Argonaute bypasses cellular obstacles without hindrance during target search
Thijs Cui (Kavli institute of nanoscience Delft)
Misha Klein (TU Delft - BN/Chirlmin Joo Lab)
Jorrit W. Hegge (Wageningen University & Research)
Stanley D. Chandradoss (TU Delft - BN/Chirlmin Joo Lab, Kavli institute of nanoscience Delft)
John van der Oost (Wageningen University & Research)
Martin Depken (Kavli institute of nanoscience Delft, TU Delft - BN/Martin Depken Lab)
Chirlmin Joo (Kavli institute of nanoscience Delft, TU Delft - BN/Chirlmin Joo Lab)
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Abstract
Argonaute (Ago) proteins are key players in both gene regulation (eukaryotes) and host defense (prokaryotes). Acting on single-stranded nucleic-acid substrates, Ago relies on base pairing between a small nucleic-acid guide and its complementary target sequences for specificity. To efficiently scan nucleic-acid chains for targets, Ago diffuses laterally along the substrate and must bypass secondary structures as well as protein barriers. Using single-molecule FRET in conjunction with kinetic modelling, we reveal that target scanning is mediated through loose protein-nucleic acid interactions, allowing Ago to slide short distances over secondary structures, as well as to bypass protein barriers via intersegmental transfer. Our combined single-molecule experiment and kinetic modelling approach may serve as a platform to dissect search processes and study the effect of sequence on search kinetics for other nucleic acid-guided proteins.
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