Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

Abstract

For the first time, a metal-mediated base pair has been used to modulate the affinity of an aptamer towards its target. In particular, two artificial imidazole 2’-deoxyribonucleosides (Im) were incorporated into various positions of an established ATP-binding aptamer (ATP, adenosine triphosphate), resulting in the formation of three aptamer derivatives bearing Im:Im mispairs with a reduced ATP affinity. A fluorescence spectroscopy assay and a binding assay with immobilized ATP were used to evaluate the aptamer derivatives. Upon the addition of one Ag(I) ion per mispair, stabilizing Im–Ag(I)–Im base pairs were formed. As a result, the affinity of the aptamer derivative towards ATP is restored again. The silver(I)-mediated base-pair formation was particularly suitable to modulate the aptamer function when the Im:Im mispairs (and hence the resulting metal-mediated base pairs) were located close to the ATP-binding pocket of the aptamer. Being able to trigger the aptamer function opens new possibilities for applications of oligonucleotides.

Metal-mediated DNA base pairing of easily prepared 2-oxo-imidazole-4-carboxylate nucleotides

“…[12][13][14][15][16][17] The newly introduced metal-mediated base pairs impart unique properties to the modied DNA, depending on the inherent nature of the metal. In addition to metal-dependent thermal stabilisation of duplexes, DNA-templated metal assembly, [18][19][20][21][22][23] modulation of charge transfer, [24][25][26][27] molecular sensing [28][29][30] and metaldependent control of DNAzymes and aptamers [31][32][33][34][35][36][37] have been reported. Therefore, nding appropriate ligand-type nucleobases that can specically and strongly bind to a certain metal ion and form metal-mediated base pairs is important to achieve these functions.…”

Towards polymerase-mediated synthesis of artificial RNA–DNA metal base pairs

“…3,4 These metal base pairs have advanced as promising candidates for a number of applications including the development of nanomolecular devices, 5 ion sensors and biosensing devices 6,7 and metal nanowires and nanodevices [8][9][10] as well as for the allosteric control of functional nucleic acids. [11][12][13][14] The formation of metal base pairs mainly occurs by annealing short synthetic oligonucleotides together with specific metal cations. While this approach has allowed the identification of metal base pairs based on natural and modified nucleotides, it is restricted in oligonucleotide size and in terms of diversity of functional groups that can be explored due to the rather harsh conditions imposed by solid-phase synthesis.…”

Enzymatic construction of metal-mediated nucleic acid base pairs

“…In this context, functional nucleic acids, i.e., aptamers and DNAzymes, are particularly adapted to sense metal cations. [22][23][24] Finally, an interest towards the electrical conductance of DNA strands containing metal base pairs has been raised 19 because intraduplex metal complexes could act as charge-carriers for electron transportation in DNA. The incorporation of metal base pairs in nucleic acids has been initially performed by application of a chemical strategy that involves the construction of oligonucleotides through automated solid-phase synthesis with phosphoramidite building blocks.…”