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.