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Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

Published on: February 19, 2019

A fluorescence-based screen for ribosome binding antibiotics.

Derrick Watkins¹, F A Norris, Sunil Kumar

¹NUBAD, LLC., Greenville, SC 29605, USA.

Analytical Biochemistry

|December 25, 2012

Summary

This summary is machine-generated.

New antibacterial drug discovery requires high-throughput screening. This study introduces a novel assay using fluorescein-conjugated neomycin (F-neo) to efficiently identify compounds with high affinity for the bacterial ribosome A-site.

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Last Updated: May 15, 2026

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Single Molecule Fluorescence Energy Transfer Study of Ribosome Protein Synthesis

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Published on: July 6, 2021

Area of Science:

Microbiology
Drug Discovery
Biochemistry

Background:

Rising antibiotic resistance necessitates novel antibacterial agents.
The bacterial ribosome A-site is a promising target for new antibiotics.
High-throughput screening is crucial for identifying high-affinity binders.

Purpose of the Study:

To develop a novel assay for high-throughput screening of potential antibacterial drugs.
To identify compounds that bind with high affinity to the bacterial ribosome A-site.
To utilize a fluorescein-conjugated neomycin (F-neo) probe for binding affinity determination.

Main Methods:

Development of a fluorescence-based assay using F-neo as a probe.
Measuring fluorescence changes upon F-neo binding to the Escherichia coli ribosomal A-site.
Assessing assay robustness and reproducibility using Z'-factor analysis.

Main Results:

F-neo binding to the ribosomal A-site caused a significant decrease in fluorescence.
The fluorescence change is attributed to alterations in the probe's pK(a) due to the electrostatic environment.
The assay demonstrated high reproducibility (Z'-factor > 0.80) and is adaptable for high-throughput screening.

Conclusions:

The developed F-neo assay is a robust and reproducible method for screening antibacterial compound libraries.
This assay facilitates the identification of novel antibacterial agents targeting the bacterial ribosome A-site.
The assay's adaptability to high-throughput formats will accelerate drug discovery efforts.