Binding properties and conformational dynamics of reversible amidines with DNA from a theoretical view

Abstract We present here molecular dynamics simulations and DNA conformational dynamics for three reversible amidine-DNA adducts. Our simulation results indicated that a DNA molecule bound by a reversible amidine produced a narrow and deep minor groove. The N–H and C–H groups in binding regions from reversible amidines play important roles on functioning as H-bond donors to N or O atoms of nucleobase located on the floor of the minor groove of DNA. DNA conformational dynamics in the vicinity of binding region were influenced significantly by the reversible amidine on a nanosecond time scale. The obtained results demonstrated that influence of the central heterocycle is greater than that of tail part for reversible amidines binding affinity to DNA. All of these findings provide useful information to better understand the binding properties and conformation dynamics of the reversible amidines with DNA.