Fourier transform techniques have been used to analyze the distributio
ns of all ten independent DNA dinucleotide steps in two eukaryotic gen
omes and one prokaryotic genome, for periodicities of approximate to 2
to 500 bp. The results reveal systematic deviations from random expec
tation for certain dinucleotide steps over this entire range of period
icities, together with striking peaks at certain spatial periodicities
for particular dinucleotide steps. Several dinucleotides yield peaks
at a periodicity of approximate to 10.2 bp that are unique to the euka
ryotic genomes. Certain members of this set of dinucleotide signals we
re previously identified as involved in nucleosome positioning, while
others were previously unrecognized. In real-space, these dinucleotide
s are uncorrelated or even anticorrelated (relative to random expectat
ion) at distances of 10 and 11 bp, despite having greater than random
spectral power at the corresponding periodicity Real-space correlation
s of these dinucleotides at distances of 10 and 11 bp are suppressed b
y another spectral component, a 3 bp periodicity attributed to codons,
which has a local minimum probability at approximate to 10.5 bp. When
the two eukaryotic genomes are encoded for the signal ''AA or TT'', t
he peak at approximate to 10.2 bp periodicity is strengthened, whereas
for the prokaryotic genome such a peak remains absent. For the Caenor
habditis elegans genome, this peak becomes the dominant feature in the
transform, surpassing a peak owing to the existence of codons in both
height and integrated intensity. These results suggest that the requi
rements of chromosome structure place significant constraints on eukar
yotic genome organization; they reveal additional signals that may be
related to nucleosome positioning; and they reveal a wealth of additio
nal new non-random aspects of genome sequence organization. (C) 1996 A
cademic Press Limited