Homing Endonucleases: Methods and Protocols

1. Homing Endonucleases: From Genetic Anomalies to Programmable Genomic Clippers

Marlene Belfort and Richard P. Bonocora

2. Bioinformatic Identification of Homing Endonucleases and Their Target Sites

Eyal Privman

3. PCR-Based Bioprospecting for Homing Endonucleases in Fungal Mitochondrial rRNA Genes

Mohamed Hafez, Tuhin Kumar Guha, Chen Shen, Jyothi Sethuraman, and Georg Hausner

4. Mapping Homing Endonuclease Cleavage Sites Using In Vitro Generated Protein

Richard P. Bonocora and Marlene Belfort

5. Mapping Free-Standing Homing Endonuclease Promoters Using 5'RLM-RACE

Ewan A. Gibb

6. PCR Analysis of Chloroplast Double-Strand Break (DSB) Repair Products Induced by I-CreII in Chlamydomonas and Arabidopsis

Taegun Kwon, Obed W. Odom, Weihua Qiu, and David L. Herrin

7. A Two-Plasmid Bacterial Selection System for Characterization and Engineering of Homing Endonucleases

Ning Sun and Huimin Zhao

8. Rapid Screening of Endonuclease Target Site Preference Using a Modified Bacterial Two-Plasmid Selection

Jason M. Wolfs, Benjamin P. Kleinstiver, and David R. Edgell

9. A Yeast-Based Recombination Assay for Homing Endonuclease Activity

Jean-Charles Epinat

10. Rapid Determination of Homing Endonuclease DNA Binding Specificity Profile

Lei Zhao and Barry L. Stoddard

11. Quantifying the Information Content of Homing Endonuclease Target Sites by Single Base Pair Profiling

Joshua I. Friedman, Hui Li, and Raymond J. Monnat, Jr.

12. Homing Endonuclease Target Site Specificity Defined by Sequential Enrichment and Next-Generation Sequencing of Highly Complex Target Site Libraries

Hui Li and Raymond J. Monnat, Jr.

13. Homing Endonuclease Target Determination Using SELEX Adapted for Yeast Surface Display

Kyle Jacoby and Andrew M. Scharenberg

14. Engineering and Flow-Cytometric Analysis of Chimeric LAGLIDADG Homing Endonucleases from Homologous I-OnuI-Family Enzymes

Sarah K. Baxter, Andrew M. Scharenberg, and Abigail R. Lambert

15. Bioinformatics Identification of Coevolving Residues

Russell J. Dickson and Gregory B. Gloor

16. Identification and Analysis of Genomic Homing Endonuclease Target Sites

Stefan Pellenz and Raymond J. Monnat, Jr.

17. Redesigning the Specificity of Protein-DNA Interactions with Rosetta

Summer Thyme and David Baker