Combined Monte Carlo and quantum mechanics study of the hydration of the guanine-cytosine base pair

We present a computer simulation study of the hydration of the guanine-cytosine (GC) hydrogen-bonded complex. Using first principles density-functional theory, with gradient-corrected exchange-correlation and Monte Carlo simulation, we include thermal contribution, structural effects, solvent polarization, and the water-water and water-GC hydrogen bond interaction to show that the GC interaction in an aqueous environment is weakened to about $70\%$ of the value obtained for an isolated complex. We also analyze in detail the preferred hydration sites of the GC pair and show that on the average it makes around five hydrogen bonds with water.

Figure 1

(Color online) Guanine-cytosine base pair and definition of the indices. The bottom shows the lateral view with the interplanar angle of $7°$.

Figure 2

(Color online) Superposition of 75 configurations of the GC pair obtained from the Monte Carlo simulation in gas phase (top) and in aqueous solution (bottom).

Figure 3

Histogram of the number of hydrogen bonds formed between the GC pair and the solvent water molecules obtained from the Monte Carlo simulation.

Figure 4

(Color online) Illustration showing one typical configuration of the Monte Carlo simulation, with five water molecules hydrogen-bonded to the GC pair.

Figure 5

(Color online) Illustration of the network of nearest hydrogen-bonded water molecules around the GC pair, obtained from the Monte Carlo simulations.

Figure 6

Convergence of the calculated average binding energy with the number of Monte Carlo configurations. The error bar is the statistical error. The top is obtained using the simulation for the isolated GC pair (gas) and the bottom is for the GC pair in the aqueous environment. See the text and Table .

Figure 7

Histogram of the calculated dipole moment for the Monte Carlo configurations of the GC pair in water.