Effect of Target Length on Specificity and Sensitivity of OligonucleotideMicroarrays: A Comparison between Dendrimer and Modified PCR basedLabelling Methods

摘要

DNA microarrays are widely used as end point detectors for gene expression analysis. Several methods havebeen developed for target labelling to enable quantification but without taking target length into consideration. Here wehighlight the importance of choosing the optimum target length that would ensure specificity without compromising sensitivityof the assay. For this, eight plasmids that are identical to each other except for a closely related 23 bp unique reporter(UR) sequence were used to examine the hybridization efficiency for these URs. Targets of various lengths weregenerated and labelled as follows: full length and 330 bases transcripts using a dendrimer labelling method, 120 bp ampliconsby the modified PCR end labelling method and synthetic labelled targets of 33 bases. This report also shows the advantagesof using the modified PCR method over other labelling methods in generating labelled amplicons of the desiredlengths to maximize hybridization efficiency.