The specificity of molecular binding between the "target" and the "probe" m
olecule, for example, between antigen and antibody or between two complemen
tary deoxyribonucleic acid (DNA) sequences, is the principle of affinity as
says. In the assay, the target is mixed with the fluorescence-labeled probe
, so that the probe binds to the target to form a target-probe complex. The
n, the bound complex is separated from the free (unbound) probe somehow (bo
und/free (BF) separation), and the fluorescence emission from the separated
complex is measured to obtain the target concentration in the original sam
ple. In this paper, we propose and experimentally demonstrate the use of di
electrophoresis (DEP) for such B/F separations. Using DEP chromatography, D
EP characteristics of various biomolecules are measured, and: 1) separation
of lambda -DNA (48.5 kbp) and oligonucleotide (22base) and 2) quantitative
detection of antigen-antibody bindings, are demonstrated. Using the triple
complex formation to facilitate DEP separation, a method is developed to d
etect B/F binding by a direct observation of the separation pattern on the
microelectrode system. It is applied for: 1) quantitative detection of alph
a-fetoprotein, the diagnostic marker of liver cancer, through antigen-antib
ody reaction and 2) the detection of DNA sequence through hybridization. Th
e methods developed here are compatible with micro fabrication, and suitabl
e for affinity assays in micro-total analysis systems.