Separation of single-stranded DNAs using DNA conjugates having different migration properties in capillary electrophoresis

A probe-regulated simultaneous separation (PRESS) using capillary electrophoresis (CE) was developed for separating single-stranded (ss) DNAs. We synthesized two DNA conjugate probes, -(5′-TGTGTGTGT-3′)p-AAmq- and -(5′-GCCACCAGC-3′)m-AAmn-, by copolymerizing 5′-methacryloyl-modified ssDNA with acrylamide (AAm), and characterized them in detail. The two probes showed lower electrophoretic mobilities than 5′-methacryloyl-modified ssDNAs. Furthermore, -(5′-TGTGTGTGT-3′)p-AAmq- showed slightly faster electrophoretic mobility toward the anode than -(5′-GCCACCAGC-3′)m-AAmn- due to its higher molar fraction of negatively-charged ssDNA. We successfully separated target ssDNAs having the same chain length by using two ssDNA conjugate probes that showed different electrophoretic mobilities, although the separation of these ssDNAs was difficult in conventional capillary electrophoresis systems.