Accounting units in DNA

Chargaff's first parity rule (%A = %T and %G = %C) is explained by the Wats on-Crick model for duplex DNA in which complementary base pairs form indivi dual 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 s ingle strands were examined by moving windows of various sizes along sequen ces 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 IO kb, wherea s W base accounting requires regions in excess of 100 kb. Accounting requir es the entire genome (190 kb) in the case of Vaccinia virus, which has an o verall "Chargaff difference" of only 0.086% (i.e. only one in 1162 bases do es not have a potential pairing partner in the same strand). Among the chro mosomes of Saccharomyces cerevisiae, the total Chargaff differences for the W bases and for the S bases are usually correlated. In general, Chargaff d ifferences for a natural sequence and its shuffled counterpart diverge maxi mally when 1 kb sequence windows are employed. This should be the optimum w indow size for examining correlations between Chargaff differences and sequ ence features which have arisen through natural selection. We propose that Chargaffs second parity rule reflects the evolution of genome-wide stem-loo p potential as part of short- and long-range accounting processes which wor k together to sustain the integrity of various levels of information in DNA . (C) 1999 Academic Press.