This paper presents electrokinetically based microfluidic integration of isolation and amplification of target-binding nucleic acids. A microfluidic device is used that consists of two microchambers for nucleic acid isolation and amplification connected by a microchannel filled with agarose gel. In the device, target-binding DNA strands are isolated and amplified on surfaces while gel-based electrophoresis is used to transfer the strands between chambers, eliminating the need for complicated flow control components. Experimental results show that the device has the potential to rapidly isolate and amplify nucleic acids in random mixtures against a variety of biological targets, such as biomolecules and cells, with increased binding affinity.