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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 Structure01:23

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-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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...
Nucleic acids02:43

Nucleic acids

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, the...

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Related Experiment Videos

Modeling RNA loops using sequence homology and geometric constraints.

Christian Schudoma1, Patrick May, Dirk Walther

  • 1Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany. schudoma@mpimp-golm.mpg.de

Bioinformatics (Oxford, England)
|April 30, 2010
PubMed
Summary

RLooM is a new web application for modeling RNA loops using homology. It enables users to insert or replace loop structures in existing RNA molecules, with a searchable loop database.

Related Experiment Videos

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • RNA loop regions are critical for RNA structure and function.
  • Understanding RNA loop structures is essential for molecular biology research.

Purpose of the Study:

  • To develop a user-friendly tool for RNA loop modeling.
  • To provide a comprehensive database of RNA loop structures.

Main Methods:

  • Development of RLooM, a web application using Python, MySQL, and Apache.
  • Homology-based modeling of RNA loops utilizing Protein Data Bank (PDB) templates.
  • Implementation of a web interface for database access and loop modeling.

Main Results:

  • RLooM facilitates the insertion and replacement of RNA loop structures based on desired sequences.
  • A comprehensive database of RNA loops from PDB structures is accessible via the web interface.
  • The tool supports homology-based modeling for RNA loop regions.

Conclusions:

  • RLooM is a valuable resource for researchers studying RNA structure and function.
  • The application simplifies the process of RNA loop modeling and analysis.
  • Accessible via a web interface, RLooM enhances the study of RNA structural elements.