What is a DNA microarray?
A DNA microarray is a chip or slide that has been printed with a large number of DNA spots. Each spot is usually homogenous in its DNA composition (eg. each spot consists of multiple single strands of the same DNA sequence). The number of spots on a slide can be numerous and they can be densely packed (up to thousands per centimeter). The spots can be printed using a variety of techniques, such as photo-lithography, pin spotting, piezoelectric printing, and even electric gradient/node placement. The DNA microarray essentially acts like a massive, multiple probe hybridization. (Filter probe hybridization is a common molecular biology tool used to find a certain DNA/RNA sequence from a Northern/Southern blot.) DNA microarrays are very useful in determining which genes are being transcribed in a certain cell or tissue (and in what amount).

Microarrays are usually read by fluorescence. This is done by attaching a fluorescent tag onto the target cDNA, which fluoresces when it is excited by a laser in a scanning device. The problem is that the intensity of the fluorescence to cDNA density per spot is not a linear function, therefore making it difficult to get an exact quantification of gene expression.

My Research

I propose that by using biotin labeled targets, which are conjugated to gold colloidal streptavidin after hybridization , it is possible to quantify the amount of hybridization on a particular microarray spot using atomic force microscopy (AFM). By attaching a 10-20 nm gold probe sphere to the target DNA, it should be possible to observe the amount hybridized using the AFM to see the colloidal gold.

I have done a little bit of preliminary work with the AFM and the colloidal gold. Here are some pictures of the colloidal gold under the AFM.

This is a two dimensional view of the slide as taken with the AFM. The surface artifacts are colloidal gold probes.

Here is a three dimensional view of the slide. The colloidal gold artifacts are more prominent.