Book of Abstracts: Albany 2005
Molecular Modeling for Biogenic Polyamines Bindings to B-DNA and A-RNA Duplex
Biogenic polyamines, such as putrescine, spermidine and spermine, are small organic polycations involved in numerous diverse biological processes. These compounds play an important role in nucleic acid function due to their bindings to DNA and RNA. We now report the results of molecular modeling, capillary electrophoresis, FTIR, and CD spectroscopic analysis of calf-thymus DNA and transfer RNA interactions with biogenic polyamine, spermine, spermidine, putrescine, and inorganic cobalt-hexamine cations in aqueous solution at physiological conditions.
Major and minor groove bindings with inter- and intra-molecular interactions were observed for biogenic polyamines, while cobalt-hexamine binding was mainly to the G-C base pair and the backbone phosphate groups. The stability of the complexes formed were of the order KSpm = 2.3 × 105 M-1 > KSpd = 1.4 × 105 M-1 > and KPut = 1.02 × 105 M-1 and KCo = 1.8 × 105 M-1 and KCo = 9.2 × 104 M-1 for DNA and KSpm = 8.7 × 105 M-1 > KSpd = 6.1 × 105 M-1 > and KPut = 1.5 × 105 M-1 and KCo = 2.1 × 105 M-1 and KCo = 1.2 × 105 M-1 for tRNA adducts. No major alterations of B-DNA or A-RNA were observed for biogenic polyamines, while cobalt(III)hexamine induced a partial B-DNA to A-DNA transition. DNA condensation was also observed for cobalt(III)hexamine cation, whereas organic polyamines induced duplex stabilization. The Hill coefficients indicate a positive cooperativity binding for biogenic polyamines and a negative cooperativity for cobalt(III)hexamine (1).
References and Footnotes
Department of Chemistry-Biology