Binding of 9-N-Butyladenine by Carboxylic Acids: Evidence that Hoogsteen Binding Can Dominate in Solution

Abstract

1 H NMR titration of 9-N-butyladenine (1) with a series of 11 representative carboxylic acids has been carried out in CDCl 3 by following the chemical shifts of δ H-2 and δ H-8 of 1 to determine the association constants for the Watson-Crick and the Hoogsteen modes of binding. Compound 1 has been found to bind carboxylic acids through the Watson-Crick (WC) site or the Hoogsteen (HG) site. The binding of carboxylic acids from the WC site shifts the δ H-2 signal upfield, whereas the binding from the HG site shifts the δ H-8 signal downfield. Analyses of binding-induced shifts of δ H-2 and δ H-8 of 1 in the presence of the carboxylic acids have indicated a distinct preference for the HG site by aromatic carboxylic acids, such as benzoic acid and monobenzyl isophthalate. On the other hand, aliphatic acids such as 4-nitrophenylacetic acid and propanoic acid are found to prefer the WC site for complexing 1. Binding affinities of a few alkenoic and alkynoic acids were also determined. In addition to the complexes (1/acid) of 1:1 stoichiometry, the possibility of a 1:2 complexation between 1 and the carboxylic acids is addressed. A possible rationale for the upfield shift of H-2 (of 1) upon binding by a carboxylic acid is discussed. The K a 's were found to increase in general with enhanced acidity of the carboxylic acids. However, the pK a values of the acids do not appear to determine the site-specificity of the binding of 1.