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About 10,000 papers for “Stop codon”

Stop Codon

National Human Genome Research Institute (NHGRI) · Definitions · 2019

A stop codon is a trinucleotide sequence within a messenger RNA (mRNA) molecule that signals a halt to protein synthesis.T he genetic code describes the relationship between the sequence of DNA bases (A, C, G, and T ) in a gene and the corresponding protein sequence that it encodes.T he cell reads the sequence of the gene in groups of three bases.Of the 64 possible combinations of three bases, 61 specify an amino acid, while the remaining three combinations are stop codons.

Cited by 0Open access

Stop Codon.

Cíntia Bittar (406933), Ana Carolina Gomes Jardim (406934), Lilian Hiromi Tomonari Yamasaki (406935) et al. · Figshare · 2015

<p>Graphic representation of sites where stop codons were identified. Pink – more than one occurrence; purple-one occurrence. NZL1 (GenBank accession number D17763) – reference sequence for genotype 3 was used for the graphic representation. CRS – cytoplasmic retention site; PKR-Bd – PKR binding region; ISDR – IFN sensitivity determining region; NLS – nuclear localization signal; V3– variable region 3.</p>

Cited by 0Open access

Stop codon neighborhood inserts.

Clara S. Chan (164398), Irwin Jungreis (394965), Manolis Kellis (55372) · Figshare · 2015

<p>Stop codon neighborhood DNA sequences inserted between Renilla and Firefly luciferase genes in parental dual luciferase reporter plasmid (with stop codons shown in boldface).</p>

Cited by 0Open access

Silent Stop Codon Mutation

National Cancer Institute · Definitions · 2020

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Cited by 0Open access

Prokaryotic post stop-codon sequences

Nieuwkoop, Thijs, Creutzburg, Sjoerd Constantijn Arnoud, Van Der Oost, John · Socio-Environmental Systems Modeling · 2022

The invention relates to methods of modulating gene expression in prokaryotes. The invention further relates to a prokaryotic expression cassette, a method of expressing a protein of interest in a prokaryotic cell, and to a prokaryotic cell comprising the prokaryotic expression cassette according to the invention.

Cited by 0Open access

Stop codon reversal assay v1

is Sparrow · 2024

This protocol is used to characterize viral RNA polymerase based directed evolution tools via fluctuation analysis to calculate the mutation rate. It is specific to the stop codon reversal of the aadA gene, which we use to characterize the mutational power of the tool.

Cited by 0Open access

Therapeutics Based on Stop Codon Readthrough

Kim M. Keeling, Xiaojiao Xue, Gwen Gunn et al. · Annual Review of Genomics and Human Genetics · 2014

Nonsense suppression therapy encompasses approaches aimed at suppressing translation termination at in-frame premature termination codons (PTCs, also known as nonsense mutations) to restore deficient protein function. In this review, we examine the current status of PTC suppression as a therapy for genetic diseases caused by nonsense mutations. We discuss what is currently known about the mechanism of PTC suppression as well as therapeutic approaches under development to suppress PTCs. The approaches considered include readthrough drugs, suppressor tRNAs, PTC pseudouridylation, and inhibition of nonsense-mediated mRNA decay. We also discuss the barriers that currently limit the clinical application of nonsense suppression therapy and suggest how some of these difficulties may be overcome. Finally, we consider how PTC suppression may play a role in the clinical treatment of genetic diseases caused by nonsense mutations.

Cited by 303Open access

A tripeptide discriminator for stop codon recognition

Yoshikazu Nakamura, Koichi Ito · FEBS Letters · 2002

Only recently has it been established that a tripeptide in the bacterial release factors (RFs), RF1 and RF2, is responsible for the stop codon recognition. This functional mimic of the anticodon of tRNA is referred to as a tripeptide 'anticodon' or a tripeptide discriminator. Here we review the experimental background and process leading to this discovery, and strengthen functional evidence for the tripeptide determinant for deciphering stop codons in mRNAs in prokaryotes.

Cited by 36

Gene of Interest with STOP codon v1

Warren van Loggerenberg · 2025

You will need to define a reference (“wild-type”, “WT”) sequence for your gene of interest. This protocol describes how to obtain the open reading frame (ORF) from the human ORFeome 8.1/9.1 collection and add a stop codon. Before beginning you will need to design primers specific to your ORF of interest to enable cloning of the amplified product into pDONR223.

Cited by 0Open access

Evolutionary Dynamics of Abundant Stop Codon Readthrough

Irwin Jungreis, Clara S. Chan, Robert M. Waterhouse et al. · Molecular Biology and Evolution · 2016

Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede.

Cited by 74Open access

Investigating stop codon readthrough in Saccharomyces cerevisiae

Kwon, Amy · Scholarship@Western (Western University) · 2021

Stop codon readthrough occurs via genetic and epigenetic mechanisms, resulting in a longer polypeptide chain at the C-terminus. Although these readthroughs may seem like an error made by translational mechanisms, evidence from yeast suggests that stop codon readthrough has an impact on various cellular processes. Readthrough has the potential to create genetic diversity, similar to RNA splicing, mRNA editing, and protein modification. The diversity created by translational readthrough may result in a beneficial change in phenotype, and thus have a role in evolution and adaptability. Translational readthrough is observed in organisms such as yeast and E. coli but may also occur in more complex organisms such as humans. Because readthrough has the potential to cause phenotypical change, errors in the process may contribute to disease.

Cited by 0Open access

Synthetic Approach to Stop-Codon Scanning Mutagenesis

Lihua Nie (1945795), Jason J. Lavinder (590616), Mohosin Sarkar (587040) et al. · Figshare · 2016

A general combinatorial mutagenesis strategy using common dimethoxytrityl-protected mononucleotide phosphoramidites and a single orthogonally protected trinucleotide phosphoramidite (Fmoc-TAG; Fmoc = 9-fluorenylmethoxycarbonyl) was developed to scan a gene with the TAG <i>amber</i> stop codon with complete synthetic control. In combination with stop-codon suppressors that insert natural (e.g., alanine) or unnatural (e.g., <i>p</i>-benzoylphenylalanine, Bpa) amino acids, a single DNA library can be used to incorporate different amino acids for diverse purposes. Here, we scanned TAG codons through part of the gene for a model four-helix bundle protein, Rop, which regulates the copy number of ColE1 plasmids. Alanine was incorporated into Rop for mapping its binding site using an in vivo activity screen, and subtle but important differences from in vitro gel-shift studies of Rop function are evident. As a test, Bpa was incorporated using a Phe14 <i>amber</i> mutant isolated from the scanning library. Surprisingly, Phe14Bpa-Rop is weakly active, despite the critical role of Phe14 in Rop activity. Bpa is a photoaffinity label unnatural amino acid that can form covalent bonds with adjacent molecules upon UV irradiation. Irradiation of Phe14Bpa-Rop, which is a dimer in solution like wild-type Rop, results in covalent dimers, trimers, and tetramers. This suggests that Phe14Bpa-Rop weakly associates as a tetramer in solution and highlights the use of Bpa cross-linking as a means of trapping weak and transient interactions.

Cited by 0Open access