Nucleic Acids Research, Vol 26, Issue 11 2797-2802, Copyright © 1998 by Oxford University Press
O Tu, T Knott, M Marsh, K Bechtol, D Harris, D Barker and J Bashkin
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. One of
the advantages inherent in fluorescent detection methods is the ability to
perform multi-color analyses. Unfortunately, labeling DNA fragments with
different fluorescent tags generally induces disparate relative
electrophoretic mobilities for the fragments. Mobility-shift corrections
must therefore be applied to the electrophoretic data to compensate for
these effects. These corrections may lead to increased errors 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 mobility of
end-labeled DNA fragments. We have used a cyanine dye family as a paradigm
and high-resolution capillary array electrophoresis (CAE) as the
instrumentation platform. Our goals are to develop a general 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 capillary electrophoresis
instrumentation.
ARTICLES
The influence of fluorescent dye structure on the electrophoretic mobility of end-labeled DNA
Molecular Dynamics, Sunnyvale, CA 94086, USA and Amersham International, Amersham, UK.
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