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Related Concept Videos

RNA Structure01:23

RNA Structure

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...
RNA Structure01:19

RNA Structure

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.
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...
RNA Structure01:23

RNA Structure

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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

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Related Experiment Video

Updated: May 30, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

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

Published on: December 9, 2022

Fast flexible modeling of RNA structure using internal coordinates.

Samuel Coulbourn Flores1, Michael A Sherman, Christopher M Bruns

  • 1Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden. samuelfloresc@gmail.com

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|July 23, 2011
PubMed
Summary

RNABuilder efficiently models large RNA structures using internal coordinates, integrating experimental data for accurate predictions. This method offers a chemically accurate and economical approach for complex molecular modeling challenges.

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Related Experiment Videos

Last Updated: May 30, 2026

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Published on: December 9, 2022

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Accurate modeling of large macromolecules like RNA is computationally expensive and challenging.
  • Existing methods like molecular dynamics (MD) and fragment-based assembly have limitations in accuracy, cost, and incorporating experimental data.
  • Coarse-grained methods offer efficiency but struggle with atomic detail realization.

Purpose of the Study:

  • To develop a novel molecular modeling algorithm, RNABuilder, for accurate and economical prediction of large RNA structures.
  • To enable the incorporation of experimental information into the modeling process.
  • To overcome limitations of existing computational methods for RNA structure prediction.

Main Methods:

  • RNABuilder operates in internal coordinate space (dihedral angles), reducing computational cost.
  • The algorithm allows for user-defined forces to incorporate experimental constraints.
  • It supports the specification of Leontis-Westhof basepairs as primitives for model construction.
  • Application to a 160-base RNA molecule using secondary structure and experimental data.

Main Results:

  • RNABuilder successfully predicted the structure of a 160-base RNA molecule.
  • The predicted structure achieved a Root Mean Square Deviation (RMSD) of 10.2 Angstroms compared to the known structure.
  • The modeling process demonstrated low computational expense.

Conclusions:

  • RNABuilder provides a chemically accurate and computationally economical method for large RNA structure modeling.
  • The algorithm effectively integrates experimental data and handles complex basepairing interactions.
  • This approach offers a significant advancement for predicting novel RNA structures and dynamics.