Parallel fabrication of RNA microarrays by mechanical transfer from a DNA master

A new method for fabrication of RNA microarrays is described. The approach involves cohybridization of a short, biotinylated DNA oligonucleotide and an RNA probe sequence to DNA templates spotted onto a master array. Next, the short DNA sequence and the RNA probe are linked using a T4 DNA ligase. Finally, a poly(dimethylsiloxane) (PDMS) monolith modified on the surface with streptavidin is brought into conformal contact with the master array. This results in binding of the biotinylated DNA/RNA oligonucleotides to the PDMS surface. When the two substrates are mechanically separated, the DNA/RNA oligonucleotides transfer to the PDMS replica, and the DNA oligonucleotides remaining on the master array are ready to template another RNA replica array. This sequence can be repeated for at least 18 cycles using a single master array. RNA arrays consisting of up to three different oligonucleotide sequences and consisting of up to 2500 individual approximately 70 microm spots have been prepared.