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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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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.

Julie Bernauer1, Xuhui Huang, Adelene Y L Sim

  • 1INRIA AMIB Bioinformatique, Laboratoire d'Informatique (LIX), Ecole Polytechnique, 91128 Palaiseau, France. julie.bernauer@inria.fr

RNA (New York, N.Y.)
|April 28, 2011
PubMed
Summary
This summary is machine-generated.

Researchers developed new knowledge-based potentials to predict RNA structures. These potentials effectively identify native-like RNA conformations, improving upon existing methods for RNA structure prediction.

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Molecular Modeling

Background:

  • Ribonucleic acid (RNA) molecules are crucial for gene regulation, and their structures provide insights into biological functions.
  • Predicting RNA structure, especially nonhelical regions, remains challenging despite advancements in prediction methods.
  • Knowledge-based potentials have shown success in protein structure prediction.

Purpose of the Study:

  • To develop and evaluate two differentiable knowledge-based potentials for RNA structure prediction.
  • To assess the ability of these potentials to identify native-like RNA conformations from near-native models.
  • To compare the performance of the new potentials against existing parameterized potentials.

Main Methods:

  • Derived two differentiable knowledge-based potentials from a curated dataset of RNA structures.
  • Utilized both all-atom and coarse-grained representations for the potentials.
  • Tested the potentials on near-native RNA models generated by three independent methods.

Main Results:

  • The developed knowledge-based potentials successfully distinguished native RNA structures from near-native models.
  • Both all-atom and coarse-grained potentials identified native-like conformations effectively.
  • The all-atom potential outperformed a highly regarded parameterized potential in discriminating near-native conformations.

Conclusions:

  • Differentiable knowledge-based potentials are effective for identifying native-like RNA conformations.
  • These potentials offer an improvement over existing methods for RNA structure prediction.
  • The differentiable nature of the potentials suggests utility in RNA structure refinement and molecular dynamics simulations.