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Related Concept Videos

RNA Structure01:23

RNA Structure

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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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RNA Structure01:23

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RNA Structure01:19

RNA Structure

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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.
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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...
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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
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Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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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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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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Analyzing and Building Nucleic Acid Structures with 3DNA
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Motif server: web server for undesignable RNA motifs and structures.

Apoorv Malik1, Tianshuo Zhou1, Wei Yu Tang2

  • 1School of EECS, Oregon State University, Corvallis, OR 97330, USA.

Journal of Molecular Biology
|March 27, 2026
PubMed
Summary
This summary is machine-generated.

Identifying "undesignable structures" in RNA design is crucial. Our new motif server helps researchers find and visualize these structures, improving RNA nanostructure design by avoiding unachievable motifs.

Keywords:
RNA designdesignabilityinverse foldingstructural motifundesignability

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Area of Science:

  • Computational Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • RNA sequence design aims to create RNA molecules that fold into specific secondary structures for diverse applications.
  • The minimum free energy (MFE) criterion identifies certain RNA structures as 'undesignable' because no sequence can stably form them.
  • Previous research established methods for identifying undesignable structures and introduced 'minimal undesignable motifs' within them.

Purpose of the Study:

  • To develop a user-friendly tool for visualizing undesignable RNA structures and motifs.
  • To provide an interactive platform for identifying and analyzing undesignable motifs in user-provided RNA structures.
  • To create a database of known undesignable RNA structures and minimal undesignable motifs to aid RNA design.

Main Methods:

  • Development of a motif server incorporating a database of undesignable RNA structures and motifs.
  • Implementation of an interactive demo tool for on-the-fly computation and visualization of undesignable motifs.
  • Utilizing theoretical findings on rival structures and minimal undesignable motifs for server functionality.

Main Results:

  • A functional motif server is available, offering visualization of undesignable RNA structures and motifs.
  • The server allows users to input new RNA structures and receive immediate identification and visualization of any undesignable motifs.
  • A comprehensive database of undesignable structures and unique minimal undesignable motifs has been established.

Conclusions:

  • The motif server serves as a valuable resource for the RNA research community.
  • It enhances RNA nanostructure design by highlighting motifs that are difficult or impossible to achieve.
  • The tool facilitates exploration, analysis, and identification of critical motifs in RNA secondary structure design.