Accounting units in DNA

Chargaff's first parity rule (%A=%T and %G=%C) is explained by the Watson-Crick model for duplex DNA in which complementary base pairs form individual accounting units. Chargaff's second parity rule is that the first rule also applies to single strands of DNA. The limits of accounting units in single strands were examined by moving windows of various sizes along sequences and counting the relative proportions of A and T (the W bases), and of C and G (the S bases). Shuffled sequences account, on average, over shorter regions than the corresponding natural sequence. For an E. coli segment, S base accounting is, on average, contained within a region of 10 kb, whereas W base accounting requires regions in excess of 100 kb. Accounting requires the entire genome (190 kb) in the case of Vaccinia virus, which has an overall "Chargaff difference" of only 0.086% (i.e. only one in 1162 bases does not have a potential pairing partner in the same strand). Among the chromosomes of Saccharomyces cerevisiae, the total Chargaff differences for the W bases and for the S bases are usually correlated. In general, Chargaff differences for a natural sequence and its shuffled counterpart diverge maximally when 1 kb sequence windows are employed. This should be the optimum window size for examining correlations between Chargaff differences and sequence features which have arisen through natural selection. We propose that Chargaff's second parity rule reflects the evolution of genome-wide stem-loop potential as part of short- and long-range accounting processes which work together to sustain the integrity of various levels of information in DNA.