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

Abstract

AbstractA 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 > 106 units, are sorted into a three‐tiered well‐ordered fractal/Fibonacci 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.