Theoretical Explanation of Mouse Satellite DNA Renaturation Kinetics

Abstract

DNA base sequence complexity is commonly calculated from k′₂, the observed second order rate constant of renaturation corrected to constant molecular weight and defined renaturation conditions^1–4. Several investigators have cautioned that k′₂ is influenced by base pair mismatching in the reacting DNA sequences^5–7, but no other serious difficulties have been noticed in using k′₂ values to measure base sequence complexity except for the case of mouse satellite DNA. Waring et al.³ and Flamm et al.⁸ calculated a repeat length of 350 nucleotides from k′₂ measurements, but Southern⁹ found a repeating unit of approximately twelve nucleotides by analysis of pyrimidine tracts. Hutton and Wetmur¹⁰ have recently shown that the kinetic complexity of mouse satellite DNA defies conventional analysis: the apparent repeat size calculated from k′₂ depends upon the DNA fragment size. I shall show that for a particular kind of DNA structure, of which mouse satellite DNA is an example, the usual method of calculating base sequence complexity from k′₂ cannot be used. The difficulty stems from an altered molecular weight dependence of k₂ for DNA repeated sequences which are shorter than the length of the reacting DNA strands.