Simulation of the interactions between Tröger bases and DNA

Journal of the Brazilian Chemical Society

Netz, Paulo A.¹  Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil¹  Ricci, Clarisse G.¹ 

关键词: DNA;    molecular dynamics;    Tröger bases;   

DOI  :  10.1590/S0103-50532012000700019

学科分类：化学（综合）

来源: SciELO

【 摘 要 】

Tröger bases are a class of molecules that, due to its geometry, bind enantioselectively to DNA. Molecular dynamic simulations were performed with levorotatory isomers of proflavine and phenanthroline substituted Tröger bases. Starting with the bases docked in DNA, the distortions they promote in the double helix were investigated in two possible modes: intercalation and minor groove binding. In the intercalation complexes, they presented long residence times and distorted the double helix leading to partial unwinding and to non-canonical values of some backbone angles. In the minor groove complexes, they displayed high mobility, leading to a change in the binding mode, interacting with the minor groove mainly through the diazocin bridge. The results suggested the intercalation of one substituent (with additional contacts in the minor groove) as the preferential binding mode for these Tröger bases, while minor groove binding may explain the weaker binding observed for the dextrorotatory isomers.

【 授权许可】

Unknown