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Related Concept Videos

RNA Structure01:23

RNA Structure

79.7K
Overview
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...
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RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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.
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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...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

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The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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Related Experiment Video

Updated: Mar 5, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Fast, clash-free RNA conformational morphing using molecular junctions.

Amélie Héliou1, Dominik Budday2, Rasmus Fonseca3,4

  • 1LIX, Ecole Polytechnique, CNRS, Inria, Université Paris-Saclay, Palaiseau, France.

Bioinformatics (Oxford, England)
|March 24, 2017
PubMed
Summary

This study introduces a new kinematics-based method to model the dynamic 3D structures of non-coding ribonucleic acids (ncRNAs). The approach efficiently morphs RNA molecules between conformations while preserving secondary structure, aiding in understanding ncRNA flexibility.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Non-coding ribonucleic acids (ncRNAs) are vital functional molecules that lack protein-coding sequences.
  • ncRNAs exhibit significant conformational flexibility, enabling diverse molecular interactions.
  • Probing the complex three-dimensional (3D) conformational landscape of ncRNAs presents experimental and computational challenges.

Purpose of the Study:

  • To develop a computational method for modeling ncRNA conformational dynamics.
  • To efficiently morph RNA molecules between different conformational substates while maintaining structural integrity.
  • To investigate the role of molecular junctions in modulating 3D structural rearrangements in ncRNAs.

Main Methods:

  • A kinematics-based procedure representing RNA as a kinematic linkage with rigid bodies and rotatable bonds.
  • Incorporation of base-pair hydrogen bonds as constraints to maintain secondary structure.
  • Development of a secondary-structure constraint manifold to guide conformational transitions.

Main Results:

  • The procedure successfully morphs RNA molecules between conformational substates, avoiding inter-atomic clashes.
  • The method preserves RNA secondary structure throughout the morphing process.
  • The algorithm achieves low all-atom RMSD to target conformations using minimal atomic adjustments, outperforming peer algorithms.

Conclusions:

  • Molecular junctions play a key role in orchestrating 3D structural rearrangements in ncRNAs.
  • Preserved secondary structure elements effectively guide large portions of the molecule during conformational transitions.
  • This kinematics-based approach offers an efficient way to explore the conformational landscape of ncRNAs.