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

The linkage between magnesium binding and RNA folding.

Vinod K Misra1, David E Draper

  • 1Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA. vmisra@umich.edu

Journal of Molecular Biology
|April 17, 2002
PubMed
Summary

This study introduces a new theoretical model for magnesium ion (Mg2+) binding to RNA, explaining how Mg2+ stabilizes RNA folding through diffuse and site binding. The model accurately predicts RNA folding energetics without fitted parameters.

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

Monoallelic and biallelic KDM5A variants identified in patients with autism spectrum disorder.

HGG advances·2026
Same author

Pathogenic Variants in <i>MPDZ</i> are Associated with a Syndromic Neurodevelopmental Disorder: A Case Report and Review of the Literature.

Journal of child neurology·2025
Same author

Biallelic variants in SLC4A10 encoding a sodium-dependent bicarbonate transporter lead to a neurodevelopmental disorder.

Genetics in medicine : official journal of the American College of Medical Genetics·2023
Same author

Spliceosome malfunction causes neurodevelopmental disorders with overlapping features.

The Journal of clinical investigation·2023
Same author

Functional insight into a neurodevelopmental disorder caused by missense variants in an RNA-binding protein, RBM10.

Journal of human genetics·2023
Same author

Consolidation of the clinical and genetic definition of a <i>SOX4-</i>related neurodevelopmental syndrome.

Journal of medical genetics·2022

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Current models for magnesium ion (Mg2+) binding to RNA rely on empirical thermodynamics with unjustified assumptions.
  • A precise theoretical framework is needed to understand the energetics of Mg2+ interaction with folded and unfolded RNA states.
  • Magnesium ions are crucial for RNA structure and function, influencing folding pathways and stability.

Purpose of the Study:

  • To develop a rigorous theoretical model for the linkage between RNA folding and magnesium ion binding.
  • To elucidate the distinct binding modes of Mg2+ and their contributions to RNA stabilization.
  • To validate the model using experimental systems like yeast tRNA(Phe) and an rRNA fragment.

Main Methods:

  • Development of a theoretical model based on the non-linear Poisson-Boltzmann (NLPB) equation.

Related Experiment Videos

  • Description of Mg2+ binding through two modes: diffuse binding (hydrated ions) and site binding (partially desolvated ions).
  • Application and validation of the NLPB model to yeast tRNA(Phe) and a 58-nucleotide rRNA fragment.

    • Main Results:

    • The NLPB model accurately describes stoichiometric and energetic linkage between Mg2+ binding and RNA folding for both systems.
    • Mg2+ stabilization arises from diffuse binding to secondary structures in intermediate states and dominant diffuse binding in native states.
    • Site binding contributes to stabilization in the rRNA fragment, particularly at sites of high electrostatic potential.

    Conclusions:

    • The NLPB model provides a physically well-defined description of Mg2+ mediated RNA folding without fitted parameters.
    • Diffuse Mg2+ binding is key for stabilizing intermediate and native RNA states, while site binding plays a specific role in some RNAs.
    • Experimental data on Mg2+-RNA interactions may require reinterpretation in light of these findings.