DNA in phosphorus atom representation: the heteronomous double helices of poly(dA).poly(dT) and poly(dG).poly(dC) and simulation of the yeast genome and of a human chromosome DNA.
We extracted phosphorus atom coordinates from the database of DNA crystal structures and calculated geometrical parameters needed to reproduce the crystal structures in the phosphorus atom representation. Using the geometrical parameters we wrote a piece of software assigning the phosphorus atom coordinates to the DNA of any nucleotide sequence. The software demonstrates non-negligible influence of the primary structure on DNA helicity, which may stand behind the heteromonous double helices of poly(dA).poly(dT) and poly(dG).poly(dC). In addition, the software is so simple that it makes possible to simulate the "crystal" structures of not only viral DNAs, but also the whole genome of Saccharomyces cerevisiae as well as the DNA human chromosome 22 having dozens of megabases in length.
Hanzálek
Petr
P
Institute of Biophysics of the Academy of Sciences, of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.
Kypr
Jaroslav
J
D002892:Chromosomes, Human, Pair 22 / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry*; D004271:DNA, Fungal / Q000737:chemistry; D016678:Genome; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010758:Phosphorus / Q000737:chemistry*; D011066:Poly C / Q000235:genetics; D011068:Poly G / Q000235:genetics; D011067:Poly dA-dT / Q000235:genetics; D017434:Protein Structure, Tertiary; D012441:Saccharomyces cerevisiae / Q000235:genetics*
D004271:DNA, Fungal; D011068:Poly G; C023826:poly(dC); C026628:poly(dG); D011067:Poly dA-dT; D010758:Phosphorus; D011066:Poly C; D004247:DNA