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 analysing the migration time of heterogeneous oligo-DNA with a gel filled capillary using the Gauss least-squares method for the observation functions, assuming that the migration time of oligo-DNA is dependent on its base composition and chain length. By using the coefficients obtained, the migration time of oligo-DNA of any known sequence that does not have a secondary structure can be estimated with an accuracy of less than 0.5-mer of cytidine. In addition, from the deviation of the actual migration time from the calculated migration time in certain specially designed base sequences, the existence of a secondary structure such as a hairpin structure was strongly suggested even in the presence of 7 M urea. From the investigation of the effects of secondary structure on migration time, it was concluded that this approach will give qualitative information on secondary structure, which may be applicable in work such as single strand conformational polymorphism (SSCP) analysis or antisense DNA analysis, in which secondary structure plays an important role in accelerating or decelerating migration times. The results of the analysis also predict the apparent chain length reversal from short to long together with a reduction in the actual chain length in DNA sequencing using capillary electrophoresis.