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Related Concept Videos

Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
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The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
Improving Translational Accuracy02:07

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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.
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Related Experiment Video

Updated: May 26, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Glutamine codon-driven translational readthrough reveals context-dependent stop codon decoding fidelity.

Jessica M Leslie1, Kaitlin Morse1, Sarah Swerdlow1

  • 1Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720.

Biorxiv : the Preprint Server for Biology
|May 25, 2026
PubMed
Summary
This summary is machine-generated.

Yeast stop codon readthrough is influenced by glutamine codon context and abundance. A QXQ motif and overall glutamine content amplify readthrough, with glutamine insertion confirmed by mass spectrometry.

Keywords:
[PSI+] prionglutamine codonpolyQpreMATure stop codonribosome profilingtRNAGlntranslational readthroughtranslational termination

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Published on: December 21, 2017

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • The canonical genetic code can deviate, with stop codons reassigned to glutamine in some eukaryotes.
  • Transfer RNA (tRNA) for glutamine mediates stop codon readthrough in organisms with the canonical code.
  • The specific sequence elements and mechanisms driving this decoding remain unclear.

Purpose of the Study:

  • To investigate the factors governing premature stop codon readthrough efficiency in Saccharomyces cerevisiae.
  • To elucidate the mechanistic basis of tRNA(Gln)-mediated stop codon readthrough.

Main Methods:

  • Ribosome profiling to assess translation dynamics.
  • Quantitative immunoblotting to measure protein levels.
  • Mass spectrometry to identify amino acid incorporation at stop codons.

Main Results:

  • Readthrough efficiency depends on both local glutamine codon context (e.g., QXQ motif) and global mRNA glutamine codon content.
  • Glutamine is specifically inserted at premature stop codons, not miscoded in flanking regions.
  • Increased glutamine codon abundance correlates with amplified readthrough.

Conclusions:

  • tRNA(Gln) competes with release factors, driving readthrough at premature stops.
  • Evolutionary selection favors stronger stop codon contexts for proteins with C-terminal glutamine repeats to ensure termination fidelity.