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Related Concept Videos

RNA Structure01:23

RNA Structure

71.6K
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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Nucleic Acid Structure01:25

Nucleic Acid Structure

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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...
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Nucleic Acids and Nucleotides01:20

Nucleic Acids and Nucleotides

9.0K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and have instructions for its functioning. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Deoxyribonucleic Acid (DNA)
DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and the organelles such as chloroplasts and mitochondria....
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Nucleic acids02:43

Nucleic acids

163.5K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
163.5K
The Nucleolus02:55

The Nucleolus

8.9K
The nucleolus is the most prominent substructure of the nucleus. When it was first discovered, it was considered to be an isolated organelle that forms fibrils and granules. In 1931, the relationship between the nucleolus and chromosomes was first described by Heitz. He observed that the appearance and size of nucleolus varies depending on the stage of the cell cycle. He also noticed constricted regions on different chromosomes clustered together at definite cell cycle stages. These regions,...
8.9K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

10.7K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
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Related Experiment Video

Updated: Jul 15, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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NuFold: A Novel Tertiary RNA Structure Prediction Method Using Deep Learning with Flexible Nucleobase Center

Yuki Kagaya1, Zicong Zhang2, Nabil Ibtehaz2

  • 1Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.

Biorxiv : the Preprint Server for Biology
|October 4, 2023
PubMed
Summary
This summary is machine-generated.

Predicting RNA tertiary structures is crucial for understanding RNA function. NuFold, a novel deep learning method, accurately forecasts these complex 3D RNA structures, bridging the gap between sequence data and structural insights.

Keywords:
RNA structure predictionmachine learningstructure biology

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Area of Science:

  • Molecular Biology
  • Computational Biology
  • Bioinformatics

Background:

  • RNA molecules perform diverse biological functions beyond messenger RNA (mRNA) in the central dogma.
  • The rapid growth of genomic data outpaces experimental determination of three-dimensional (3D) RNA structures, creating a significant data gap.
  • Experimental methods for RNA structure determination are costly and time-consuming.

Approach:

  • A novel computational approach utilizing the deep learning architecture NuFold is proposed.
  • NuFold accurately predicts RNA tertiary structures.
  • The model employs a nucleobase center representation to capture all nucleotide conformations.

Key Points:

  • NuFold offers a cost-effective and efficient solution for RNA structure prediction.
  • The nucleobase center representation enhances the accuracy of predicting nucleotide conformations.
  • This method addresses the disparity between available RNA sequence data and structural information.

Conclusions:

  • NuFold significantly advances the field of RNA structure prediction.
  • The approach facilitates a deeper understanding of RNA function through accurate structural insights.
  • This computational tool is vital for researchers working with large RNA sequence datasets.