Jc. O'Brien et al., Preparation and characterization of self-assembled double-stranded DNA (dsDNA) microarrays for protein : dsDNA screening using atomic force microscopy, LANGMUIR, 16(24), 2000, pp. 9559-9567
We report details on the development of a self-assembled, double-stranded D
NA (dsDNA) microarray fabrication strategy suitable for protein:dsDNA scree
ning using the atomic force microscope (AFM). Using disulfide-modified dsDN
A (26-mer) synthesized to contain the recognition sequence for ECoR1, we ha
ve created micron-sized mixed monolayer surfaces where both the spatial ori
entation and packing density of the immobilized oligonucleotides, two criti
cal parameters for screening protein:dsDNA interactions, are controlled. Be
fore exposure to ECoR1, the topography of microarrays that were composed of
26-mers containing the recognition sequence for EcoR1 was 8.8 nm +/- 1.5 n
m (n = 5), a value consistent with that predicted by X-ray diffraction stud
ies. After enzyme digestion, the topography of the microarray decreased to
4.3 nm +/- 0.8 nm (n = 14), a value consistent with predictions based on th
e position of the recognition sequence within the oligonucleotides. In cont
rast, the topography of microarrays that were composed of 26-mers that did
not contain the recognition sequence for ECoR1 remained essentially the sam
e before (8.9 nm +/- 1.5 nm (n = 5)) and after (8.3 nm +/- 1.4 nm (n = 5))
exposure to ECoR1. Furthermore, because the dsDNA were synthesized to inclu
de a fluorescein moiety above the recognition sequence, the loss of fluores
cence after exposure to ECoR1 was also used to detect enzymatic cleavage. W
e believe that this technology holds promise as a tool for the rapid and fa
cile screening of multiple protein interactions using massively parallel ds
DNA microarrays.