NDLI: Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel

Content Provider	PubMed Central
Author	Zhang, Xinyue Xu, Xiaojun Yang, Zhiyu Burcke, Andrew J. Gates, Kent S. Chen, Shi-jie Gu, Li-qun
Abstract	Pseudoknots are a fundamental RNA tertiary structure with important roles in regulation of mRNA translation. Molecular force spectroscopic approaches such as optical tweezers can track the pseudoknot’s unfolding intermediate states by pulling the RNA chain from both ends, but the kinetic unfolding pathway induced by this method may be different from that in vivo, which occurs during translation and proceeds from the 5′ to 3′ end. Here we developed a ribosome-mimicking, nanopore pulling assay for dissecting the vectorial unfolding mechanism of pseudoknots. The pseudoknot unfolding pathway in the nanopore, either from the 5′ to 3′ end or in the reverse direction, can be controlled by a DNA leader that is attached to the pseudoknot at the 5′ or 3′ ends. The different nanopore conductance between DNA and RNA translocation serves as a marker for the position and structure of the unfolding RNA in the pore. With this design, we provided evidence that the pseudoknot unfolding is a two-step, multistate, metal ion-regulated process depending on the pulling direction. Most notably, unfolding in both directions is rate-limited by the unzipping of the first helix domain (first step), which is Helix-1 in the 5′ → 3′ direction and Helix-2 in the 3′ → 5′ direction, suggesting that the initial unfolding step in either pulling direction needs to overcome an energy barrier contributed by the noncanonical triplex base-pairs and coaxial stacking interactions for the tertiary structure stabilization. These findings provide new insights into RNA vectorial unfolding mechanisms, which play an important role in biological functions including frameshifting.
Related Links	http://dx.doi.org/10.1021/jacs.5b07910
Ending Page	15752
Page Count	11
Starting Page	15742
File Format	PDF
ISSN	00027863
e-ISSN	15205126
Journal	Journal of the American Chemical Society
Issue Number	50
Volume Number	137
Language	English
Publisher Date	2015-12-23
Access Restriction	Open
Subject Keyword	Colloid and Surface Chemistry Biochemistry Chemistry(all) Catalysis Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Chemistry Colloid and Surface Chemistry Biochemistry Catalysis

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