Figure 2.

Three basic types of microarrays: (A) Spotted arrays on glass, (B) self assembled arrays and (C) in-situ synthesized arrays.

A. With spotted arrays, a “pen” (or multiple pens) are dipped into solutions containing the DNA of interest and physically deposited on a 1“x 3” glass microscope slide. Typically the glass slide surface is coated with something to help retain the DNA such as polylysine {DeRisi, 1997 #28191}, a silane {Call, 2001 #28277} or a chemically reactive surface {Rogers, 1999 #28278} (to which chemically reactive oligos or PCR products would be added).

B. Self assembled arrays can be created by applying a collection of beads containing a diverse set of oligos to a surface with pits the size of the beads. After the array is constructed a series of hybridizations determine which oligo is in what position on each unique array (Ferguson et al., 2000; Michael et al., 1998; Steemers et al., 2000; Walt, 2000) (Gunderson et al., 2004).

C1 and C2. In-situ synthesized arrays can be produced by inkjet oligo synthesis methods (C1) or by photolithographic methods such as used by Affymetrix (C2).