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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...
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-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...
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...

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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A structure-based flexible search method for motifs in RNA.

Isana Veksler-Lublinsky1, Michal Ziv-Ukelson, Danny Barash

  • 1Department of Computer Science, Ben-Gurion University, Beer Sheva, Israel.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|September 7, 2007
PubMed
Summary

A new tool, Structural RNA Motif Search (STRMS), efficiently finds non-coding RNA (ncRNA) motifs by prioritizing secondary structure. It identifies novel riboswitch candidates and known RNA structures in large databases.

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Non-coding RNAs (ncRNAs) play crucial roles in gene regulation.
  • Current methods for discovering ncRNA motifs often prioritize primary sequence over secondary structure.
  • A flexible, structure-based approach is needed for efficient ncRNA motif discovery.

Purpose of the Study:

  • To develop a novel RNA motif search tool, STRMS (Structural RNA Motif Search).
  • To enable filtering of sequence databases based on secondary structure first, incorporating sequence and pseudoknot constraints.
  • To provide a fine-tunable tool for discovering diverse RNA motifs.

Main Methods:

  • STRMS accepts RNA secondary structure, sequence constraints, and pseudoknot information as input.
  • It employs a combination of pre-folding and an O(mn) RNA pattern matching algorithm based on subtree homeomorphism.
  • An extension allows for the consideration of pseudoknots, with an O(n^2 log n) complexity for riboswitch analysis.

Main Results:

  • STRMS successfully identified novel purine bacterial riboswitch candidates in large sequence databases.
  • The tool demonstrated high sensitivity in detecting known riboswitches and transfer RNAs (tRNAs).
  • STRMS generates graphical representations of query and hit structures, aiding in analysis.

Conclusions:

  • STRMS offers a flexible and efficient structure-based approach for RNA motif discovery.
  • The tool is effective in identifying both known and novel RNA motifs, including riboswitches and tRNAs.
  • STRMS advances the field of ncRNA motif identification and analysis.