AI Article Synopsis
- RNA plays a critical role in various biological functions, but pinpointing its effective sequences and structures is challenging.
- The new method called mutational interference mapping experiment (MIME) allows researchers to determine the key sequences and structures of RNA at a single-nucleotide level through random mutagenesis, functional selection, and next-gen sequencing.
- Using MIME, researchers successfully identified how the HIV-1 Pr55(Gag) protein binds to the viral genomic RNA, revealing important base-pairing patterns and RNA structural motifs necessary for this interaction.
Article Abstract
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.
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| http://dx.doi.org/10.1038/nmeth.3490 | DOI Listing |
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