In recent years, much information has been revealed concerning the essential role of helicases, the enzymes that utilize the energy derived from nucleoside triphosphate hydrolysis to unwind the double stranded helical structure of nucleic acids. In this book, the topic is explored by leading international scientists who have contributed significantly to our current understanding of helicases and the ways in which they function. Chapters include methods for the production and purification of helicases from different species, as well as detailed studies of helicase activities, including NTP binding and hydrolysis, nucleic acid binding and unwinding, and translocation along nucleic acid substrates.
Contents Preface Contributors Helicases: An overview Mohamed Abdelhaleem Fluorescent biosensors to investigate helicase activity Martin Webb Single molecule FRET analysis of helicase functions Eli Rothenberg and Taekjip Ha Kinetics of Motor Protein Translocation on Single Stranded DNA Christopher Fischer, Lake Wooten, Eric Tomko and Timothy Lohman Experimental and computational analysis of DNA unwinding and polymerization kinetics Manjula Pandey, Mikhail Levin and Smita Patel Protein displacement by helicases Laxmi Yeruva and Kevin Raney In vivo Investigation of Protein-Protein Interactions for Helicases Using Tandem Affinity Purification Matthew Jessulat, Terry Buist, Md Alamgir, Mohsen Hooshyar, Jianhua Xu, Hiroyuki Aoki, M. Clelia Ganoza, Gareth Butland and Ashkan Golshani Mapping genomic targets of DNA helicases by chromatin immunoprecipitation in Saccharomyces cerevisiae Jennifer Cobb and Haico van Attikum Methods to Study How Replication Fork Helicases Unwind DNA Daniel L. Kaplan and Irina Bruck Simple enzymatic assays for the in vitro motor activity of transcription termination factor Rho from Escherichia coli Marc Boudvillain, Celine Walmacq, Annie Schwartz and Frederique Jacquinot Single-molecule studies of RecBCD Thomas Perkins and Hung-Wen Li Mutational analysis of Bloom helicase Xu Guang Xi In vivo analysis of Drosophila BLM helicase function during DNA double-strand gap repair Mitch McVey Purification and characterization of RecQ helicases of plants Daniela Kobbe, Manfred Focke and Holger Puchta Fluorometric assay of hepatitis C virus NS3 helicase activity Mariusz Krawczyk, Anna Stankiewicz-Drogon, Anne-Lise Haenni and Anna Boguszewska-Chachulska A Method to Simultaneously Monitor Hepatitis C Virus NS3 Helicase and Protease Activities David Frick, Olya Ginzburg and Angela Lam Computer Modeling of Helicases Using Elastic Network Model Wenjun Zheng Duplex unwinding with DEAD-box proteins Eckhard Jankowsky and Andrea Putnam Analysis of the RNA helicase p68 (Ddx5) as a transcriptional regulator Samantha Nicol and Frances Fuller-Pace A method to study the role of DDX3 RNA helicase in HIV-1 Chia-Yen Chen, Venkat Yedavalli and Kuan-The Jeang Molecular characterization of nuclear DNA helicase II (RNA helicase A) Suisheng Zhang and Frank Grosse Regulation of inter- and intramolecular interaction of RNA, DNA and proteins by MLE Hyangyee Oh, Andrew Parrott, Yongkyu Park and Chee-Gun Lee Biochemical characterization of human Upf1 helicase Zhihong Cheng, Gaku Morisawa and Haiwei Song Assays of the helicase, ATPase and exoribonuclease activities of the yeast mitochondrial degradosome. Michal Malecki, Piotr Stepien, Pawel Golik Characterization of the Helicase Activity and Anti-Telomerase Properties of Yeast Pif1p in vitro Jean-Baptiste Boule and Virginia A. Zakian A method to confer salinity stress tolerance to plants by helicase overexpression Narendra Tuteja A method to inhibit the growth of Plasmodium falciparum by double-stranded RNA-mediated gene silencing of helicases Renu Tuteja
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