Capillary electrophoretic behavior and conformational analysis of triplet-repeat DNA

Abstract

Recently, much attention has been focused on the association of the higher order structure of genomic DNA, human gene, and mRNA with genetic and common diseases. For example, a change in the higher order structure of genomic DNA or mRNA induced by an expansion of trinucleotide repeats may cause some inherited neuromuscular diseases, called triplet-repeat diseases. We investigated the capillary electrophoretic behavior for triplet-repeat DNA fragments in detail and found that even a large triplet-repeat DNA fragment moves much faster than a small random-sequence DNA fragment within a capillary filled with a polymer solution. We proposed modified reptation theory to help understand such an unusual electrophoretic behavior, succeeded to estimate the drastic change in the persistence length of the triplet repeat DNA fragment, and elucidated the higher order structure of the human gene associated with genetic and common diseases. It showed that triplet-repeat DNA fragments are Jess flexible than single-stranded standard DNA fragments because of the higher order structures formed by the characteristic GC-rich sequences of triplet-repeat DNA fragments. In this study we established new method to investigate and elucidate the higher order structures of genomic DNA, human gene, and mRNA by capillary electrophoresis with high speed, high accuracy, and high sensitivity.