Metal Coordination to Ligand-Modified Peptide Nucleic Acid Triplexes

Three's a crowd - stabilisation, structure, and applications of DNA triplexes

DNA is a strikingly flexible molecule and can form a variety of secondary structures, including the triple helix, which is the subject of this review. The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex forming oligonucleotide (TFO) to a DNA duplex. As the TFO will bind to the duplex with sequence specificity, there is significant interest in developing TFOs with potential therapeutic applications, including using TFOs as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies, which may increase triplex stability or in vivo degradation, is essential - these areas will be discussed in this review. Ruthenium polypyridyl complexes, which are able to photooxidise DNA and act as luminescent DNA probes, may serve as a suitable photophysical payload for a TFO system and the developments in this area in the context of DNA triplexes will also be reviewed.

A Catalogue of Orthogonal Complementary Ligand Pairings for Palladium(II) Complexes

Molecular recognition is a form of information transfer, seen in the base pairing in DNA which is derived from the identity (acceptor or donor) and number of hydrogen bond sites within each base. Here we report bis‐ligand palladium(II) complexes that exhibit similar complementarity. Pd(II) has square planar four‐coordinate geometry, giving control over ligand orientation and denticity. Pairings were developed using ligand denticity (3 : 1 or 2 : 2), and hydrogen bond capability (AA:DD or AD:DA) or lack thereof. Five pairings were investigated, with two sets of four being found fully orthogonal. The two 3 : 1 pairings exhibited limited ligand exchange. The extent of this exchange varied dependant on solvent from 2 : 1 (desired to undesired) to 6 : 1. A reliable and varied set of ligand pairs have therefore been developed for bis‐ligand coordination sphere engineering in pursuit of sorting for complex molecular architectures and molecular‐level information storage and transfer events.

Metal-Binding Foldamers

Sequence-defined oligomeric molecules with discrete folding propensities, termed foldamers, are a versatile source of agents with tailored structure and function. An inspiration for the development of the foldamer paradigm are natural biomacromolecules, the sequence-encoded folding of which is the basis of life. Metal ions and clusters are common features in proteins, where the role of metal varies from supporting structure to enabling function. The ubiquity of metals in natural systems suggests promise for metals in the context of folded artificial backbones. In this Minireview, we highlight efforts to realize this potential through a survey of published work on the design, synthesis, and characterization of metal-binding foldamers.

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

Metal-mediated base pairs involving artificial nucleobases have emerged as a promising means for the site-specific functionalization of nucleic acids with metal ions. In this context, a GNA-appended (GNA: glycol nucleic acid) nucleoside analogue containing the artificial nucleobase 1H-imidazo[4,5-f][1,10]phenanthroline (P) has already been applied successfully in a variety of homo- and heteroleptic metal-mediated base pairs, mainly involving Ag(I) ions. Herein, we report a thorough investigation of the Hg(II)-binding properties of P when incorporated into antiparallel-stranded DNA duplexes. The artificial nucleobase P is able to form Hg(II)-mediated homoleptic base pairs of the type P-Hg(II)-P with a [2 + 2] coordination environment. In addition, the heteroleptic P-Hg(II)-T pair was investigated. The addition of a stoichiometric amount of Hg(II) to a duplex comprising either a P:P pair or a P:T pair stabilizes the DNA duplex by 4.3 °C and 14.5 °C, respectively. The P-Hg(II)-T base pair, hence, represents the most stabilizing non-organometallic Hg(II)-mediated base pair reported to date. The formation of the Hg(II)-mediated base pairs was investigated by means of temperature-dependent UV spectroscopy and CD spectroscopy.

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

The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of Ag^I -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.