Non-random circular permutation of phage P22 DNA

Abstract

Phage P22 is known to have a linear duplex chromosome that is circularly permuted and terminally repeated. We have found, by constructing a partial denaturation map of mature P22 DNA, that circular permutation in P22 DNA is restricted: all of the ends of the mature DNA fall within 20% of each other on the physical map. The limited distribution of ends can be explained by the “headful” packaging model of Streisinger et al. (1967), with the additional specifications that: 1. (a) the intracellular precursor DNA is no longer than ten times the length of mature phage DNA; 2. (b) encapsulation of DNA starts at a unique site; 3. (c) encapsulation proceeds sequentially therefrom. This model is supported by the denaturation maps of two deletion phage DNAs. We found, as expected from our model, that the extent of permutation is a direct function of the length of terminal repetition. An independent demonstration of this relation between permutation and terminal repetition was done by denaturation-self-reannealing experiments using wild type and deletion phage DNAs. In the case of phage with large terminal repetitions (16%), we can discern discrete classes of molecules (using denaturation mapping), which we interpret as the first, second, etc. headful cut from the intracellular DNA concatemer.