Related Experiment Video
Updated: Dec 30, 2025
Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
Published on: September 19, 2017
Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg2+ Ion Bound at the Double Mg-Clamp
Aodong Zou1,2, Sangyun Lee3, Jingyuan Li2
1Department of Engineering Mechanics , Zhejiang University , Hangzhou 310027 , China.
Abstract:
It has been known that the binding of two Mg2+ ions to the phosphate groups of RNA is essential for enhancing the stability of a three-way junction oligomeric prohead RNA (3WJ-pRNA). Here, we investigate the coupling between binding of two Mg2+ ions and the stability of the complex structure by calculating the rupture force of 3WJ-pRNA using steered molecular dynamics simulations. Our simulations showed that the mechanical stability of the pRNA structure is largely retained with a single Mg2+ ion bound. Because of a strong electrostatic repulsion between the adjacent Mg2+ ions, the rupture force with two Mg2+ ions bound is smaller than the sum of the rupture forces with either one of Mg2+ ions bound. Our results suggest that binding of the second Mg2+ ion could be redundant for maintaining the rigidity of 3WJ-pRNA, which allows 3WJ-pRNA to have a flexible working range of Mg2+ concentration in a cell.
More Related Videos
10:11Author Spotlight: Investigating the Motion Dynamics of the Eukaryotic Replisome Components at the Single-Molecule Level
Published on: July 26, 2024
07:37Author Spotlight: Unraveling the Dynamics of Eukaryotic DNA Replication Through Single-Molecule Visualization
Published on: September 27, 2024
Related Concept Videos
03:01The Replisome
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
01:03Single-Strand DNA Binding Proteins
00:58DNA Packaging
01:25Nucleic Acid Structure
DNA Structure
DNA...
01:19RNA Structure
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
01:23RNA Structure
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...