homopolymer Regions: Template #773 and Others
82(4)
Discussion
86(2)
Do Not Dilute
87(1)
Blending Works for Some Templates
87(1)
Primer Proximity
88(1)
Conclusion
88(3)
Improving Sequence Results from Difficult Templates with Phi 29 DNA Polymerase and Nucleotide Analogs: the TempliPhi™ Sequence Resolver Kit
91(18)
Haiguang Xiao
Carl W. Fuller
Materials and Methods
94(1)
Results
94(12)
Non-Repetitive Sequences Composed of Just Two Nucleotides
100(4)
Homopolymer Repeat Sequences
104(2)
Discussion
106(3)
Sequencing Through Various Secondary Structures: Detailed Studies of pDEST Vectors and Other DNA Templates with Hairpins
109(16)
Tony Li
Mostafa Ait-Zahra
Paul Wu
Jan Kieleczawa
Materials and Methods
110(1)
Results and Discussion
110(11)
Re-Sequencing of Other pDEST Vectors
117(1)
Sequencing of Other Hairpin Structures
118(3)
Conclusions
121(4)
Transcriptional Sequencing as a Tool for Reading Difficult-to-Read Templates
125(16)
Masanori Suzuki
Materials and Methods
126(10)
Overview of Transcriptional Sequencing
127(1)
Advantages of Transcriptional Sequencing
128(3)
Characteristics of Modified RNAP
131(1)
Sequencing of Difficult-to-Read Templates by the Transcriptional Sequencing Method
132(3)
Multiple Displacement Amplification (MDA)-TS
135(1)
Conclusions
136(5)
Bias-Free Cloning of ``Unclonable'' DNA for Simplified Genomic Finishing
141(22)
Ronald Godiska
David Mead
Vinay Dhodda
Rebecca Hochstein
Attila Karsi
Nikolai Ravin
Chengcang Wu
Materials and Methods
143(1)
Transcription-Free Cloning with the Linear pJAZZ Vector
143(1)
Results
144(8)
Vector Construction
144(2)
Cloning Large AT-Rich DNA
146(3)
Cloning Large GC-Rich DNA
149(1)
Repetitive DNA
149(1)
Efficient Library Construction and Assembly
149(1)
Cloning of Large PCR Products
149(1)
Lack of Size Bias
150(2)
Size Limit of Inserts
152(1)
Random Shear BAC Library Construction
152(4)
Random Shearing of Undigestable Genomic DNA
153(1)
Cloning Large Inserts in a Random Shear BAC Library
153(2)
Amplification of Copy Number in the Random Shear Library
155(1)
Summary
156(7)
Bioinformatics Tools to Aid Sequencing of Difficult Templates
163(16)
Jan Kieleczawa
Bharath Lakshmanan
Donald Koffman
Aaron Kitzmiller
GC Module
166(1)
Examine Repeats Module
167(8)
Summary
175(4)
Index 179
Dr. Jan Kieleczawa earned his masters and Ph.D. degrees from the University of Wroclaw (Poland) and his M.B.A. from Oakdale College. Currently, he heads the DNA Sequencing Group at Wyeth Research in Cambridge, MA. His research interest involve developing methods of sequencing numerous types of difficult DNA templates.