ArticleNucleic acids research2007
Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch.Nucleic acids research · 2019Article
- Coarse-grained dynamic RNA titration simulations.Interface focus · 2019Article
- Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome.Nucleic acids research · 2019Article
- An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding.Journal of chemical theory and computation · 2018Article
- Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition.Scientific reports · 2016Article
- A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders.Nucleic acids research · 2013Article
- Determining RNA three-dimensional structures using low-resolution data.Journal of structural biology · 2012Article
- Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme.Structure (London, England : 1993) · 2010Article
- Computational exploration of mobile ion distributions around RNA duplex.The journal of physical chemistry. B · 2010Article
- An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods.Journal of chemical theory and computation · 2010Article
- Modulating RNA structure and catalysis: lessons from small cleaving ribozymes.Cellular and molecular life sciences : CMLS · 2009Review
- Defining the syntax for self-assembling RNA tertiary architectures.Nucleic acids symposium series (2004) · 2009Article
- The UA_handle: a versatile submotif in stable RNA architectures.Nucleic acids research · 2009Article
- The GA-minor submotif as a case study of RNA modularity, prediction, and design.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
3 authors.
Funding
Abstract
The T-loop motif is an important recurrent RNA structural building block consisting of a U-turn sub-motif and a UA trans Watson-Crick/Hoogsteen base pair. In the presence of a hairpin stem, the UA non-canonical base pair becomes part of the UA-handle motif. To probe the hierarchical organization and energy landscape of the T-loop, we performed replica exchange molecular dynamics (REMD) simulations of the T-loop in isolation and as part of a hairpin. Our simulations reveal that the isolated T-loop adopts coil conformers stabilized by base stacking. The T-loop hairpin shows a highly rugged energy landscape featuring multiple local minima with a transition state for folding consisting of partially zipped states. The U-turn displays a high conformational flexibility both when the T-loop is in isolation and as part of a hairpin. On the other hand, the stability of the UA non-canonical base pair is enhanced in the presence of the UA-handle. This motif is apparently a key component for stabilizing the T-loop, while the U-turn is mostly involved in long-range interaction. Our results suggest that the stability and folding of small RNA motifs are highly dependent on local context.
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