Fractal displays of genomic DNA. I. Eco RI fractal lattice of buffalo rat

Abstract

A complex multidimensional DNA structure is obtained when treating the elements of the Eco RI restriction set of buffalo rat as a cascade of self-similar units. Fifteen of the 16 (about 94%) Eco RI repeat families, ranging in length from 2300 to 83 nucleotides and in frequency from 500 to >lo6 units, are sorted into a three-tiered well-ordered fractaliFibonacci lattice. On the first level, 11 fractal dimensions are defined as unique collinear collections of repeat DNA families in a "graph-invariant'' plot of log(fragment length) : log(frequency). On the second level, the individual dimensional arrays are clustered as groups, each sharing, at last, one common vertex. On the third level, the entire display is scaled along a stepwise log to the base 6 expansion. This study represents the first successful attempt to unify an "entire" set of repeat DNAs into a single motif, in effect confirming the contention that select repeat DNAs provide a framework for the discrete packaging and unpackaging of genomic information.