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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: Nov 27, 2025

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

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Three-Color Imaging Enables Simultaneous Screening of Multiple RNA Targets on Small Molecule Microarrays.

Deondre Jordan¹, Mo Yang¹, John S Schneekloth¹

¹Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland.

Current Protocols in Chemical Biology

|December 4, 2020

Summary

This study introduces a new method for screening small molecule ligands against multiple RNA targets simultaneously using multi-color imaging on small molecule microarrays (SMMs). This approach enhances drug discovery by evaluating compound specificity against various RNA structures efficiently.

Keywords:

RNA target SMM high throughput screening multi-color imaging small molecule microarray

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Last Updated: Nov 27, 2025

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

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Published on: August 3, 2011

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Published on: August 6, 2014

Rapid Colorimetric Assays to Qualitatively Distinguish RNA and DNA in Biomolecular Samples

Rapid Colorimetric Assays to Qualitatively Distinguish RNA and DNA in Biomolecular Samples

Published on: February 4, 2013

Area of Science:

Biochemistry
Molecular Biology
Drug Discovery

Background:

Small molecule microarray (SMM) technology is vital for high-throughput screening in drug discovery.
RNA molecules with complex structures offer attractive targets for novel therapeutics due to suitable binding pockets.
Previous SMM applications focused on screening single RNA targets.

Purpose of the Study:

To develop and report a novel SMM screening protocol for simultaneous investigation of multiple RNA targets.
To enable the evaluation of small molecule ligand specificity against diverse RNA structures.
To facilitate the identification of specific RNA-targeting compounds in drug discovery.

Main Methods:

Utilized small molecule microarray (SMM) technology.
Developed a multi-color imaging approach for simultaneous RNA screening.
Employed fluorophore-labeled RNA mixtures for detection.
Applied maleimide chemistry for RNA labeling.

Main Results:

Successfully demonstrated simultaneous screening of multiple RNA targets on SMMs.
Enabled simultaneous observation of fluorescence signals for each RNA binding event.
Facilitated easy evaluation of compound specificity against target RNAs versus abundant RNAs (e.g., tRNA, rRNA).

Conclusions:

The developed multi-color SMM protocol is effective for high-throughput screening of small molecule ligands against multiple RNA targets.
This method enhances the efficiency and specificity assessment in RNA-targeted drug discovery.
The protocol allows for the identification of specific binders among numerous potential interactions.