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Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.
Abstract
Helical elements separated by bulges frequently undergo transitions between unstacked
and coaxially stacked conformations during the folding and function of non-coding
RNAs. Here, we examine the dynamic properties of poly-pyrimidine bulges of varying
length (n = 1, 2, 3, 4 and 7) across a range of Mg2+ concentrations using HIV-1 TAR
RNA as a model system and solution NMR spectroscopy. In the absence of Mg2+ (25 mM
monovalent salt), helices linked by bulges with n ≥ 3 residues adopt predominantly
unstacked conformations (stacked population < 15%) whereas 1-bulge and 2-bulge motifs
adopt predominantly stacked conformations (stacked population > 74%). The 2-bulge
motif is biased toward linear conformations and increasing the bulge length leads
to broader inter-helical distributions and structures that are on average more kinked.
In the presence of 3 mM Mg2+, the helices predominantly coaxially stack (stacked population
> 84%), regardless of bulge length, and the midpoint for the Mg2+-dependent stacking
transition does not vary substantially (within 3-fold) with bulge length. In the absence
of Mg2+, the difference between the free energy of inter-helical coaxial stacking
across the bulge variants is estimated to be ≈2.9 kcal/mol, based on an NMR chemical
shift mapping approach, with stacking being more energetically disfavored for the
longer bulges. This difference decreases to ≈0.4 kcal/mol in the presence of 3 mM
Mg2+ NMR residual dipolar coupling and resonance intensity data show increased dynamics
in the stacked state with increasing bulge length in the presence of Mg2+ We propose
that Mg2+ helps to neutralize the growing electrostatic repulsion in the stacked state
with increasing bulge length thereby increasing the number of coaxial conformations
that are sampled. Energetically compensated inter-helical stacking dynamics may help
to maximize the conformational adaptability of RNA and allow a wide range of conformations
to be optimally stabilized by proteins and ligands.
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Journal articlePermalink
https://hdl.handle.net/10161/17418Published Version (Please cite this version)
10.1261/rna.066258.118Publication Info
Merriman, Dawn K; Yuan, Jiayi; Shi, Honglue; Majumdar, Ananya; Herschlag, Daniel;
& Al-Hashimi, Hashim M (2018). Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles
with minimal impact on stacking energetics. RNA (New York, N.Y.). pp. rna.066258.118-rna.066258.118. 10.1261/rna.066258.118. Retrieved from https://hdl.handle.net/10161/17418.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Hashim Al-Hashimi
Adjunct Professor in the Department of Biochemistry
Honglue Shi
Student
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