Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

tRNA Activation02:26

tRNA Activation

Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Biosynthesis of Nucleic Acids01:28

Biosynthesis of Nucleic Acids

Nucleic acid biosynthesis is a fundamental biochemical process that produces the purine and pyrimidine nucleotides essential for DNA and RNA synthesis. This pathway maintains a balanced nucleotide pool, preventing imbalances that could jeopardize genetic integrity and cellular function. Given the crucial role of nucleotides, their synthesis is tightly regulated to ensure proper cellular homeostasis.Purine BiosynthesisThe biosynthesis of purine nucleotides begins with ribose-5-phosphate, a...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET.

Nature protocols·2026
Same author

Capsid flexibility during Ty1 virus-like particle assembly.

bioRxiv : the preprint server for biology·2025
Same author

MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers.

The Journal of biological chemistry·2025
Same author

Assembly of respiratory syncytial virus matrix protein lattice and its coordination with fusion glycoprotein trimers.

Nature communications·2024
Same author

Correlative montage parallel array cryo-tomography for in situ structural cell biology.

Nature methods·2023
Same author

Micropatterning Transmission Electron Microscopy Grids to Direct Cell Positioning within Whole-Cell Cryo-Electron Tomography Workflows.

Journal of visualized experiments : JoVE·2021

Related Experiment Video

Updated: May 27, 2026

A Purification and In Vitro Activity Assay for a (p)ppGpp Synthetase from Clostridium difficile
09:53

A Purification and In Vitro Activity Assay for a (p)ppGpp Synthetase from Clostridium difficile

Published on: November 3, 2018

Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements.

Bryan S Sibert1, Jeffrey R Patton

  • 1Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, SC 29208, USA.

Nucleic Acids Research
|November 22, 2011
PubMed
Summary

Pseudouridine synthase 1 (Pus1p) modifies RNA, but its recognition mechanism is unclear. This study found that base pairing in the anticodon stem-loop and the TΨC stem-loop are crucial for Pus1p to modify tRNA(Ser) at position 28.

More Related Videos

Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli
07:26

Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli

Published on: December 26, 2020

Functional Complementation Analysis (FCA): A Laboratory Exercise Designed and Implemented to Supplement the Teaching of Biochemical Pathways
09:27

Functional Complementation Analysis (FCA): A Laboratory Exercise Designed and Implemented to Supplement the Teaching of Biochemical Pathways

Published on: June 24, 2016

Related Experiment Videos

Last Updated: May 27, 2026

A Purification and In Vitro Activity Assay for a (p)ppGpp Synthetase from Clostridium difficile
09:53

A Purification and In Vitro Activity Assay for a (p)ppGpp Synthetase from Clostridium difficile

Published on: November 3, 2018

Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli
07:26

Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli

Published on: December 26, 2020

Functional Complementation Analysis (FCA): A Laboratory Exercise Designed and Implemented to Supplement the Teaching of Biochemical Pathways
09:27

Functional Complementation Analysis (FCA): A Laboratory Exercise Designed and Implemented to Supplement the Teaching of Biochemical Pathways

Published on: June 24, 2016

Area of Science:

  • Biochemistry
  • Molecular Biology
  • RNA Modification

Background:

  • Pseudouridine synthase 1 (Pus1p) is an enzyme responsible for pseudouridylation, a key RNA modification.
  • Pus1p exhibits unusual substrate specificity, modifying various RNA types and positions without a clear consensus sequence or structure.
  • Understanding Pus1p's recognition mechanism is vital for elucidating its role in RNA function and regulation.

Purpose of the Study:

  • To identify the structural and sequence elements of human tRNA(Ser) essential for pseudouridine (Ψ) formation at position 28.
  • To investigate the role of the anticodon stem-loop (ASL) and TΨC stem-loop in Pus1p-mediated modification.

Main Methods:

  • Site-directed mutagenesis of human tRNA(Ser) to alter ASL stem and loop structures.
  • Deletion analysis to assess the contribution of the TΨC stem-loop.
  • Construction and testing of a mini-substrate containing the ASL and TΨC stem-loop.

Main Results:

  • Point mutations in the ASL stem significantly impacted Ψ formation at U28, with compensatory mutations restoring modification levels.
  • Deletion of the TΨC stem-loop abolished modification, indicating its importance.
  • A mini-substrate with the ASL and TΨC stem-loop showed significant Ψ formation at U28.
  • Retention of base pairing in the ASL stem (at least 3/5 bp) was necessary, but the TΨC loop sequence was not critical.

Conclusions:

  • Base pairing within the anticodon stem-loop is a critical determinant for Pus1p recognition and modification at position 28.
  • The TΨC stem-loop acts as a necessary structural element for efficient modification of the ASL.
  • Pus1p's substrate recognition involves complex structural features rather than a simple sequence motif.