Chargaff’s Second Parity Rule

Abstract

Prose, poetry and palindromes can be seen as informational devices that trade-off increasing degrees of redundancy in order to increase error-detecting power. The most extreme of these is the palindrome which, if a general restriction, would severely compromise the normal transfer of information between humans, while greatly decreasing the chances of error. That hereditary information in the form of DNA sequences is palindrome-like, suggests that evolutionary pressures for error-detection may be at least as powerful as those for the encoding of primary messages. Given limits on genome space, there are potential conflicts between different forms and levels of information. Classical Darwinian selective forces in the environment acting on an organism’s form and function provide extrinsic constraint, but genomes are also under intrinsic constraint. In palindromes there is a one-to-one pairing relationship between symbols (letters, bases). In DNA this finds expression as Chargaff’s second parity rule (PR2), namely Chargaff’s first parity rule for duplex DNA (PR1) also applies, to a close approximation, to single-stranded DNA. Selective forces generating the PR2 equivalences may have acted at higher oligomer levels than that of single bases. Diminished PR2 equivalences in protein-coding regions suggests diminished potential for secondary structure (stem-loops) in these regions. The intra-chromosomal ‘accounting’ that generated the mathematical regularities noted by Chargaff, may have been supplemented by inter-chromosomal ‘accounting.’