Printing microarray slides requires three (3) distinct components: genetic content (probe), deposition, and slide chemistry. Purified cDNA or oligonucleotide probes can be deposited (spotted, printed) onto a solid surface that is capable of binding nucleic acids. The deposition chemistry involves a chemical reaction between molecular groups on the glass surface and the probe, resulting in the formation of covalent bonds that bind the probe to the glass array. Both aldehyde and amine slides are available and each has a unique surface chemistry to enhance binding. Aldehyde slides link amine modified nucleic acids to aldehyde chemistry on slides (e.g., Telechem slides) and amine slides contain amine groups which are introduced to slides by treating cleaned slides with an aminosilane, such as 3-aminopropyltrimethoxysilane (e.g., Corning CMT-GAPS). Unmodified DNA can attach to the amine-modified slides via interactions between negatively charged phosphate groups on the DNA and the positively charged slide surface. The interaction ensures denaturation of the DNA, as well as increasing its binding affinity.

In addition to spotting solution and surface chemistry, environmental regulation is necessary to ensure uniform spot morphology, density, and reproducibility.