Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Predicting Molecular Geometry

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries

Noncovalent Attractions in Biomolecules

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

Noncovalent Attractions in Biomolecules

Noncovalent Attractions in Biomolecules

You might also read

Related Articles

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

Sort by

Same author

Building RNA coarse-grained force fields: Design principles and training strategies.

Biophysical journal·2026

Same author

Increased risk of ischemic stroke in cervical cancer patients received radiotherapy: A nationwide population-based study.

Taiwanese journal of obstetrics & gynecology·2026

Same author

Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch.

Nature communications·2026

Same author

Template-based RNA structure prediction advanced through a blind code competition.

bioRxiv : the preprint server for biology·2026

Same author

Blind prediction of complex water and ion ensembles around RNA in CASP16.

bioRxiv : the preprint server for biology·2025

Same author

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.

Proteins·2025

Search research articles

Related Experiment Video

Updated: Mar 16, 2026

Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example

Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example

Published on: December 3, 2014

Predicting Molecular Crowding Effects in Ion-RNA Interactions.

Tao Yu^1,2, Yuhong Zhu^1,3, Zhaojian He¹

¹Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States.

The Journal of Physical Chemistry. B

|August 5, 2016

Summary

This summary is machine-generated.

This study introduces a new model for molecular crowding effects on ion-RNA interactions. The model predicts that crowding increases RNA instability by reducing ion binding and altering the dielectric environment.

More Related Videos

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Related Experiment Videos

Last Updated: Mar 16, 2026

Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example

Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example

Published on: December 3, 2014

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Area of Science:

Statistical mechanics
Biophysics
Computational chemistry

Background:

Molecular crowding significantly impacts biological systems, including ion-RNA interactions.
Understanding these effects is crucial for predicting RNA structure and function.

Purpose of the Study:

To develop a novel statistical mechanical model predicting molecular crowding effects on ion-RNA interactions.
To elucidate the mechanisms by which crowders influence ion binding and RNA stability.

Main Methods:

A hybrid approach sampling discrete crowder distributions near RNA and continuous mean-field distributions in bulk solvent.
Incorporation of the tightly bound ion (TBI) model to account for ion fluctuation and correlation effects.
Application to simple RNA structures like helices.

Main Results:

Crowding leads to increased free energy and decreased ion binding to RNA.
Crowding effects contribute to RNA structure destabilization.
Key mechanisms include crowder-ion competition and reduced dielectric constant.

Conclusions:

The developed model provides a framework for understanding crowding effects on ion-RNA interactions.
Crowding generally destabilizes RNA structures.
The model can be extended for more complex RNA systems and crowders.