THE INFLUENCE OF FLUORESCENT DYE STRUCTURE ON THE ELECTROPHORETIC MOBILITY OF END-LABELED DNA

Over the past 10 years, fluorescent end-labeling of DNA fragments has evolved into the preferred method of DNA detection for a wide variety of applications, including DNA sequencing and PCR fragment analysis. O ne of the advantages inherent in fluorescent detection methods is the ability to perform multi-color analyses, Unfortunately, labeling DNA f ragments with different fluorescent tags generally induces disparate r elative electrophoretic mobilities for the fragments. mobility-shift c orrections must therefore be applied to the electrophoretic data to co mpensate for these effects. These corrections may lead to increased er rors in the estimation of DNA fragment sizes and reduced confidence in DNA sequence information, Here, we present a systematic study of the relationship between dye structure and the resultant electrophoretic m obility of end-labeled DNA fragments. We have used a cyanine dye famil y as a paradigm and high-resolution capillary array electrophoresis (C AE) as the instrumentation platform. Our goals are to develop a genera l understanding of the effects of dyes on DNA electrophoretic mobility and to synthesize a family of DNA end-labels that impart identically matched mobility influences on DNA fragments. Such matched sets could be used in DNA sequencing and fragment sizing applications on capillar y electrophoresis instrumentation.