Metal-mediated base pairs in parallel-stranded DNA

Abstract

In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine–Ag(I)–cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.

Atomic Structure of a Fluorescent Ag8 Cluster Templated by a Multistranded DNA Scaffold

“…The zipper is stabilized by metal-mediated base pairs with C(4)C(5)C(6) from strands A and B (Fig. 2C, Tables S3, S4) [34][35] . Each silver interacts with the endocyclic N3 nitrogen of two in-register cytosines with near linear geometry, similar to available non-emissive, zipper-like metallobase pair-containing structures [36][37] .…”

A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding

“…A recent development is the structural elucidation of various heavy metal-bound DNA containing mismatched base pairs (Table 1 ). Although not directly relevant to biology, metal-containing DNA has great application potential in areas such as nanotechnology and may become important tools for biological research ( 34–37 ). Of particular importance is the interaction between T:T or C:T base pairs and Hg II .…”

Stable Hg(II)-mediated base pairs with a phenanthroline-derived nucleobase surrogate in antiparallel-stranded DNA

“…A higher affinity of the artificial nucleosides towards a particular metal ion and the wide structural flexibility offered by them represent their largest advantages. Similarly, other nucleic acid topologies and nucleic acid analogues have been probed with respect to the site-specific incorporation of metal ions in analogy to metal-mediated base-pair formation [28][29][30][31]. Several promising applications have already been established in this area, including the construction of structures with a modified electrical response [32,33], switchable devices [34], responsive devices [35,36], regulated primer extension [37], the specific detection of canonical nucleobases [38,39], the generation of DNA-templated metal nanoclusters [40], an expansion of genetic four-letter code [41], etc.…”