Contiguous Silver(I)-Mediated Base Pairs of Imidazophenanthroline and Canonical Nucleobases in DNA Duplexes: Formation of Classical Duplexes versus Homodimer Formation

Abstract

Metal-mediated base pairs represent a topical alternative to canonical hydrogen-bonded base pairs. In this context, the ligand 1Himidazo[4,5-f ][1,10]phenanthroline (P) was introduced as an artificial nucleobase in a glycol nucleic acid-based nucleoside analogue into a DNA oligonucleotide in a way that the oligonucleotide contains a central block of six contiguous P residues. The ability to engage in Ag + -mediated base pairing was evaluated with respect to the four canonical nucleosides in positions complementary to P. Highly stabilizing Ag + -mediated base pairs were formed with cytosine and guanine (i.e., P−Ag + −C and P−Ag + −G base pairs), whereas the analogous base pairs with thymine and adenine were much less stable and hence formed incompletely. Surprisingly, the intermediate formation of a homodimeric duplex of the P-containing oligonucleotide was observed in all cases, albeit to a different extent. The homodimer is composed of P−Ag + −P base pairs and 18 overhanging mismatched canonical nucleobases. It demonstrates the obstacles present when designing metal-mediated base pairs as metal complexation may take place irrespective of the surrounding natural base pairs. Homodimer formation was found to be particularly prominent when the designated metal-mediated base pairs are of low stability, suggesting that homodimers and regular duplexes are formed in a competing manner.

Synthesis, structure and luminescence of two europium complexes of diphenylimidazophenanthrolines

“…Imidazo[4,5- f ][1,10]phenanthroline and its derivatives are excellent chelators in coordination chemistry. 2,3 Possessing planar rigid moieties and deficit electron conjugated systems, they can serve as an “antenna” to sensitize the luminescence of the coordinated lanthanide ions. The luminescent properties can be functionally tuned by altering the pending groups to the imidazole moiety, which imparts versatility to these ligands and their complexes.…”