Stabilizing effect of dangling bases on a short RNA double helix as determined by proton nuclear magnetic resonance spectroscopy

Romaniuk, Paul J.; Hughes, Donald W.; Gregoire, Rene J.; Neilson, Thomas; Bell, Russell A.

doi:10.1021/ja00480a076

Cited by 35 publications

(26 citation statements)

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“…The reversal in E FRET occurs at lower salt when the construct contains longer 24 bp helices as opposed to 12 bp helices. Although end-fraying may be a concern for such short duplexes, we expect this effect to be more pronounced for the 12 bp construct, where the dye is much closer to the blunt end (fraying at the end closest to the junction is less likely due to the stabilizing effect of the linker (35)). The agreement between the E FRET values for both constructs, at the extremes of salt, suggests that fraying does not contribute substantially to the measured effects.…”

Section: Effect Of Helix Lengthmentioning

confidence: 96%

Tuning RNA Flexibility with Helix Length and Junction Sequence

Sutton

Pollack

2015

Biophysical Journal

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The increasing awareness of RNA's central role in biology calls for a new understanding of how RNAs, like proteins, recognize biological partners. Because RNA is inherently flexible, it assumes a variety of conformations. This conformational flexibility can be a critical aspect of how RNA attracts and binds molecular partners. Structurally, RNA consists of rigid basepaired duplexes, separated by flexible non-basepaired regions. Here, using an RNA system consisting of two short helices, connected by a single-stranded (non-basepaired) junction, we explore the role of helix length and junction sequence in determining the range of conformations available to a model RNA. Single-molecule Förster resonance energy transfer reports on the RNA conformation as a function of either mono- or divalent ion concentration. Electrostatic repulsion between helices dominates at low salt concentration, whereas junction sequence effects determine the conformations at high salt concentration. Near physiological salt concentrations, RNA conformation is sensitive to both helix length and junction sequence, suggesting a means for sensitively tuning RNA conformations.

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Section: Effect Of Helix Lengthmentioning

confidence: 96%

Tuning RNA Flexibility with Helix Length and Junction Sequence

Sutton

Pollack

2015

Biophysical Journal

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“…We do not have the complete physical-chemical (or combinatorial) tools necessary for such an undertaking. Even in solution, we neglect the 359 Nucleic Acids Research stabilizing effects of Mg+2 ions and of free dangling ends (25,26). Nonetheless, the calculation was exactly carried out within a well defined framework, i.e.…”

Section: The Thermodynamic Approach To Rna Foldingmentioning

confidence: 99%

Secondary structure model for the complete simian virus 40 Late precursor mRNA

1982

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Structures for all sequences containing less than 1790 nucleotides in the 2600 nucleotide late region of the SV40 virus have been computed and saved on magnetic tape. Previously the longest sequence whose secondary structure was calculated in a single computer run contained 950 nucleotides. In the past, analysis of long molecules required numerous repeated, partially overlapping computations on much shorter segments. The structure obtained for the late half of the SV40 is Y-shaped with two unequal arms. It has 52 short hairpins. Two long range interactions between nucleotides near 650 and 1350 and between 1450 and 2450 appear to play an important role. The first is within the 16S intron; the second is in the 3' exon. The 5' and 3' ends of the molecule are close to each other and are found in the major elongated stem in the vicinity of the fork.

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“…Additional analysis demonstrated that nearly all helix ends in other classes of structured RNAs are involved in end-stacking ( Table S1 ). Provided that helix ends fray [20] , [21] , [22] , such preponderance of end-stacking in structured RNAs reflects its significance not merely in protecting short canonical RNA helices against fraying as indicated by earlier studies [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [27] , [28] , [29] , [30] , [31] , [32] .…”

Section: Resultsmentioning

confidence: 88%

“…Together with basepairing interactions, base-stacking contributes significantly to the stability of DNA and RNA helices [11] , [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] . While internal basepairs are stacked on both sides, the ends of RNA secondary structure helices are stacked on their internal side and exposed to the loop side, potentially susceptible to fraying in that their imino protons exchange with solvent [20] , [21] , [22] .…”

Section: Introductionmentioning

confidence: 99%

Helix Capping in RNA Structure

Lee¹,

Gutell

2014

PLoS ONE

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Helices are an essential element in defining the three-dimensional architecture of structured RNAs. While internal basepairs in a canonical helix stack on both sides, the ends of the helix stack on only one side and are exposed to the loop side, thus susceptible to fraying unless they are protected. While coaxial stacking has long been known to stabilize helix ends by directly stacking two canonical helices coaxially, based on analysis of helix-loop junctions in RNA crystal structures, herein we describe helix capping, topological stacking of a helix end with a basepair or an unpaired nucleotide from the loop side, which in turn protects helix ends. Beyond the topological protection of helix ends against fraying, helix capping should confer greater stability onto the resulting composite helices. Our analysis also reveals that this general motif is associated with the formation of tertiary structure interactions. Greater knowledge about the dynamics at the helix-junctions in the secondary structure should enhance the prediction of RNA secondary structure with a richer set of energetic rules and help better understand the folding of a secondary structure into its three-dimensional structure. These together suggest that helix capping likely play a fundamental role in driving RNA folding.

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Stabilizing effect of dangling bases on a short RNA double helix as determined by proton nuclear magnetic resonance spectroscopy

Cited by 35 publications

References 0 publications

Tuning RNA Flexibility with Helix Length and Junction Sequence

Tuning RNA Flexibility with Helix Length and Junction Sequence

Secondary structure model for the complete simian virus 40 Late precursor mRNA

Helix Capping in RNA Structure

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