Abstract:
:To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) 'seed' region and performed all-atom molecular dynamics simulations of the resulting Ago-miRNA:mRNA ternary complexes. Our simulations reveal that many modifications, including combinations of multiple G:U wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuations that do not affect overall complex stability. These results are further supported by analyses of HITS-CLIP data. Lastly, introduction of disruptive mutations revealed a bending motion of the PAZ domain along the L1/L2 'hinge' and a subsequent opening of the nucleic-acid-binding channel. Our findings suggest that the spectrum of a miRNA's admissible targets is different from what is currently anticipated by the canonical seed-model. Moreover, they provide a likely explanation for the previously reported sequence-dependent regulation of unintended targeting by siRNAs.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Xia Z,Clark P,Huynh T,Loher P,Zhao Y,Chen HW,Ren P,Rigoutsos I,Zhou Rdoi
10.1038/srep00569subject
Has Abstractpub_date
2012-01-01 00:00:00pages
569issn
2045-2322journal_volume
2pub_type
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