Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

RNA multi-structure landscapes. A study based on temperature dependent partition functions

S Bonhoeffer1, J S McCaskill, P F Stadler

  • 1Institut für Theoretische Chemie, Universität Wien, Austria.

European Biophysics Journal : EBJ
|January 1, 1993
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Efficacy of a Mouthwash Containing CHX and CPC in SARS-CoV-2-Positive Patients: A Randomized Controlled Clinical Trial.

Journal of dental research·2023
Same author

Durable memories and efficient neural coding through mnemonic training using the method of loci.

Science advances·2021
Same author

Adherence to oral anticoagulant treatment and risk factor assessment six months after DC-conversion of atrial fibrillation.

Scandinavian cardiovascular journal : SCJ·2020
Same author

Static patella tilt and axial engagement in knee extension are mainly influenced by knee torsion, the tibial tubercle-trochlear groove distance (TTTG), and trochlear dysplasia but not by femoral or tibial torsion.

Knee surgery, sports traumatology, arthroscopy : official journal of the ESSKA·2019
Same author

Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa.

BMC evolutionary biology·2018
Same author

[Reconstruction of the medial patellofemoral ligament using autologous gracilis tendon in an implant-free technique on the patellar side].

Operative Orthopadie und Traumatologie·2015
Same journal

Disruption of bacterial membranes by plant extracts of celandine and dandelion: microbiological and langmuir monolayer studies.

European biophysics journal : EBJ·2026
Same journal

Challenging cases for AlphaFold: two multidomain proteins with zinc-binding-, phosphorylation- or dimerization-driven conformational changes.

European biophysics journal : EBJ·2026
Same journal

In sample pH measurement by <sup>31</sup>P phosphate NMR: application to measure the intrinsic GTPase activity of Rab1a.

European biophysics journal : EBJ·2026
Same journal

The MOlecular-Scale Biophysics Research Infrastructure (MOSBRI) Project and its Outcomes.

European biophysics journal : EBJ·2026
Same journal

Bitter taste TAS2R14 and TAS2R46 receptors bound to G proteins: comparison of cryo-EM, AlphaFold, and molecular dynamics structures.

European biophysics journal : EBJ·2026
Same journal

Homologous series of N-acylmelatonins: synthesis, biophysical studies, enhanced antioxidant, antimicrobial and anticancer activities.

European biophysics journal : EBJ·2026
See all related articles

Investigating RNA folding landscapes using partition function calculations reveals that RNA sequences explore multiple structures, influencing evolution. This thermodynamic approach offers a comprehensive view beyond minimal free energy predictions.

Area of Science:

  • Computational Biology
  • Biophysics
  • Bioinformatics

Background:

  • Traditional RNA folding analysis often relies on minimal free energy predictions.
  • The partition function algorithm provides a more comprehensive thermodynamic view of RNA secondary structures.
  • Understanding RNA folding landscapes is crucial for predicting RNA function and evolution.

Purpose of the Study:

  • To statistically analyze RNA folding landscapes using the partition function.
  • To quantify landscape ruggedness using free energy pair correlations and structural distances.
  • To compare landscape properties between full GCAU and GC-only sequences.

Main Methods:

  • Utilized the partition function algorithm (McCaskill 1990) to calculate thermodynamic properties of RNA folding.

Related Experiment Videos

  • Computed pair correlation functions of free energies against Hamming distance to assess landscape ruggedness.
  • Introduced and computed metric distances for RNA structure ensembles.

    • Main Results:

    • RNA folding landscapes are smoother for the full GCAU alphabet compared to GC-only sequences.
    • Correlation lengths scale with chain lengths for both landscape types.
    • Multi-structure landscapes show increased correlation lengths near the melting temperature.

    Conclusions:

    • The partition function approach offers a richer understanding of RNA folding thermodynamics than minimal free energy methods.
    • RNA sequence evolution may be influenced by the exploration of multiple structures in finite populations.
    • Landscape properties are sensitive to sequence composition and temperature.