guanosine-monophosphate and guanylyl-(3--5-)-cytidine

Monte Carlo computer simulation techniques may be used to predict structural properties of solvent networks in helical fragments of nucleic acids, provided that suitable potential functions are available to describe the interactions between nucleic acid atoms, water and counterions. Previous studies have shown that simple non-bonded and point charge parameters are adequate for mononuclear ions such as sodium and calcium. In this study a model interaction potential for the polynuclear ammonium ion is evaluated. The parameters used take account of the distribution of charge over the constituent atoms in the ion. Simulations are carried out on the ammonium salt of a small nucleic acid crystal hydrate and a comparison is made between the predicted and experimental results. It is shown that the simulated structure is in reasonable agreement with experiment. It is therefore feasible to use this potential in studies of ammonium-containing bimolecular systems.

Topics: Computer Simulation; Crystallography; Cytidine; Dinucleoside Phosphates; DNA; Guanosine Monophosphate; Models, Biological; Monte Carlo Method; Nucleic Acid Conformation; Operations Research; Quaternary Ammonium Compounds

A knowledge of structural and energetic aspects of water- and ion-nucleic acid interactions is essential for the understanding of the role of solvent and counterions in stabilising the various helical forms of nucleic acids. In this study, Monte Carlo computer simulation techniques have been used to predict structural properties of solvent networks in small nucleic acid crystal hydrates containing the ions sodium, ammonium and calcium. Appropriate parameters to describe the interaction potentials of the ions are added to those previously developed for water and nucleic acid atoms. A comparison is made between the predicted and experimental results and it is concluded that the potential functions used lead to simulated solvent structure in reasonable agreement with experimental data, at least in the cases of sodium and calcium. It is now feasible to use these functions in studies of hydration of larger helical fragments of nucleic acids of more direct biological interest.

Topics: Calcium; Computer Simulation; Crystallization; Cytidine; Dinucleoside Phosphates; DNA; Guanosine Monophosphate; Models, Chemical; Monte Carlo Method; Nucleic Acid Conformation; Operations Research; Quaternary Ammonium Compounds; Sodium; Water