Molecular recognition of Watson-Crick-like purine-purine base pairs.

Nucleic acid duplexes containing non-Watson–Crick base pairs are of interest to several fields including structural biology, supramolecular chemistry, origin of life, and synthetic biology. An early observation of a natural non-Watson–Crick base pair was the tRNA–mRNA adenine–inosine wobble pair, and it is now known that purine–purine pairs occur frequently in natural RNAs, including ribosomes and tRNAs. Crick even proposed that purine–purine base pairs might have been the original mode of information transfer in early life, a proposal that recently received support from the observation that duplexes with only purine–purine pairs can be as stable as Watson–Crick duplexes. Given that small-molecule recognition of nucleic acids is an important element of drug development, biochemical assays, and rationally designed molecular assemblies, and because intercalation might have played a role in the origin of nucleic acids, we have explored the interaction of several nucleic acid intercalators with DNA purine–purine duplexes. Here, we demonstrate the ability of some small molecules to bind duplexes containing guanine–isoguanine and adenine–inosine base pairs (Scheme 1A) with selectivity over duplexes with Watson–Crick base pairs (Scheme 1B), and vice versa. This selectivity is consistent with the structural differences expected between these two classes of duplexes, which arise from differences in base-pair size and shape and helix groove geometry. This study represents, to the best of our knowledge, the first demonstration of selective binding of small molecules to an informational, but non-Watson–Crick, duplex. Ethidium, proflavine, and ellipticine are three classical intercalators of Watson–Crick DNA. These molecules are each characterized by a single positive charge and a planar, multicyclic surface that is approximately the size of a Watson–Crick base pair (Scheme 1C). However, the structures of these molecules differ in other respects, thereby providing a means to explore the potential for shape-selective binding to purine– purine base pairs. The representative purine–purine duplex used in this study, Pu·Pu, was formed from self-complementary dodecamers with the nucleotide sequence d(#AGIAG#IA#IG) (I, inosine; #, isoguanine). For all the small-molecule ligands investigated, binding to Pu·Pu was compared with binding to the analogous Watson–Crick duplex, WC, with C in place of #, and T in place of I, that is, d(CAGTAGCTACTG). Pu·Pu causes a 41 nm red shift of the longest-wavelength absorbance bands of ethidium, which is the same as the shift observed when ethidium binds to WC. The shapes of these two red-shifted absorbance bands are also virtually identical (Figure 1A). This result suggests a common binding mode of ethidium by Pu·Pu and WC. The same phenomenon is observed for proflavine, which gives a red shift of 22 nm upon binding to either Pu·Pu or WC (Figure 1B). Although such spectral changes are not definitive indicators of binding mode, red shifts in the longest-wavelength absorption bands are consistent with an intercalative mode of binding. Similarly, ellipticine binding to Pu·Pu is accompanied by changes in its lonScheme 1. A) Purine–purine base pairs. B) Watson–Crick base pairs. C) Smallmolecule ligands used in this study.