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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...
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Properties and determinants of codon decoding time distributions.

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    PubMed
    Summary
    This summary is machine-generated.

    Ribosome profiling reveals distinct codon footprint distributions across five organisms, correlating with tRNA abundance and suggesting three translation elongation sub-steps. This codon-centric view aids future translation and transcription studies.

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    Area of Science:

    • Molecular Biology
    • Genomics
    • Biophysics

    Background:

    • Codon decoding time influences protein characteristics and abundance.
    • Ribosome profiling, a next-generation sequencing technique, measures ribosome density at codon resolution.
    • This method provides footprint counts reflecting ribosome probability at each nucleotide.

    Purpose of the Study:

    • To investigate novel properties of codon footprint count distributions using large-scale ribosomal profiling data from five organisms.
    • To analyze basic properties of these distributions and their relationship with tRNA abundance.

    Main Methods:

    • Large-scale analysis of ribosomal profiling data.
    • Comparative genomic analysis focusing on codon distribution.
    • Statistical analysis of footprint count distributions.

    Main Results:

    • Codon footprint count distributions exhibit distinct patterns across organisms.
    • These distributions are generally conserved within the open reading frame (ORF) but vary at the 5' and 3' ends.
    • Specific distribution properties correlate with the abundance of cognate tRNA molecules.

    Conclusions:

    • The translation elongation stage may involve three distinct biophysical sub-steps.
    • A codon-distribution-centric approach is advantageous for analyzing ribosome profiling data.
    • The developed methods can be applied to future research in translation and transcription elongation.