Binding of non-intercalating antibiotics to B-DNA: a theoretical study taking into account nucleic acid flexibility.
A detailed theoretical study has been made for five antibiotics which all bind selectively to AT sequences in the minor groove of B-DNA: SN-18071, NSC-101327, distamycin-2, distamycin-3 and netropsin. The optimal complexes were found for systems in which the flexibility of DNA, as well as that of the antibiotics, was taken into account. Explicit, mobile counterions and a dielectric function modelling aqueous solution were also included. The binding geometries of the most strongly interacting antibiotics, distamycin-3 and netropsin, are compared in considerable detail and it is shown that notable differences exist between them. The results for netropsin are also discussed in the light of recent disagreements concerning its exact binding location within DNA.
Lavery
R
R
Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique associé au C.N.R.S., Paris, France.
Zakrzewska
K
K
Pullman
B
B
D000900:Anti-Bacterial Agents; D001665:Binding Sites; D004247:DNA; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011067:Poly dA-dT; D013816:Thermodynamics
D000900:Anti-Bacterial Agents; D011067:Poly dA-dT; D004247:DNA