Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.
dc.contributor.author | Merriman, Dawn K | |
dc.contributor.author | Yuan, Jiayi | |
dc.contributor.author | Shi, Honglue | |
dc.contributor.author | Majumdar, Ananya | |
dc.contributor.author | Herschlag, Daniel | |
dc.contributor.author | Al-Hashimi, Hashim M | |
dc.date.accessioned | 2018-09-18T03:02:43Z | |
dc.date.available | 2018-09-18T03:02:43Z | |
dc.date.issued | 2018-07-16 | |
dc.date.updated | 2018-09-18T03:02:42Z | |
dc.description.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. | |
dc.identifier | rna.066258.118 | |
dc.identifier.issn | 1355-8382 | |
dc.identifier.issn | 1469-9001 | |
dc.identifier.uri | ||
dc.language | eng | |
dc.publisher | Cold Spring Harbor Laboratory | |
dc.relation.ispartof | RNA (New York, N.Y.) | |
dc.relation.isversionof | 10.1261/rna.066258.118 | |
dc.subject | HIV | |
dc.subject | NMR | |
dc.subject | RNA Folding | |
dc.subject | RNA bulges | |
dc.subject | RNA dynamics | |
dc.title | Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. | |
dc.type | Journal article | |
pubs.begin-page | rna.066258.118 | |
pubs.end-page | rna.066258.118 | |
pubs.organisational-group | School of Medicine | |
pubs.organisational-group | Duke | |
pubs.organisational-group | Biochemistry | |
pubs.organisational-group | Basic Science Departments | |
pubs.organisational-group | Student | |
pubs.organisational-group | Chemistry | |
pubs.organisational-group | Trinity College of Arts & Sciences | |
pubs.publication-status | Published |
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