SIMULTANEOUS DETERMINATION OF THE MIGRATION COEFFICIENT OF EACH BASE IN HETEROGENEOUS OLIGO-DNA BY GEL-FILLED CAPILLARY ELECTROPHORESIS

The direct determination of migration coefficients was achieved by ana lysing the migration time of heterogeneous oligo-DNA with a gel filled capillary using the Gauss least-squares method for the observation fu nctions, assuming that the migration time of oligo-DNA is dependent on its base composition and chain length. By using the coefficients obta ined, the migration time of oligo-DNA of any known sequence that does not have a secondary structure can be estimated with an accuracy of le ss than 0.5-mer of cytidine. In addition, from the deviation of the ac tual migration time from the calculated migration time in certain spec ially designed base sequences, the existence of a secondary structure such as a hairpin structure was strongly suggested even in the presenc e of 7 M urea. From the investigation of the effects of secondary stru cture on migration time, it was concluded that this approach will give qualitative information on secondary structure, which may be applicab le in work such as single strand conformational polymorphism (SSCP) an alysis or antisense DNA analysis, in which secondary structure plays a n important role in accelerating or decelerating migration times. The results of the analysis also predict the apparent chain length reversa l from short to long together with a reduction in the actual chain len gth in DNA sequencing using capillary electrophoresis.