Figure 6. An overview of the cDNA array assay.

ERDC TN-DOER-C19

December 2000

Isolate mRNA population

AAAUGUCGGA...

Convert to labeled cDNA

AAAUGUCGGA...

(PCR)

TTTACAGCCT...

Hybridize to array

TTTACAGCCT...

AAATGTCGGA...

Array membrane

Detection of labeled cDNA

(radiometric, chemiluminescent,

or fluorescent detection)

Treated

Control

Compare control and treated arrays to

determine which genes have been up or

down regulated (increase or decreased

signal compared to control array)

Figure 6. An overview of the cDNA array assay. The mRNA populations are isolated from control and

treated cell cultures (a partial sequence shown to the right as an example), converted to

tagged cDNA (shown in green), and hybridized to the cDNA bound to the array (one of the

genes on the array shown in blue)

models for risk assessment than is presently possible (Corton et al. 1999; Nuwaysir et al. 1999;

Rockett and Dix 1999). The mechanistic information obtained from the arrays can also be valuable

in determining which samples require further examination with more time-consuming and expen-

sive bioassays, and can direct the type of bioassay (e.g., survival, growth and reproduction,

genotoxicity) that should be conducted. Additionally, use of the cDNA arrays to test sediment ex-

tracts can help direct the development and/or use of other assays. For example, screening of typical

dredged sediments with cDNA arrays may indicate that certain endpoints (e.g., metal-responsive

genes) consistently show positive responses and warrant further evaluation with cell-based assays,

which can provide high throughput screens due to their compatibility with the 96-well microtiter

plate format. Alternatively, initial screening of a site with cDNA arrays may indicate that a certain

contaminant class is of concern, whereupon the appropriate cell-based assays can be utilized to