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Mutational interference mapping experiment (MIME) for studying RNA structure and function

Smyth, Redmond P., Despons, Laurence, Huili, Gong, Bernacchi, Serena, Hijnen, Marcel, Mak, Johnson, Jossinet, Fabrice, Weixi, Li, Paillart, Jean-Christophe, von Kleist, Max and Marquet, Roland 2015, Mutational interference mapping experiment (MIME) for studying RNA structure and function, Nature methods, vol. 12, no. 9, pp. 866-872, doi: 10.1038/nmeth.3490.

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Title Mutational interference mapping experiment (MIME) for studying RNA structure and function
Author(s) Smyth, Redmond P.
Despons, Laurence
Huili, Gong
Bernacchi, Serena
Hijnen, Marcel
Mak, JohnsonORCID iD for Mak, Johnson orcid.org/0000-0002-5229-5707
Jossinet, Fabrice
Weixi, Li
Paillart, Jean-Christophe
von Kleist, Max
Marquet, Roland
Journal name Nature methods
Volume number 12
Issue number 9
Start page 866
End page 872
Total pages 7
Publisher Nature Publishing Group
Place of publication New York, NY
Publication date 2015-09
ISSN 1548-7105
Keyword(s) Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Biochemistry & Molecular Biology
HUMAN-IMMUNODEFICIENCY-VIRUS
HIV-1 RNA
PROTEIN INTERACTIONS
GENOME DIMERIZATION
BINDING-SPECIFICITY
SECONDARY STRUCTURE
MINIMAL REGION
TYPE-1 GAG
SEQUENCE
IDENTIFICATION
Summary RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.
Language eng
DOI 10.1038/nmeth.3490
Field of Research 110804 Medical Virology
Socio Economic Objective 920109 Infectious Diseases
HERDC Research category C1 Refereed article in a scholarly journal
Grant ID NHMRC 1025273
NHMRC 543107
ARC FT100100297
Copyright notice ©2015, Nature Publishing Group
Persistent URL http://hdl.handle.net/10536/DRO/DU:30078126

Document type: Journal Article
Collection: School of Medicine
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Created: Thu, 22 Oct 2015, 10:08:13 EST

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