DNA Repair Protocols

ISBN-13: 9781617799976 / Angielski / Twarda / 2012 / 631 str.

Lotte Bjergb K.

Opis

Current knowledge of the mechanisms that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly successful Methods in Molecular Biology? series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, DNA Repair Protocols, Third Edition provides expert guidance for DNA repair, recombination, and replication.

Recenzje

From the book reviews:

"This book covers important aspects of the eukaryotic response to genomic insults and the most recent and advanced protocols on DNA repair, recombination, and replication. ... The intended audience is researchers in the field of DNA repair. In my judgment, graduate students, postdoctorals, and researchers in the field of molecular biology, especially those with a focus on DNA repair, will find this book extremely useful." (Omer Iqbal, Doody's Book Reviews, February, 2013)

Spis treści

1. DNA repair: Front and Center and Not Going Away!

Vilhelm A. Bohr

 

Part I. Identification of Repair Genes and Generation of Repair Mutants

 

2. Identification of Genes Required for Damage Survival using a Cell Based RNAi Screen against the Drosophila Genome

Dashnamoorthy Ravi and Alexander James Roy Bishop

 

3. Isolating Genes Involved with Genotoxic Drug Response in the Nematode Caenorhabditis elegans using Genome-wide RNAi Screening 

Lone Vedel Schøler, Tine Hørning Møller, Steffen Nørgaard, Lotte Vestergaard and Anders Olsen.

 

4. Establishment of the DNA Repair-defective Mutants in DT40 Cells

Masamichi Ishiai, Emi Uchida, and Minoru Takata

 

 

Part II. Assessing DNA Damage and Repair

 

5. Electrophoretic Mobility Shift Assays for

Protein-DNA Complexes Involved in DNA Repair

Chun Tsai, PhD, Vaughn Smider, Byung Joon Hwang,  and Gilbert Chu

 

6. The Comet Assay A Sensitive Genotoxicity Test for the Detection of DNA Damage and Repair

Günter Speit and Andreas Rothfuss

 

7. Detection of DNA Damage by Comet Fluorescence in situ Hybridization (Comet-FISH)

W. Schlörmann and M. Glei

 

8. Quantitative DNA Damage and Repair Measurement with the Yeast Comet Assay

Rui Oliveira and Björn Johansson

 

9. Analysis of DNA Damage and Repair in Nuclear and Mitochondrial DNA of Animal Cells using Quantitative PCR

Amy M. Furda,  Amanda Smith Bess,  Joel N. Meyer, Bennett Van Houten

 

Part III. Repair of Incorrect or Damaged DNA Bases

 

10. In vitro DNA Mismatch Repair in Human Cells

Liya Gu, Charles M. Ensor, and Guo-Min Li

 

11. Eukaryotic DNA Mismatch Repair in vitro

Fenghua Yuan, Limin Song, Fengsong Liu, Liya Gu, Yanbin Zhang

 

12.  Immuno-slot Blot Assay for Detection of UVR-mediated DNA Damage

Mahsa Karbaschi, Nigel J. Brady, Mark D. Evans, and Marcus S. Cooke

 

13.  Quantification of DNA Photoproductions in Mammalian Cell DNAUsing Radioimmunoassay

Thomas R. Berton and David L. Mitchell

 

14. Measuring the Formation and Repair of UV Damage at the DNA Sequence Level by Ligation-mediated PCR

Ahmad Besaratinia and Gerd P. Pfeifer

 

15. Construction of Plasmids Containing Site-specific DNA Interstrand Crosslinks for Biochemical and Cell Biological Studies

Milica Enoiu, The Vinh Ho, David T. Long, Johannes C. Walter, and Orlando D. Schärer

 

16. Replication-coupled DNA Interstrand Crosslink Repair in  Xenopus Egg Extracts

Puck Knipscheer, Markus Räschle, Orlando D. Schärer, and Johannes C. Walter

 

17.  In Vitro Base Excision Repair using Mammalian Cell Extracts

Jason L. Parsons and Grigory L. Dianov^,

 

18.  Using Arabidopsis Cell Extracts to Monitor Repair of DNA Base Damage in vitro

Dolores Córdoba-Cañero, Teresa Roldán-Arjona and Rafael R. Ariza

 

19.  In vitro monitoring of Base Excision Repair in Saccharomyces cerevisiae

Simone Moertl and Fred Ahne

 

20. Mitochondrial Base Excision Repair Assays

Ricardo Gredilla and Tinna Stevnsner

 

Part IV. DNA Strand Breakage and Repair

 

21. O-Hydroxylamine-Coupled Alkaline Gel Electrophoresis Assay for the Detection and Measurement of DNA Single-Strand Breaks

April M. Luke and Jun Nakamura

 

22.  DNA Double Stand Break Damage and Repair Assessed by Pulse-field Gel
Electrophoresis

Helen E. Bryant

 

23. Quantitative Amplification of Single Stranded DNA (QAOS)

Eva-Maria Holstein and David Lydall

 

24. Simple, Non-radioactive Measurement of Single-stranded DNA at Telomeric, Sub-telomeric and Genomic Loci in Budding Yeast

James M Dewar and David Lydall

 

25. Monitoring DNA Recombination Initiated by HO Endonuclease

Neal Sugawara and James E. Haber

 

26. Monitoring I-SceI Induced Double Strand Break Repair in DT40 Cells

David du Plessis and Julian E. Sale

 

27. I-SceI-based Assays to Examine Distinct Repair Outcomes of Mammalian Chromosomal Double Strand Breaks

Amanda Gunn and Jeremy M. Stark

 

28. Studying Repair of a Single Protein-bound Nick in vivo using the Flp-nick System

Ida Nielsen, Anni H. Andersen, and Lotte Bjergbæk

 

29. Measurement of Diversification in the Immunoglobulin Light Chain Gene of DT40 Cells

Julian E. Sale

 

30. Live cell microscopy of DNA damage response in Saccharomyces cerevisiae

Sonia Silva, Irene Gallina, Nadine Eckert-Boulet and Michael Lisby

 

31. Use of Gene Targeting to Study Recombination in Mammalian Cell DNA

Repair Mutants

Jennifer J. Rahn, Gerald M. Adair and Rodney S. Nairn

 

32. In vitro Rejoining of Double Strand Breaks in Genomic DNA

George Iliakis, Emil Mladenov and Nge Cheong

 

33. An In Vitro DNA Double-Strand Break Repair Assay Based on End Joining of Defined Duplex Oligonucleotides

Kamal Datta, Shubhadeep Purkayasth, Ronald D. Neumann, and Thomas A. Winters

 

 

Part V. DNA Damage Tolerance and Checkpoints

 

34. Assays of Bypass Replication of Genotoxic Lesions in Cell-Free Extracts

Nana Nikolaishvili-Feinberg and Marila Cordeiro-Stone

 

35. Quantitative Measurement of Translesion DNA Synthesis in Mammalian Cells

Omer Ziv, Noam Diamant, Sigal Shachar, Ayal Hendel and Zvi Livneh

 

36. Detection of PCNA Modifications in Saccharomyces cerevisiae

Adelina A. Davies and Helle D. Ulrich

 

37. In vitro PCNA Modification Assays

Joanne L. Parker and Helle D. Ulrich

 

38. Analysis of Inhibition of DNA Replication in Irradiated Cells using the SV40 Based in vitro assay of DNA Replication

George Iliakis, Emil Mladenov, Ya Wang and Hong Yan Wang

 

39. CHK1 Kinase Activity Assay

Hongyan Wang and Ya Wang

 

40. Histone H2AX Phosphorylation: A Marker for DNA Damage

Arishya Sharma Kamini Singh, and Alexandru Almasan