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Related Concept Videos

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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...

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Related Experiment Video

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RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Detecting conserved secondary structures in RNA molecules using constrained structural alignment.

Mugdha Khaladkar1, Vandanaben Patel, Vivian Bellofatto

  • 1Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.

Computational Biology and Chemistry
|May 13, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces an efficient method for constrained structural alignment in RNA molecules. The approach enhances the detection of conserved RNA secondary structures and structural motifs, improving biological relevance.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Constrained sequence alignment is well-researched, but constrained structural alignment is less explored.
  • Existing methods for RNA structural alignment often lack the ability to incorporate specific biological constraints.
  • Identifying conserved RNA secondary structures is crucial for understanding RNA function.

Purpose of the Study:

  • To develop an efficient method for constrained structural alignment of RNA molecules.
  • To apply this method for detecting conserved secondary structures (structural motifs) in RNA.
  • To provide biologically meaningful alignment scores by incorporating user-defined constraints.

Main Methods:

  • Developed an efficient algorithm for constrained structural alignment combining sequence and structural RNA information.
  • Implemented a method to find optimal local alignments between query and subject RNA secondary structures.
  • Incorporated user-annotated conserved regions (constraints) into the alignment process.
  • Developed a statistical measure to assess the significance of alignment scores.

Main Results:

  • The proposed method effectively detects conserved RNA secondary structures and structural motifs.
  • Experimental results demonstrate the method's superiority over existing techniques.
  • The method successfully identified internal ribosome entry sites in hepatitis C virus and Trypanosoma brucei RNA.

Conclusions:

  • The developed method offers an efficient and effective approach for constrained structural alignment in RNA.
  • This technique enhances the biological relevance of RNA structural alignments by incorporating constraints.
  • The method shows significant promise for applications in RNA motif discovery and functional analysis.