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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...
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...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Related Experiment Video

Updated: Jun 18, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Folding 3-noncrossing RNA pseudoknot structures.

Fenix W D Huang1, Wade W J Peng, Christian M Reidys

  • 1Center for Combinatorics, LPMC-TJKLC, Tianjin, PR China.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|December 5, 2009
PubMed
Summary
This summary is machine-generated.

We introduce Cross, a novel algorithm for RNA folding that accurately predicts minimum free energy structures. This method ensures 3-noncrossing and canonical RNA structures, crucial for biological function.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Predicting RNA secondary structure is vital for understanding RNA function.
  • Existing algorithms often struggle with complex structures like pseudoknots.
  • Accurate RNA structure prediction requires efficient and precise computational methods.

Purpose of the Study:

  • To present a novel ab initio RNA folding algorithm named Cross.
  • To generate RNA structures that are minimum free energy (mfe), 3-noncrossing, and canonical.
  • To incorporate a specific concept of pseudoknots and loop-based energy parameters.

Main Methods:

  • The Cross algorithm employs a three-subroutine approach.
  • Subroutine 1: Inductive construction of motifs and their shadows.
  • Subroutine 2: Generation of rooted skeleta-trees.
  • Subroutine 3: Saturation of skeleta using context-dependent dynamic programming.

Main Results:

  • The algorithm generates minimum free energy (mfe) RNA structures.
  • Ensures 3-noncrossing RNA structures, where no three arcs mutually cross.
  • Produces canonical RNA structures with stacks of size two or greater.
  • Accounts for pseudoknots using a novel loop-based energy model.

Conclusions:

  • The Cross algorithm offers a new approach to predicting complex RNA secondary structures.
  • It provides a robust method for generating biologically relevant RNA conformations.
  • This work advances computational methods for RNA structure analysis.