Abstract
BackgroundChargaff's rule of DNA base composition, stating that DNA comprises equal amounts of adenine and thymine (%A = %T) and of guanine and cytosine (%C = %G), is well known because it was fundamental to the conception of the Watson-Crick model of DNA structure. His second parity rule stating that the base proportions of double-stranded DNA are also reflected in single-stranded DNA (%A = %T, %C = %G) is more obscure, likely because its biological basis and significance are still unresolved. Within each strand, the symmetry of single nucleotide composition extends even further, being demonstrated in the balance of di-, tri-, and multi-nucleotides with their respective complementary oligonucleotides.ResultsHere, we propose that inversions are sufficient to account for the symmetry within each single-stranded DNA. Human mitochondrial DNA does not demonstrate such intra-strand parity, and we consider how its different functional drivers may relate to our theory. This concept is supported by the recent observation that inversions occur frequently.ConclusionAlong with chromosomal duplications, inversions must have been shaping the architecture of genomes since the origin of life.
Highlights
Chargaff's rule of DNA base composition, stating that DNA comprises equal amounts of adenine and thymine (%A = %T) and of guanine and cytosine (%C = %G), is well known because it was fundamental to the conception of the Watson-Crick model of DNA structure
An and Tn are defined as the frequency of any particular oligonucleotide sequence and its reverse complementary sequence, respectively, in the same strand after n inversions (n > 0)
Inversions or interchromosomal rearrangements could render the duplicated gene nonfunctional due to its release from interaction with its promoter or other regulatory elements. This may be one reason why many inverted and interchromosomal segmental duplications are found in the human genome [25,26]
Summary
Chargaff's rule of DNA base composition, stating that DNA comprises equal amounts of adenine and thymine (%A = %T) and of guanine and cytosine (%C = %G), is well known because it was fundamental to the conception of the Watson-Crick model of DNA structure. His second parity rule stating that the base proportions of double-stranded DNA are reflected in single-stranded DNA (%A = %T, %C = %G) is more obscure, likely because its biological basis and significance are still unresolved. In spite of these anomalies, any violation of the second parity phenomena is generally small in magnitude [8,20]
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