PCR protocols / edited by John M.S. Bartlett and David Stirling.

Contributor(s): Bartlett, John M. S | Stirling, David
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 226.Publisher: Totowa, N.J. : Humana Press, ©2003Edition: 2nd edDescription: 1 online resource (xvii, 545 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781592593842; 0896036421; 9780896036420; 1592593844; 1280842601; 9781280842603; 9786610842605; 6610842604Subject(s): Polymerase chain reaction -- Laboratory manuals | Polymerase Chain Reaction | Nucleic Acid Amplification Techniques | Genetic Techniques | Investigative Techniques | Analytical, Diagnostic and Therapeutic Techniques and Equipment | Réaction en chaîne de la polymérase -- Manuels de laboratoire | SCIENCE -- Life Sciences -- Biochemistry | Polymerase chain reaction | Polymerase kettingreactie | Wetenschappelijke technieken | Genética | Genética molecularGenre/Form: Electronic books. | Laboratory manuals. Additional physical formats: Print version:: PCR protocols.DDC classification: 572/.43 LOC classification: QP606.D46 | P3595 2003Other classification: 35.75 Online resources: Click here to access online
Contents:
A short history of the polymerase chain reaction / J.M. Bartlett and D. Stirling -- Pcr patent issues / P. Carroll and D. Casimir -- Equipping and establishing a pcr laboratory / S. McDonagh -- Quality control in pcr / D. Stirling -- Extraction of nucleic acid templates / J.M. Bartlett -- Extraction of DNA from whole blood / J.M. Bartlett and A. White -- DNA extraction from tissue / H. Pearson and D. Stirling -- Extraction of DNA from microdissected archival tissues / J.J. Going -- Rna extraction from blood / H. Pearson -- Rna extraction from frozen tissue / J.M. Bartlett -- Rna extraction from tissue sections / H. Pearson -- Dual DNA/rna extraction / D. Stirling and J.M. Bartlett -- DNA extraction from fungi, yeast, and bacteria / D. Stirling -- Isolation of rna viruses from biological materials / S. McDonagh -- Extraction of ancient DNA / W.M. Schmerer -- DNA extraction from plasma and serum / D. Stirling -- Technical notes for the detection of nucleic acids / J.M. Bartlett -- Technical notes for the recovery and purification of pcr products from acrylamide gels / D. Stirling -- Pcr primer design / D.L. Hyndman and M. Mitsuhashi -- Optimization of polymerase chain reactions / H. Grunenwald -- Subcycling pcr for long-distance amplifications of regions with high and low guanine-cystine content: Amplification of the intron 22 inversion of the fviii gene / D. Stirling -- Rapid amplification of cdna ends / X. Wang and W.S. Young, 3rd -- Randomly amplified polymorphic DNA fingerprinting: The basics / R.S. Dassanayake and L.P. Samaranayake -- Microsphere-based single nucleotide polymorphism genotyping / M.A. Iannone [and others] -- Ligase chain reaction / W.H. Benjamin, Jr., K.R. Smith and K.B. Waites -- Nested rt-pcr in a single closed tube / A. Olmos [and others] -- Direct pcr from serum: Application to viral genome detection / K. Abe -- Long pcr amplification of large fragments of viral genomes: A technical overview / R. Tellier [and others] -- Long pcr methodology / R. Tellier [and others] -- Qualitative and quantitative pcr: A technical overview / D. Stirling -- Ultrasensitive pcr detection of tumor cells in myeloma / F.W. Cremer and M. Moos -- Ultrasensitive quantitative pcr to detect rna viruses / S. McDonagh -- Quantitative pcr for camp ri alpha mrna: Use of site-directed mutation and pcr mimics / J.M. Bartlett -- Quantitation of multiple rna species / R. Kerr -- Differential display: A technical overview / J.M. Bartlett -- Au-differential display, reproducibility of a differential mrna display targeted to au motifs / O. Dominguez [and others] -- Pcr fluorescence differential display / K. Khalturin, S. Kuznetsov and T.C. Bosch -- Microarray analysis using rna arbitrarily primed pcr / S. Ringquist [and others] -- Oligonucleotide arrays for genotyping: Enzymatic methods for typing single nucleotide polymorphisms and short tandem repeats / S. Case-Green, C. Pritchard and E. Southern -- Serial analysis of gene expression / K.A. Oien -- Mutation and polymorphism detection: A technical overview / J. Edwards and J.M. Bartlett -- Combining multiplex and touchdown pcr for microsatellite analysis / K. Rithidech and J.J. Dunn -- Detection of microsatellite instability and loss of heterozygosity using DNA extracted from formalin-fixed paraffin-embedded tumor material by fluorescence-based multiplex microsatellite pcr / J. Edwards and J.M. Bartlett -- Reduction of shadow band synthesis during pcr amplification of repetitive sequences from modern and ancient DNA / W.M. Schmerer -- Degenerate oligonucleotide-primed pcr / M. Aubele and J. Smida -- Mutation detection using rt-pcr-rflp / H. Nakashima, M. Akahoshi and Y. Tanaka -- Multiplex amplification refractory mutation system for the detection of prothrombotic polymorphisms / D. Stirling -- Pcr-sscp analysis of polymorphism: A simple and sensitive method for detecting differences between short segments of DNA / M. Han and M.A. Robinson -- Sequencing: A technical overview / D. Stirling -- Preparation and direct automated cycle sequencing of pcr products / S.E. Daniels -- Nonradioactive pcr sequencing using digoxigenin / S. Kosel [and others] -- Direct sequencing by thermal asymmetric pcr / G.R. Mazars and C. Theillet -- Analysis of nucleotide sequence variations by solid-phase minisequencing / A. Suomalainen and A.C. Syvanen -- Direct sequencing with highly degenerate and inosine-containing primers / Z. Shen [and others] -- Determination of unknown genomic sequences without cloning / J.P. Quivy and P.B. Becker -- Cloning pcr products for sequencing in m13 vectors / D. Walsh -- DNA rescue by the vectorette method / M.A. McAleer, A.J. Coffey and I. Dunham -- Technical notes for sequencing difficult templates / D. Stirling -- Pcr-based detection of nucleic acids in chromosomes, cells, and tissues: Technical considerations on prins and in situ pcr and comparison with in situ hybridization / E.J. Speel, F.C. Ramaekers and A.H. Hopman -- Cycling primed in situ amplification / J.H. Bull and L. Paskins -- Direct and indirect in situ pcr / K.H. Wiedorn and T. Goldmann -- Reverse transcriptase in situ pcr: New methods in cellular interrogation / M. Gilchrist and A.D. Befus -- Primed in situ nucleic acid labeling combined with immunocytochemistry to simultaneously localize DNA and proteins in cells and chromosomes / E.J. Speel, F.C. Ramaekers and A.H. Hopman -- Cloning and mutagenesis: A technical overview / H. Pearson and D. Stirling -- Using t4 DNA polymerase to generate clonable pcr products / K. Wang -- A t-linker strategy for modification and directional cloning of pcr products / R.M. Horton, R. Raju and B.M. Conti-Fine -- Cloning gene family members using pcr with degenerate oligonucleotide primers / G.M. Preston -- Cdna libraries from a low amount of cells / P. Ravassard [and others] -- Creation of chimeric junctions, deletions, and insertions by pcr / G. Pont-Kingdon -- Recombination and site-directed mutagenesis using recombination pcr / D.H. Jones and S.C. Winistorfer -- Megaprimer pcr: Application in mutagenesis and gene fusion / E. Burke and S. Barik.
Action note: digitized 2010 committed to preserveSummary: Drawing on the proven qualities of the much praised and widely used first edition, John M.S. Bartlett and David Stirling have thoroughly updated and dramatically expanded the number of protocols to take advantage of the newest technologies used in all branches of research and clinical medicine today. These successful methods include real-time PCR, SNP analysis, nested PCR, direct PCR, and long-range PCR. Among the highlights are chapters on genome profiling by SAGE, differential display and chip technologies, the amplification of whole genome DNA by random degenerate oligonucleotide PCR, and the refinement of PCR methods for the analysis of fragmented DNA from fixed tissues. In situ PCR methods and their application in parallel with other methods, such as immunohistochemistry, are also included. Each fully tested protocol is described in step-by-step detail by an established expert in the field and includes a background introduction outlining the principle behind the technique, equipment and reagent lists, tips on troubleshooting and avoiding known pitfalls, and, where needed, a discussion of the interpretation and use of results. Cutting-edge and highly practical, PCR Protocols, Second Edition provides both novice and experienced investigators with an up-to-date compendium of powerful PCR methods for easy reference and consultation in the day-to-day performance of PCR-based experimentation, one that will enhance understanding of PCR, satisfy current needs, and point to powerful future applications.
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Includes bibliographical references and index.

A short history of the polymerase chain reaction / J.M. Bartlett and D. Stirling -- Pcr patent issues / P. Carroll and D. Casimir -- Equipping and establishing a pcr laboratory / S. McDonagh -- Quality control in pcr / D. Stirling -- Extraction of nucleic acid templates / J.M. Bartlett -- Extraction of DNA from whole blood / J.M. Bartlett and A. White -- DNA extraction from tissue / H. Pearson and D. Stirling -- Extraction of DNA from microdissected archival tissues / J.J. Going -- Rna extraction from blood / H. Pearson -- Rna extraction from frozen tissue / J.M. Bartlett -- Rna extraction from tissue sections / H. Pearson -- Dual DNA/rna extraction / D. Stirling and J.M. Bartlett -- DNA extraction from fungi, yeast, and bacteria / D. Stirling -- Isolation of rna viruses from biological materials / S. McDonagh -- Extraction of ancient DNA / W.M. Schmerer -- DNA extraction from plasma and serum / D. Stirling -- Technical notes for the detection of nucleic acids / J.M. Bartlett -- Technical notes for the recovery and purification of pcr products from acrylamide gels / D. Stirling -- Pcr primer design / D.L. Hyndman and M. Mitsuhashi -- Optimization of polymerase chain reactions / H. Grunenwald -- Subcycling pcr for long-distance amplifications of regions with high and low guanine-cystine content: Amplification of the intron 22 inversion of the fviii gene / D. Stirling -- Rapid amplification of cdna ends / X. Wang and W.S. Young, 3rd -- Randomly amplified polymorphic DNA fingerprinting: The basics / R.S. Dassanayake and L.P. Samaranayake -- Microsphere-based single nucleotide polymorphism genotyping / M.A. Iannone [and others] -- Ligase chain reaction / W.H. Benjamin, Jr., K.R. Smith and K.B. Waites -- Nested rt-pcr in a single closed tube / A. Olmos [and others] -- Direct pcr from serum: Application to viral genome detection / K. Abe -- Long pcr amplification of large fragments of viral genomes: A technical overview / R. Tellier [and others] -- Long pcr methodology / R. Tellier [and others] -- Qualitative and quantitative pcr: A technical overview / D. Stirling -- Ultrasensitive pcr detection of tumor cells in myeloma / F.W. Cremer and M. Moos -- Ultrasensitive quantitative pcr to detect rna viruses / S. McDonagh -- Quantitative pcr for camp ri alpha mrna: Use of site-directed mutation and pcr mimics / J.M. Bartlett -- Quantitation of multiple rna species / R. Kerr -- Differential display: A technical overview / J.M. Bartlett -- Au-differential display, reproducibility of a differential mrna display targeted to au motifs / O. Dominguez [and others] -- Pcr fluorescence differential display / K. Khalturin, S. Kuznetsov and T.C. Bosch -- Microarray analysis using rna arbitrarily primed pcr / S. Ringquist [and others] -- Oligonucleotide arrays for genotyping: Enzymatic methods for typing single nucleotide polymorphisms and short tandem repeats / S. Case-Green, C. Pritchard and E. Southern -- Serial analysis of gene expression / K.A. Oien -- Mutation and polymorphism detection: A technical overview / J. Edwards and J.M. Bartlett -- Combining multiplex and touchdown pcr for microsatellite analysis / K. Rithidech and J.J. Dunn -- Detection of microsatellite instability and loss of heterozygosity using DNA extracted from formalin-fixed paraffin-embedded tumor material by fluorescence-based multiplex microsatellite pcr / J. Edwards and J.M. Bartlett -- Reduction of shadow band synthesis during pcr amplification of repetitive sequences from modern and ancient DNA / W.M. Schmerer -- Degenerate oligonucleotide-primed pcr / M. Aubele and J. Smida -- Mutation detection using rt-pcr-rflp / H. Nakashima, M. Akahoshi and Y. Tanaka -- Multiplex amplification refractory mutation system for the detection of prothrombotic polymorphisms / D. Stirling -- Pcr-sscp analysis of polymorphism: A simple and sensitive method for detecting differences between short segments of DNA / M. Han and M.A. Robinson -- Sequencing: A technical overview / D. Stirling -- Preparation and direct automated cycle sequencing of pcr products / S.E. Daniels -- Nonradioactive pcr sequencing using digoxigenin / S. Kosel [and others] -- Direct sequencing by thermal asymmetric pcr / G.R. Mazars and C. Theillet -- Analysis of nucleotide sequence variations by solid-phase minisequencing / A. Suomalainen and A.C. Syvanen -- Direct sequencing with highly degenerate and inosine-containing primers / Z. Shen [and others] -- Determination of unknown genomic sequences without cloning / J.P. Quivy and P.B. Becker -- Cloning pcr products for sequencing in m13 vectors / D. Walsh -- DNA rescue by the vectorette method / M.A. McAleer, A.J. Coffey and I. Dunham -- Technical notes for sequencing difficult templates / D. Stirling -- Pcr-based detection of nucleic acids in chromosomes, cells, and tissues: Technical considerations on prins and in situ pcr and comparison with in situ hybridization / E.J. Speel, F.C. Ramaekers and A.H. Hopman -- Cycling primed in situ amplification / J.H. Bull and L. Paskins -- Direct and indirect in situ pcr / K.H. Wiedorn and T. Goldmann -- Reverse transcriptase in situ pcr: New methods in cellular interrogation / M. Gilchrist and A.D. Befus -- Primed in situ nucleic acid labeling combined with immunocytochemistry to simultaneously localize DNA and proteins in cells and chromosomes / E.J. Speel, F.C. Ramaekers and A.H. Hopman -- Cloning and mutagenesis: A technical overview / H. Pearson and D. Stirling -- Using t4 DNA polymerase to generate clonable pcr products / K. Wang -- A t-linker strategy for modification and directional cloning of pcr products / R.M. Horton, R. Raju and B.M. Conti-Fine -- Cloning gene family members using pcr with degenerate oligonucleotide primers / G.M. Preston -- Cdna libraries from a low amount of cells / P. Ravassard [and others] -- Creation of chimeric junctions, deletions, and insertions by pcr / G. Pont-Kingdon -- Recombination and site-directed mutagenesis using recombination pcr / D.H. Jones and S.C. Winistorfer -- Megaprimer pcr: Application in mutagenesis and gene fusion / E. Burke and S. Barik.

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Drawing on the proven qualities of the much praised and widely used first edition, John M.S. Bartlett and David Stirling have thoroughly updated and dramatically expanded the number of protocols to take advantage of the newest technologies used in all branches of research and clinical medicine today. These successful methods include real-time PCR, SNP analysis, nested PCR, direct PCR, and long-range PCR. Among the highlights are chapters on genome profiling by SAGE, differential display and chip technologies, the amplification of whole genome DNA by random degenerate oligonucleotide PCR, and the refinement of PCR methods for the analysis of fragmented DNA from fixed tissues. In situ PCR methods and their application in parallel with other methods, such as immunohistochemistry, are also included. Each fully tested protocol is described in step-by-step detail by an established expert in the field and includes a background introduction outlining the principle behind the technique, equipment and reagent lists, tips on troubleshooting and avoiding known pitfalls, and, where needed, a discussion of the interpretation and use of results. Cutting-edge and highly practical, PCR Protocols, Second Edition provides both novice and experienced investigators with an up-to-date compendium of powerful PCR methods for easy reference and consultation in the day-to-day performance of PCR-based experimentation, one that will enhance understanding of PCR, satisfy current needs, and point to powerful future applications.

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