title: Theoretical evidence for the significance of certain types of DNA secondary structure in the genomes of phi X174, G4, fd, SV40 and the plasmid pBR322.
abstract: The significance of certain types of DNA secondary structure was assessed on a purely theoretical basis by analyzing their distribution over the entire genomes of bacteriophages phi X174, G4, fd, the eucaryotic virus SV40 and the E. coli plasmid pBR322. A computer program was designed to search the translated and non-translated (intercistronic) regions of these genomes for the potential of forming perfect hairpins (perfectly base paired stems: no G-T pairing; no interruptions) with small loops. The number of found occurrences was then compared to the statistically expected number. The results reveal a significant excess in each genome of perfect hairpins with stem length greater than 7 and end loops less than or equal to 20 over that expected given their nucleotide composition. For stem length of 5 to 7 the same observation holds true for the intercistronic regions, but for translated regions the number of such structures is below expectation. This suggests an evolutionary selection for these structures.
mesh_terms: D005075:Biological Evolution; D003090:Coliphages / Q000235:genetics / Q000648:ultrastructure*; D004279:DNA, Viral; D005796:Genes; D005814:Genes, Viral; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D010957:Plasmids; D013539:Simian virus 40 / Q000235:genetics / Q000648:ultrastructure*; D013329:Structure-Activity Relationship
chemical_list: D004279:DNA, Viral