Chapter title |
Probing Hfq:RNA Interactions with Hydroxyl Radical and RNase Footprinting.
|
---|---|
Chapter number | 24 |
Book title |
RNA Remodeling Proteins
|
Published in |
Methods in molecular biology, January 2015
|
DOI | 10.1007/978-1-4939-2214-7_24 |
Pubmed ID | |
Book ISBNs |
978-1-4939-2213-0, 978-1-4939-2214-7
|
Authors |
Ellis MJ, Trussler RS, Ross JA, Haniford DB, Michael J. Ellis, Ryan S. Trussler, Joseph A. Ross, David B. Haniford |
Abstract |
RNA footprinting and structure probing techniques are used to characterize the interaction between RNA-binding proteins and RNAs in vitro. Hydroxyl radical footprinting results in the identification of protein binding site(s) in an RNA. Ribonuclease (RNase) structure probing is a complementary technique that also provides information about protein binding sites, as well as RNA structure and possible protein-directed RNA remodeling. Here we provide a comprehensive protocol for studying the interaction between Hfq and an mRNA or sRNA of interest using a combination of RNase A, T1, and V1 as well as hydroxyl radical footprinting techniques. Detailed protocols for in vitro synthesis of (32)P-labeled RNA; formation of Hfq:RNA binary complex(es), RNase, and hydroxyl radical footprinting; preparation and running of sequencing gels; and data analysis are provided. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 1 | 100% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 1 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 9 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 2 | 22% |
Student > Ph. D. Student | 1 | 11% |
Unspecified | 1 | 11% |
Student > Bachelor | 1 | 11% |
Student > Doctoral Student | 1 | 11% |
Other | 0 | 0% |
Unknown | 3 | 33% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 3 | 33% |
Agricultural and Biological Sciences | 2 | 22% |
Unspecified | 1 | 11% |
Unknown | 3 | 33% |