CHROMOSOMES AS INTERDEPENDENT ACCOUNTING UNITS: THE ASSIGNED ORIENTATION OF C-ELEGANS CHROMOSOMES MINIMIZES THE TOTAL W-BASE CHARGAFF DIFFERENCE

DNAs of individual chromosomes violate, albeit perhaps by only one in a thousand bases, Chargaff's second parity rule, which is that Chargaff's first parity rule for duplex DNA A = T, G = C) applies, to a close approximation, to single stranded DNA. If the top strand of one chromosome has A > T and the top strand of another has T > A, can they complement to approach even parity A = T)? Assignment of orientation to the six chromosomes of Caenorhabditis elegans is said to have been arbitrary and, of 26(= 64) possible combinations of top T) and bottom B) strands, the GenBank orientation designated TTTTTT) is but one. Yet, for the W bases A and T) the chromosomes in the GenBank orientation complement to reduce the Chargaff difference A-T) to only 200 bases (i.e. only one in 323,658 bases does not have a potential Watson-Crick pairing partner). This suggests that the assignment was not arbitrary. However, the GenBank orientation for the S bases G and C) allows an approach to even parity less well than many other orientations, the best of which is BBBBTT indicating a disparity between the GenBank orientations of the first four autosomes and those of chromosomes V and X). Although only the euchromatic regions of Drosophila melanogaster chromosomes have been sequenced, there are orientations that allow an approach to even parity. We conclude that, with respect to their Chargaff differences, the chromosomes of C. elegans have the potential to engage in interdependent base accounting. Since this might also apply to D. melanogaster, even when heterochromatin-associated DNA rich in tandem repeats (microsatellite DNA) is excluded, then heterochromatic DNA might not normally participate in the hypothetical accounting process.