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

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

13.7K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
13.7K
Leaky Scanning02:28

Leaky Scanning

5.0K
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...
5.0K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.5K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.5K
RNA Splicing01:32

RNA Splicing

55.7K
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
55.7K
Regulation of Nuclear Protein Sorting01:45

Regulation of Nuclear Protein Sorting

2.3K
Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...
2.3K
Signal Sequences and Sorting Receptors01:41

Signal Sequences and Sorting Receptors

5.1K
Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...
5.1K

You might also read

Related Articles

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

Sort by
Same author

NMR-based conformational analysis of DNA G-quadruplex guides mapping essential structure-function relationship in protein chaperoning.

Physical chemistry chemical physics : PCCP·2026
Same author

Catalyzing Protein Folding by Chaperones.

Biology·2025
Same author

Reconstructing biological molecules with help from video gamers.

Acta crystallographica. Section D, Structural biology·2025
Same author

Quantitative Thermodynamic Characterization of Self-Assembling RNA Nanostructures.

bioRxiv : the preprint server for biology·2025
Same author

Examining the Influences of Educational Computer-Gaming Play on Older Adults' Learning Using the Biochemistry Video Game Foldit.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology·2025
Same author

Chronic RNA G-quadruplex accumulation in aging and Alzheimer's disease.

eLife·2025
Same journal

RNA polymerase II phosphorylation dynamics: from molecular mechanisms to human disease.

RNA biology·2026
Same journal

Impact of interspecies colostrum and milk replacement on circulating sncRNA dynamics of neonatal goat kids.

RNA biology·2026
Same journal

The role of RNA modifications in cancer translational control.

RNA biology·2026
Same journal

Discovery of a mutation-containing circRNA in polyglutamine disease through systematic analysis of RNAs with CAG repeats.

RNA biology·2026
Same journal

FDA-approved antisense oligonucleotide therapies for duchenne muscular dystrophy: current status and future outlook.

RNA biology·2026
Same journal

The RNA binding protein ZFP36L2 displays tissue-selective mRNA targeting in mice.

RNA biology·2026
See all related articles

Related Experiment Video

Updated: May 9, 2025

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
09:16

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

7.2K

Cleavage sequence specificity of Nsp15.

John V McGuire1, Scott Horowitz1

  • 1Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA.

RNA Biology
|May 6, 2025
PubMed
Summary
This summary is machine-generated.

Nsp15, a SARS-CoV-2 enzyme, shows a preference for uridine at the first dinucleotide position during RNA cleavage. Structural analysis suggests this specificity is influenced by interactions near the RNA sequence.

Keywords:
AlphaFoldNon-structural protein 15Nsp15RNA degradationSARS-CoV-2endoribonucleasesequence specificity

More Related Videos

Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods
10:40

Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods

Published on: December 21, 2019

25.9K
Substrate Generation for Endonucleases of CRISPR/Cas Systems
11:53

Substrate Generation for Endonucleases of CRISPR/Cas Systems

Published on: September 8, 2012

27.2K

Related Experiment Videos

Last Updated: May 9, 2025

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
09:16

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

7.2K
Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods
10:40

Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods

Published on: December 21, 2019

25.9K
Substrate Generation for Endonucleases of CRISPR/Cas Systems
11:53

Substrate Generation for Endonucleases of CRISPR/Cas Systems

Published on: September 8, 2012

27.2K

Area of Science:

  • Virology
  • Molecular Biology
  • Structural Biology

Background:

  • Nsp15 is an EndoU nuclease crucial for SARS-CoV-2 immune evasion.
  • Understanding Nsp15's sequence specificity is vital for antiviral strategies.
  • Previous studies faced challenges in fully determining Nsp15 sequence specificity.

Purpose of the Study:

  • To systematically measure the sequence specificity of the SARS-CoV-2 Nsp15 enzyme.
  • To investigate the structural basis underlying Nsp15's RNA cleavage preferences.

Main Methods:

  • A systematic approach was employed to test all 16 possible dinucleotide sequences for Nsp15 cleavage activity.
  • AlphaFold3 predictions were utilized to analyze the structural interactions governing Nsp15 specificity.
  • Cleavage assays were performed to determine Nsp15's sequence preference.

Main Results:

  • Nsp15 exhibits a clear preference for uridine (U) in the first dinucleotide position.
  • Specificity in the second dinucleotide position varied.
  • Structural analysis revealed key interactions 3' to the dinucleotide sequence and with the dinucleotides themselves, correlating with observed cleavage specificity.

Conclusions:

  • The study elucidates Nsp15's sequence specificity, highlighting a preference for U at the first position.
  • Structural insights from AlphaFold3 provide a basis for understanding these enzymatic preferences.
  • This detailed understanding of Nsp15 function can inform the development of targeted antiviral therapies against SARS-CoV-2.