Metal-mediated aggregation of DNA comprising 2,2′-bipyridine nucleoside, an asymmetrically substituted chiral bidentate ligand

Abstract

The incorporation of an artificial 5-methyl-2,2'-bipyridine nucleoside at the 5' terminus of an otherwise self-complementary oligonucleotide sequence opens up the opportunity of metal-mediated aggregation of DNA double helices triggered by the addition of the respective metal ions. Interestingly, two-dimensional aggregates (DNA monolayers) are formed in the presence of nickel(ii), whereas copper(ii) leads to the formation of three-dimensional disc-shaped structures. With iron(ii), a coexistence of both types of aggregates had been observed previously. Models are proposed in which these observations are explained based on geometrical considerations. The artificial nucleoside itself represents a rare example for a C(1)-symmetric chiral derivative of 2,2'-bipyridine, enabling the formation of four isomeric octahedral complexes.

Metal‐Modified Nucleic Acids: Metal‐Mediated Base Pairs, Triples, and Tetrads

“…Three complementary approaches have been published related to the formation of metal-stabilized three-way junctions.T he attachment of ab identate ligand such as 2,2'bipyridine at the terminus of as ingle-stranded oligonucleotide enables ametal-mediated DNAassembly in the presence of metal ions favoring an octahedral coordination geometry. [49] If this single-stranded oligonucleotide is self-complementary,t hen the resulting conjugate can aggregate through DNAd uplex formation, giving rise to metal-mediated 3WJs (Figure 6a). Depending on the experimental conditions,twodimensional and three-dimensional aggregates have been observed.…”

“…Depending on the experimental conditions,twodimensional and three-dimensional aggregates have been observed. [49] Alternatively,a na rtificial metal-modified 3WJ can be obtained by introducing a2 ,2'-bipyridine-containing nucleoside into the center of an otherwise regular DNA3 WJ Figure 5. Selected Ag I -mediated base triples.…”

“…a) Terminal attachment of a2,2'-bipyridine nucleoside for ametalmediated aggregation of 3WJs. [49] Only asmall excerpt of the aggregate is depicted.b )Central attachment of a2,2'-bipyridine for the metalstabilized formation of a3 WJ. [50] Alternative modes of attachment of the bipyridine moiety have been reported,t oo.…”

Nucleic Acids With Metal‐Mediated Base Pairs and Their Applications

“…When attached to the 5′‐end of palindromic DNA oligonucleotides, 5Me Bipy nucleoside can be used to generate DNA‐metal aggregates in the presence of Fe 2+ , Ni 2+ and Cu 2+ 47. 48 Such conjugates can be considered a first step on the way towards metal‐containing DNA nanostructures.…”

A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs

“…While the naturally occurring pyrimidine nucleosides cytidine and thymidine are known to be capable of forming silver(I)-and mercury(II)-mediated base pairs, respectively, numerous artificial nucleosides have been developed for an application in metal-mediated base pairs. These include for example hydroxypyridone, [10] salen, [11] dipicolylamine, [12] 2,2'-bipyridine, [13] imidazole [14] and triazole. [15] In particular, the imidazole-Ag + -imidazole base pair has been intensively characterized (Scheme 1a): A comparison with other azole-based nucleosides indicated that it should form highly stable metal-mediated base pairs.…”