Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligandsElectronic supplementary information (ESI) available: MALDI-TOF mass spectra of modified oligonucleotides, additional UV/VIS-spectra from filtration assays, HPLC traces, UV-melting points, and additional UV-melting curves. See DOI: 10.1039/c5ob00508f

• Main Authors: Vollmer, S, Richert, C
• Format: Article
• Language: English
• ISSN: 1477-0520; 1477-0539
• DOI: 10.1039/c5ob00508f

Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with K d values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands. Triple helices with an abasic bridge between two oligopurine segments bind ligands like ATP, FAD, and cAMP with dissociation constants as low as 30 nM.