A biochemist's most useful tool these days are molecules with a binding site on one end and a glowing fluorescent complex {of fluorine?} on the other end.

Chemists arrange molecules in a sample (possibly by GelElectrophoresis, for example, or by letting living creatures arrange them). Then they wash the sample with these fluorescent stains, and use a FluorescentMicroscope to detect the location, color, and intensity of the glow. This reveals where molecules matching the binding site appeared in the substrate.

MicroArray technology combines an FM with 3D resolution, called a LaserScanningConfocalMicroscope, with DNA strands linked to an array of tiny beads to sense the locations of fluorescent markers known to bond to specific Base sequences. Alternating baths of fluorescent markers with baths of RestrictionEnzyme's to snip the sensed sequences off can read, bead per bead, the complete sequence of the DNA strands.

http://www.cyto.purdue.edu/flowcyt/educate/confocal/524Lec4/sld004.htm