Anomalously fast migration of triplet-repeat DNA in capillary electrophoresis with linear polymer solution

Yuriko Kiba¹, Lihua Zhang, Yoshinobu Baba

¹Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, The University of Tokushima, Tokushima, Japan.

|February 6, 2003

Abstract:

We investigated the capillary electrophoretic behavior of single-stranded DNA fragments in methylcellulose solution, and found that triplet-repeat DNA showed anomalously faster mobilities than DNA markers with random sequence. Through the further study on the electrophoretic data, reptation model is proven appropriate to describe the migration of DNA under our experimental conditions. Accordingly, with the equations based on reptation theory, we could obtain the persistence length of DNA fragments and find that these values of triplet-repeat DNAs are larger than that of DNA markers with random sequence, which means the former DNAs are less flexible than the latter ones when they migrate in the electric field. This phenomenon is supposed to result from the characteristic higher-order structure formed by GC base pairs within triplet-repeat DNA, which is further proven by the resumed migration order in accordance with DNA size when the denaturant is added into the sieving matrix.

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Abstract:

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