title: [Formation of noncanonical structures in superhelical DNA. Mutual effects of various transitions].
abstract: This is a theoretical study of the problem of formation of noncanonical structures, cruciforms in palindromic regions and the Z form in purine--pyrimidine sequences, in negatively supercoiled DNA. If two such regions, one palindromic and one purine--pyrimidine, are present in the same DNA molecule of a finite length, then transitions between the regular B form and noncanonical structures in these regions will experience a considerable mutual influence. This takes place because both noncanonical structures compete for the same superhelix energy. A special attention is paid to the case when the probability of the Z form formation nonmonotonously depends on the superhelix density. Such a situation is shown to be possible for some specific interrelation between the DNA length, the length of the palindromic region and the length of the purine--pyrimidine region. The calculations show that in this case the Z form is formed first with the increasing superhelix density, that the cruciform structure is formed whereas the purine--pyrimidine region returns into the B form, and finally, the Z form is formed again. The possibility of experimental observation of such unusual behaviour is discussed.
mesh_terms: D001483:Base Sequence; D004270:DNA, Circular; D004278:DNA, Superhelical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004270:DNA, Circular; D004278:DNA, Superhelical
vernacular_title: Obrazovanie nekanonicheskikh struktur v sverkhspiral'noĭ DNK. Vzaimnoe vliianie razlichnykh perekhodov.