Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA

A study was carried out to provide a detailed comparison of the binding modes of the two complexes formed between an oligodeoxynucleotide containing a two-base bulge and SCA-[alpha]2 and provide new insights into the importance of shape and space, as opposed to simple nucleotide sequence. Results reveal that SCA-[alpha]2 has a better hand-in-glove fit at the bulge site, making it an ideal platform for the placement of moieties that could react covalently with the DNA and for generating congeners specific for bulges in RNA.