Physicochemical basis of the recognition process in nucleic acid interactions, IV. Costacking as the cause of mispairing and intercalation in nucleic acid interactions.

In the first paper of this series,' we reported the interaction between the nucleosides and r(U)n as a model for monomer-polymer interaction.Our re- sults from equilibrium dialysis indicate that only when a threshold concentration of adenosine was reached did the binding of adenosine to r(U)n to form an ordered structure take place in a cooperative manner with a stacking energy of 5-6 kcal.Since adenosine associates extensively in aqueous solution to form vertical stacks,2 we proposed that these adenosine stacks bind to r(U)n cooperatively through spe- cific hydrogen bonding.Thus, both hydrogen bonding and the stacking force are essential, with the former more related to specificity and the latter to sta- bility.The interaction of nucleotides and nucleoside triphosphates with r(C)n and r(U)n was reported in the second and third papers of this series.3 4This same system has also been studied by laboratories at the National Institutes of Health with different emphasis.5-7In the present paper, the cause of mispairing and intercalation in nucleic acid interaction has been investigated.Materials.-Solutions of r(U). (Miles Laboratories, Elkhart, Indiana) at a concentra- tion of 10 mg/ml were dialyzed against 0.01 M Tris buffer, pH 7.0, for 12 hr in a cold room before use.The exact concentration of uridine units in solution was determined from optical density measurement at 259 mu by using the molar extinction coefficient of 9.2 X 103.Adenosine, guanosine, and cytidine were A grade preparations from Sigma Chemical Company, St. Louis, Missouri and were used without further purification.Caffine was purchased from Eastman Organic Chemicals, Rochester, New York, and was dried at 1200 for 24 hr before use.CL-adenosine, HI-caffeine, and HI-BP were obtained from Nuclear-Chicago Corporation, Des Plaines, Illinois, and H'-cytidine and H3-guanosine were obtained from Schwarz BioResearch, Orangeburg, New York.Before being used, HI-guanosine was checked by paper chromatography for possible contamination of adenosine.