Methods and compositions are provided for producing arrays of polymeric binding
agents. In the subject methods, the individual polymers of the array are synthesized
using solid phase synthesis techniques on the surface of a substrate. A critical
feature of the invention is that one or more locations on the substrate surface
are spatially and temporally protected by a protective bubble during the synthesis
protocol, where the protective bubble may be produced using any convenient bubble
producing means. The bubble producing means may be a component of either a substrate
or a structure separate from the substrate. Also provided are the arrays produced
by the subject methods, kits for use in practicing the subject methods, and methods
of using the arrays in analyte detection assays, including hybridization assays,
such as gene discovery, differential gene expression and gene sequencing assays.
