Microarray synthesis instrument and method

A flow cell for synthesizing an array of oligomers, comprising:

• a chamber cover having a first surface to receive an illumination light and a second surface which is opposite to the first surface to form a first wall of an oligomer synthesis chamber in which oligomer synthesis reactions occur;
• a medium contained in the chamber;
• and
• a slide made of a material having a similar refractive index to that of the medium that is in the oligomer synthesis chamber during an illumination period, the slide having a surface on which oligomers are synthesized.

An apparatus for synthesizing arrays of oligomers such as DNA probes and polypeptides, the apparatus comprising:

• (i) a flow cell having in which monomer addition reactions can be conducted
• (ii) a substrate forming the front surface of the flow cell, the array being formed on the substrate;
• (iii) a light source providing a light beam;
• (iv) an array of optical elements placed to receive the light beam from the light source and arranged such that each element of the array can be positioned to direct light along an optical axis or to not direct light along the optical axis;
• (v) projection optics capable of receiving the light reflected from the array of optical elements along the optical axis and imaging the pattern of the optical elements onto the flow cell;
• and
• (vi) the flow cell containing a medium the index of refraction of which is matched to the index of refraction of the substrate so as to minimize light refractions at the interface between the substrate and the flow cell.