ArticleBiophysical journal2003
Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 41 citations in OpenAlex.
- Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer.Journal of chemical information and modeling · 2025Article
- Systematics for types and effects of RNA variations.RNA biology · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.Journal of computational chemistry · 2017Article
- Blind tests of RNA nearest-neighbor energy prediction.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A novel implicit solvent model for simulating the molecular dynamics of RNA.Biophysical journal · 2013Article
- Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome.RNA (New York, N.Y.) · 2011Article
- Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.Journal of computational chemistry · 2011Article
- Free energy profile of RNA hairpins: a molecular dynamics simulation study.Biophysical journal · 2010Article
- Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.Journal of the American Chemical Society · 2008Article
- Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.Biophysical journal · 2007Article
- Review
- CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.Journal of computational chemistry · 2007Article
- Molecular dynamics simulations of sarcin-ricin rRNA motif.Nucleic acids research · 2006Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Contributions of individual interactions in the GGCGCAAGCC hairpin containing a GCAA tetraloop were studied by computer simulations using base substitutions. The G in the first tetraloop position was replaced by inosine (I) or adenosine (A), and the G in the C-G basepair closing the tetraloop was replaced by I. These substitutions eliminate particular hydrogen bonds proposed in the nuclear magnetic resonance model of the GCAA tetraloop. Molecular dynamics simulations of the GCAA tetraloop in aqueous solvent displayed a well-defined hydrogen pattern between the first and last loop nucleotides (G and A) stabilized by a bridging water molecule. Substitution of G-->I in the basepair closing the tetraloop did not significantly influence the loop structure and dynamics. The ICAA loop maintained the overall structure, but displayed variation in the hydrogen-bond network within the tetraloop itself. Molecular dynamics simulations of the ACAA loop led to conformational heterogeneity of the resulting structures. Changes of hairpin formation free energy associated with substitutions of individual bases were calculated by the free energy perturbation method. The calculated decrease of the hairpin stability upon G-->I substitution in the C-G basepair closing the tetraloop was in good agreement with experimental thermodynamic data. Our theoretical estimates for G-->I and G-->A mutations located in the tetraloop suggest larger loop destabilization than corresponding experimental results. The extent of conformational sampling of the structures resulting from base substitutions and its impact on the calculated free energy was discussed.
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