Protocols for GCAT
Producing Probes for DNA Chips

3DNA Method

GCAT has negotiated a deal with Genisphere to purchase smaller packages of their 3DNA probe production kits. This method is very different from traditional approaches and sounds ideal for undergraduate purposes. The kit includes the reagents for making 5 pairs of probes (five Cy5 and five Cy3) to conduct 5 experiments. The discounted price is $295 per kit and current GCAT Members may buy more than the limit of one kit that the rest of the world faces.

Benefits of the 3DNA method include:

To learn more about 3DNA, go to the Genisphere web page

Below is the method that has worked for GCAT Members
(Written by Todd Eckdahl at Missouri Western State College)

Protocol for Probe Production Using Genisphere 3DNA
Submicro EX and Microarray Hybridization Kit
with options in red text
enough reagents for 5 microarrays

Preparation Prior to Starting Protocol

RT Reaction

Preparing the Label

Prehybridization of Microarray


Post-hybridization Washing

Materials Needed:

Small volumes of the following (<1 ml):

Get Ready Beforehand:


Reverse Transcription (~30 minutes set-up and 2 hour incubation)


Preparation of Label (~1.5 hours)

A POSSIBLE STOPPING POINT Leave precipitations at -20° C

A POSSIBLE STOPPING POINT Leave precipitations at -20° C

A POSSIBLE STOPPING POINT - Store pellets at room temp

Pre-Hybridization (~45 minutes)

Hybridization (3 days)

Post-Hybridization (~1 hour)


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