The structure of kinetoplast DNA: I. Properties of the intact multi-circular complex from Crithidia luciliae

Abstract

1. We have developed a modified isolation procedure that yields kinetoplast DNA networks containing more than 90% closed circular DNA, as judged by two criteria: 1. (a) In 0.15 M NaCl 0.015 M sodium citrate (pH 7.0), less than 10% of the intact kinetoplast DNA melts in the temperature region of sonicated kinetoplast DNA. In 7.2 M NaClO 4 the kinetoplast DNA melts with a T m 26° C higher than sonicated kinetoplast DNA. Even after complete melting in 7.2 M NaClO 4 at 90° C, the network remains intact, as judged by regain of hypochromicity on cooling and analysis in CsCl containing propidium diiodide. 2. (b) In alkaline sucrose gradients more than 90% of the kinetoplast DNA sediments in a single peak. 2. In CsCl gradients containing ethidium bromide or propidium diiodide intact kinetoplast DNA gives a single uni-modal band showing an extremely restricted dye uptake. From the position of the band relative to the bands of PM2 DNA, the superhelix density of these networks is calculated to be +3.9 twists per 1000 base pairs. The superhelix density of closed mini-circles, efficiently liberated from the networks by shear in a French press, is −0.5 twists per 1000 base pairs. We attribute the high superhelix density (the highest yet observed in any DNA) of intact networks to their compact, highly catenated structure, leading to an additional constraint on dye uptake, superimposed on the restriction due to closed circularity.