9780763733834

DNA Sequencing II: Optimizing Preparation and Cleanup

by
  • ISBN13:

    9780763733834

  • ISBN10:

    0763733830

  • Edition: 1st
  • Format: Hardcover
  • Copyright: 2006-02-25
  • Publisher: Jones & Bartlett

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Summary

Kieleczawa's second volume, DNA Sequencing II:  Optimizing the Preparation and Clean-Up, is devoted to the various methods used for extraction, clean-up, quantification, and analysis of DNA.  This volume is divided into four comprehensive sections - DNA Purification, Clean-up of DNA Fragments, Storage of DNA, and Quantifying DNA and RNA - and offers the reader an in-depth presentation of DNA technologies.  The text also touches upon the many tools and software programs that are found in a typical modern biology laboratory.  This fascinating text is a wonderful addition to your molecular biology library.

Table of Contents

Contributors xiv
Preface xvii
Foreword by Richard A. Gibbs xx
Chapter 1. Preparation of Difficult DNA Templates Using Seven Different Commercial Methods 1(14)
Jan Kieleczawa, Tony Li, and Paul Wu
Materials and Methods
2(3)
DNA Sequencing
4(1)
Results and Discussion
5(7)
Conclusions
12(3)
Chapter 2. Isolation and Use of Bacterial and P1 Bacteriophage-Derived Artificial Chromosomes 15(18)
Miguel A. Gama Sosa, Rita De Gasperi, and Gregory A. Elder
DNA Sequencing
16(1)
Transfection into Cultured Cells
17(3)
Animal Transgenesis
20(1)
Plant Transgenesis and Transformation
21(1)
Retrofitting of BAC and PAC DNAs
22(3)
Future Directions
25(1)
Conclusions
26(7)
Chapter 3. Preparation of Genomic DNA from Animal Tissues 33(14)
Gary E. Truett
Alkaline Lysis Protocols
33(6)
Proteinase K Digestion
39(1)
Isolation of High Molecular Weight DNA from Proteinase K Digests
40(1)
Isolation of DNA from Proteinase K Digests without Organic Solvents
41(1)
Isolation of Genomic DNA with Gaunidinium Salts
42(1)
Isolation of Fetal DNA from Maternal Blood
43(1)
Preparation of Genomic DNA for In Silico Hybridization
44(3)
Chapter 4. Extraction of Genomic DNA from Plant Tissues 47(14)
Zhanguo Xin and Junping Chen
Plant Materials and Reagents
48(1)
Plant Materials
48(1)
Chemicals
48(1)
Solutions and Buffers for the CTAB Method
48(1)
Solutions and Buffers for the High-Throughput Method
49(1)
Solutions and Buffers for the Commercial Kits
49(1)
PCR Conditions
49(1)
CTAB Method
49(3)
Principle
49(1)
Procedure
50(1)
Advantages of the CTAB Method
51(1)
Disadvantages of the CTAB Method
52(1)
Commercial Kits for DNA Extraction from Plants
52(2)
Principle
52(1)
Advantages and Disadvantages of Commercial Kits
52(2)
A Simple HTP DNA Extraction Method Suitable for PCR
54(4)
Principle
54(1)
Procedure
55(1)
Advantages of the Simple High-Throughput Method
56(1)
Disadvantages of the Simple HTP Method
57(1)
Conclusions
58(3)
Chapter 5. Preparation of cDNA Probes for DNA Microarrays 61(24)
Peter R. Hoyt, Mitchel J. Doktycz, and Lois Tack
Materials and Methods
62(5)
Reagents and Supplies
62(1)
Instrument Description/Configuration
63(1)
Plasmid Preparation
63(1)
PCR Product Preparation
64(1)
Gel Electrophoresis
65(1)
DNA Quantitation
65(1)
Sample Tracking
66(1)
Microarray Production and Analysis
66(1)
Results
67(13)
Discussion
80(5)
Chapter 6. Isolation of Nucleic Acids from Paraffin-Embedded Archival Tissues and Other Difficult Sources 85(14)
Evgeny N. Imyanitov, Evgeny N. Suspitsin, Konstantin G. Busby, Ekatherina Sh. Kuligina, Evgeniya V. Belogubova, Alexandr V. Togo, and Kaido P. Hanson
DNA Isolation
86(5)
Summary of Our Experience
88(3)
RNA Isolation
91(1)
Summary of Our Experience
92(1)
Protocols
92(8)
Protocol 1. Preparation of DNA-Containing Lysates from Formalin-Fixed Paraffin-Embedded Tissue Sections
92(1)
Protocol 2. Phenol-Chloroform Extraction of DNA from Formalin-Fixed Paraffin-Embedded Tissue Sections
93(1)
Protocol 3. Taq Polymerase-Driven Restoration of Partially Degraded DNA from Formalin-Fixed Paraffin-Embedded Tissue Sections
94(1)
Protocol 4. RNA Extraction from Formalin-Fixed Paraffin-Embedded Tissue Sections
94(5)
Chapter 7. Comparison of Sequencing Data for DNAs Prepared Using TempliPhi Technology and Using Traditional Preparation Protocols 99(10)
Richard Sheldon, Lloydia Reynolds, Markryan Dwyer, and Jan Kieleczawa
Materials and Methods
100(2)
DNA Isolation from Saturated Cultures
100(1)
TempliPhi DNA Amplification
101(1)
Characterization of DNA
101(1)
DNA Sequencing
101(1)
Results and Discussion
102(4)
Media Effects on the DNA Quantity
102(1)
Media Effects on a Phred Q > or equal to; 20 Score
103(2)
Effects of Denaturation Temperature and Time on Sequence Quality of TempliPhi-Derived DNA Templates from Colonies
105(1)
Summary
106(3)
Chapter 8. Whole Genome Amplification Using the Multiple Displacement Amplification Reaction 109(18)
Roger S. Lasken
A Brief History of Whole Genome Amplification Methods
111(1)
Multiple Displacement Amplification
112(2)
Laboratory Protocols for Whole Genome Amplification with MDA
114(3)
Sources of DNA Templates
114(3)
MDA Reaction Protocols
117(2)
Required Reagents and Materials
117(1)
Notes
118(1)
Commercial Whole Genome Amplification Kits
119(3)
Whole Genome Amplification Using Purified Genome DNA: 50μL MDA Reaction Volume
119(2)
Whole Genome Amplification from Blood or Cells: 50μL MDA Reaction Volume
121(1)
Troubleshooting Guide
122(5)
Genomic DNA Protocol 123 Blood and Cell Protocol
123(1)
Whole Genome Amplification from Other Biological Sample Types
124(3)
Chapter 9. Solid-Phase Nucleic Acid Purification Using Magnetic Beads 127(42)
Kevin McKernan and Erik Gustafson
Solid-Phase Nuleic Acid Purification
127(2)
Advantages of Magnetic Bead Purification in a Large Scale Sequencing Pipeline
129(2)
Throughput and Automation
129(2)
Universal Applicability of Magnetic Bead-Based Pipelines
131(1)
Description of SPRI Technologies
132(6)
Critical Factors to Magnetic Bead-Based Assays
138(1)
Selected Applications of SPRI Technology
138(18)
Plasmid Purification
138(1)
RNA Purification
139(9)
Genomic DNA Isolation
148(8)
Extending the Applications for SPRI: Bifunctional SPRI Beads
156(4)
Endotoxin Removal
160(3)
Summary
163(1)
Materials and Methods
163(6)
Chapter 10. The Sanger Institute High-Throughput Sequencing Pipeline 169(32)
Anthony P. West, Christopher M. Clee, and Jane Rogers
Materials, Software, and Equipment
171(1)
Software
172(1)
Automation Pipelines
172(3)
Liquid Handling Automation Equipment
175(4)
Colony Picking Robots
175(1)
Liquid Handling Robots
176(3)
Protocol Development
179(2)
Plasmid Isolation
181(5)
Thermal Cycling
186(6)
Labeled Sample Detection
192(1)
Sample Tracking
193(3)
Conclusion
196(5)
Chapter 11. Comparison of PCR Product Clean-Up Methods for High-Throughput Capillary Electrophoresis 201(18)
Darryl L. Irvin and Keith R. Mitchelson
Materials and Methods
202(1)
Product Cleanup
203(2)
Dilution (Diln)
203(1)
Sephadex Cleanup (Seph)
203(1)
Magnetic Bean Cleanup (MagB)
204(1)
MgSO4/Ethanol Cleanup (Mg/Eth)
205(1)
Results
205(9)
Discussion
214(5)
Chapter 12. Evaluation of Methods for Cleanup of DNA Sequencing Reactions 219(22)
Jan Kieleczawa and Katarzyna Bajson
Materials and Methods
220(3)
DNA Sequencing
222(1)
Result and Discussion
223(7)
Clean-Up Procedures
223(1)
Pre-Made Clean-Up Plates
223(2)
In-House–Prepared Clean-Up Plates
225(2)
Purification Using Magnetic Beads
227(1)
Alcohol Precipitation Clean-Up Procedures
227(3)
Stability of the Read Lengths and Signal Strength Over Time
230(1)
Repetitive Use of the Same Filter Plate
231(1)
Effects of Amount of DNA on Read Length and Signal Strength
231(1)
First Correctly Called Base and Error Distribution
232(4)
Dye-Terminator BigDye Dilution Limits
236(1)
Conclusions
236(5)
Chapter 13. Thermostable DNA Polymerases for a Wide Spectrum of Applications: Comparison of a Robust Hybrid TopoTaq to Other Enzymes 241(18)
Andrey R. Pavlov, Nadejda V. Pavlova, Sergei A. Kozyavkin, and Alexei I. Slesarev
Materials and Methods
242(1)
Examples of the Enzyme Activities
243(12)
Example 1: Comparison of Strand Displacement Activity of TopoTaq, AmpliTaq, and Stoffel Fragment
243(1)
Example 2: Dye Terminator Cycle Sequencing Using TopoTaqSq
243(2)
Example 3: PCR Amplification from G-C–Rich Templates with TopoTaq DNA Polymerase
245(2)
Example 4: PCR from Human Genomic DNA
247(1)
Example 5: Specific PCR Using DNA Amplified with Random Hexamer Primers
248
Example 6: Direct PCR DNA Amplification from Bacterial Cultures with TopoTaq DNA Polymerase
245(6)
Example 7: Production of Modified DNA with TopoTaq DNA Polymerase by PCR Amplification
251(4)
Discussion
255(4)
Chapter 14. Prolonged Storage of Plasmid DNAs Under Different Conditions: Effects on Plasmid Integrity, Spectral Characteristics and DNA Sequence Quality 259(16)
Jan Kieleczawa and Paul Wu
Materials
260(1)
Methods
261(2)
DNA Sequencing
261(1)
Agarose Gel Electrophoresis
262(1)
Spectral Analysis
263(1)
Results and Discussion
263(12)
Chapter 15. The DNA Book™: A New Method to Store and Distribute Genome Resources 275(16)
Midori Kobayashi and Yoshihide Hayashizaki
DNABook™ Technology
276(3)
Concept
276(3)
Materials and Methods
279(1)
Paper for DNA Printing
279(1)
Plasmid Preparation
279(1)
Polymerase Chain Reaction
279(1)
Recovery of Spotted DNA
279(1)
The Spotted DNA: Preservation of DNABooks
280(1)
Manufacturing the DNABook
281(1)
Printing the DNA
281(1)
Trial Production
281(5)
First DNA Sheet Published in Genome Research
281(5)
Examples of DNABooks
Progress and Problems of DNABooks
286(1)
Progress and Potential Applications of the DNABook
286(1)
FTA® Technology
286(2)
Future Considerations
288(3)
Chapter 16. Assessing the Quantity, Purity, and Integrity of RNA and DNA Following Nucleic Acid Purification 291(22)
William W. Willfinger, Karol Mackey, and Piotr Chomczynski
Overview of the Instruments and Criteria Employed to Assess the Quality of Nucleic Acid Extracts
292(1)
Assessment of Nucleic Acid Purity and Content by Spectrophotometric Methods: Theory and Assumptions
293(6)
Nucleic Acid Quantitation
299(3)
Nucleic Acid Integrity
302(1)
An Additional Absorbance Measurement Improves Nucleic Acid Purity Assessment
303(2)
Suitability of Spectrophotometric Absorbance Measurements for Evaluating Nucleic Acid Purity
305(3)
Assessment of Nucleic Acid Extracts: Summary and Conclusions
308(5)
Chapter 17. Essential Software and Other Tools Used in Modern Biology Laboratories 313(41)
Jan Kieleczawa, Deven Atnoor, Russ Carmical, Andrew Hill, Fei Lu, Ken Paynter, and Paul Wu
Determination of Quantity and Quality of DNA
314(8)
EDAS 290 Imaging System
314(8)
Databases to Store and Analyze DNA Information
322(2)
Sequence Analysis Packages
324(15)
Sequencher™: Software Overview
324(1)
Mutation Surveyor™: Software Overview
324(8)
SeqScape® Software: Overview
332(3)
Vector NTI
335(3)
DNASTAR
338(1)
Sequence Repository Databases
339(15)
Spotfire
343(2)
Ingenuity Pathways Analysis
345(1)
Other Tools
346(8)
Index 354

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