Prediction The Exchanging Route Of K~+ In Guanine-quadruplex

The existence of metal ions has great influence on the stability and conformation of DNA Quartet (guanine-quadruplex structure, G4), various studies show small monovalent cation such as K~+,Na~+,Li~+ or other ions can be found in G4. The G4 structure which coutains potassium ion is the most stable one. whether the cations presented in G4 can exchange with other cations surrounding? where is the special channel for exchanging? Considering the configuration characteristic, we designed three vibration models for K~+. First , we take a K~+ and one g-tetrad (g-tetrad-K~+) as studied object, ab initio [MP2/6-31G(d,p)] and ABEEMσπ/MM (Atom Bond Electronegativity Equalization Method atσπlevel fused into Molecular Mechanics) methods have been used to investigate the changes of structure, binding energy and total energe, when K~+ moves along the desigined routes in g-tetrad-K~+. The results indicate that ABEEMσπ/MM can accurately describe the structure and energy properties of the g-tetrad-K~+ system. the guanines in g-tetrad with K~+ adopt the parallel hydrogen bonds structure; the guanines in g-tetrad without K~+ adopt the bifurcate hydrogen bonds structure. the binding and total energe curves calculated by MP2 and ABEEMσπ/MM methods indicate that if absorb enough energy, K~+can leave fromα,β,γdirection,it is the easiest way that the K~+ moves out of the cavity along theαdirection.To approaching the practical system, we take the bigger system a K~+ and two g-tetrads(1,2-g-tetrads-K~+ and 2,3-g-tetrads-K~+), which is too big to calculate the interaction energy using MP2. ABEEMσπ/MM has been used to explore the 1,2-g-tetrads-K~+ and 2,3-g-tetrads-K~+, The changes of the binding energy and total energe from ABEEMσπ/MM, when K~+ moves in g-tetrad-K~+, 1,2-g-tetrads-K~+ and 2,3-g-tetrads-K~+ systems indicate that if absorb enough energy, it is easiest for the K~+ in G4 moves out of the cavity along theαdirection.