Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Southern Blot

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...

Western Blotting

Western Blotting

Western blotting is an analytical technique for protein identification. It has various applications in immunology and medicine, including detecting diseases like bovine spongiform encephalopathy, mad cow disease, and human and feline immunodeficiency virus from biological samples.
The technique begins with separating proteins from the sample using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), followed by protein transfer, immunoblotting, and finally, protein detection.

You might also read

Related Articles

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

Sort by

Same author

A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB.

Nucleic acids research·2025

Same author

The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation.

Nucleic acids research·2025

Same author

The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation.

bioRxiv : the preprint server for biology·2024

Same author

Prolonged exposure to insulin might cause epigenetic alteration leading to insulin resistance.

FEBS open bio·2024

Same author

A <i>POLR3B</i>-variant reveals a Pol III transcriptome response dependent on La protein/SSB.

bioRxiv : the preprint server for biology·2024

Same author

Single-Molecule Poly(A) Tail Sequencing (SM-PATseq) Using the PacBio Platform.

Methods in molecular biology (Clifton, N.J.)·2023

Same journal

Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.

RNA (New York, N.Y.)·2026

Same journal

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026

Same journal

Reduced Sensitivity to RNA Structural Differences Distinguishes Eukaryotic Pus4 from Bacterial TruB.

RNA (New York, N.Y.)·2026

Same journal

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.

RNA (New York, N.Y.)·2026

Same journal

RBM38 Regulates HORMAD1 Splicing to Enhances MEK Inhibitor Sensitivity in Breast Cancer.

RNA (New York, N.Y.)·2026

Same journal

EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides.

RNA (New York, N.Y.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 9, 2025

Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster

Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster

Published on: August 21, 2014

A versatile tRNA modification-sensitive northern blot method with enhanced performance.

Abdul Khalique¹, Sandy Mattijssen¹, Richard J Maraia¹

¹Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.

RNA (New York, N.Y.)

|December 21, 2021

Summary

This summary is machine-generated.

The positive hybridization in the absence of modification (PHAM) assay detects tRNA modifications but can be inconsistent. This study refines the PHAM method for improved reliability in quantifying tRNA hypomodifications and associated diseases.

Keywords:

TRIT1 anticodon loop modification base methylation i6A37 t6A37

More Related Videos

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues

Published on: December 5, 2016

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

Related Experiment Videos

Last Updated: Oct 9, 2025

Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster

Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster

Published on: August 21, 2014

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues

Published on: December 5, 2016

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

Area of Science:

Molecular Biology
Genetics
Biochemistry

Background:

Human cells utilize numerous post-transcriptional modifications on mitochondrial and cytosolic tRNAs, crucial for their function.
Deficiencies in tRNA modification enzymes (TMEs) are linked to various diseases, highlighting the need for accurate detection methods.
The positive hybridization in the absence of modification (PHAM) assay was previously developed to quantify tRNA modifications.

Purpose of the Study:

To address observed inconsistencies and variability in the established PHAM assay.
To provide principles and practices for enhancing the reliability and uniformity of the PHAM assay.
To validate the improved PHAM assay and offer a tool for optimizing probe and hybridization conditions.

Main Methods:

Utilized a northern blot-based assay (PHAM) that relies on differential DNA-oligo probe annealing to modified versus unmodified tRNAs.
Documented and analyzed sources of inconsistency in the PHAM assay for specific tRNAs and probes.
Developed and validated improved conditions, including a calculator tool for probe and hybridization matching.

Main Results:

Identified and documented idiosyncratic inconsistencies and variability in the PHAM assay performance.
Demonstrated quantitative validation of the refined PHAM assay using a TME deletion control.
Showcased how nearby modifications can influence apparent modification efficiency calculations.

Conclusions:

The refined PHAM assay offers improved reliability and uniformity for quantifying tRNA modifications.
Understanding and mitigating assay variability is crucial for accurate assessment of tRNA hypomodifications.
The developed tools and practices facilitate advancements in studying tRNA modification-related diseases.