Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

Sheng, Gang; Gogakos, Tasos; Wang, Jiuyu; Zhao, Hongtu; Serganov, Artem; Juranek, Stefan; Tuschl, Thomas; Patel, Dinshaw J.; Wang, Yanli

doi:10.1093/nar/gkx547

Title: Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

Journal Article · Tue Jun 27 00:00:00 EDT 2017 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkx547· OSTI ID:1430343

Sheng, Gang ^[1]; Gogakos, Tasos ^[2]; Wang, Jiuyu ^[1]; Zhao, Hongtu ^[3]; Serganov, Artem ^[2]; Juranek, Stefan ^[2]; Tuschl, Thomas ^[2]; Patel, Dinshaw J. ^[4]; Wang, Yanli ^[5]

Chinese Academy of Sciences (CAS), Beijing (China)
Rockefeller Univ., New York, NY (United States)
Chinese Academy of Sciences (CAS), Beijing (China); Univ. of Chinese Academy of Sciences, Beijing (China)
Memorial-Sloan Kettering Cancer Center, New York, NY (United States)
Chinese Academy of Sciences (CAS), Beijing (China); Univ. of Chinese Academy of Sciences, Beijing (China); Memorial-Sloan Kettering Cancer Center, New York, NY (United States); Collaborative Innovation Center of Genetics and Development, Shanghai (China)

We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6’U7’ and 6’A7’ on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6’N7’ bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson–Crick and reversed non-canonical flanking pairs. Furthermore, these structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: Natural Science Foundation of China; Chinese Ministry of Science and Technology; National Institutes of Health (NIH)

Grant/Contract Number:: 31571335; 31630015; 91440201; 2014CB910102; TR01 GM104962-01

OSTI ID:: 1430343

Journal Information:: Nucleic Acids Research, Vol. 45, Issue 15; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 15 works

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