Covalently Palladated Oligonucleotides Through Oxidative Addition of Pd⁰

Abstract

An 11‐mer oligonucleotide incorporating a central (2‐iodobenzoylamino)methyl residue has been synthesized and palladated by oxidative addition of Pd2(dba)3. UV melting profiles of the duplexes formed by the palladated oligonucleotide with its natural complements were biphasic and the higher melting temperatures (Tm) exhibited considerable hysteresis. CD spectra, in turn, resembled those of canonical B‐type double helices. Two‐step denaturation, with the “low‐Tm” melting involving only canonical base pairs and the “high‐Tm” melting involving also dissociation of a PdII‐mediated base pair, appears the most likely explanation for the observed UV melting profiles. As the latter step in all cases takes place at a higher temperature than denaturation of natural duplexes of the same length, the putative PdII‐mediated base pairs are stabilizing.

Still Elusive – Pd(II)‐Mediated Base Pairing by an Acetophenone Oxime Palladacycle within 15N‐Labelled Double‐Helical Oligonucleotides

“…RP‐HPLC analysis of the product mixture revealed several new peaks (chromatograms presented in the Supporting Information). This phenomenon has been reported before [28–30,40,41] and attributed to relatively slow ligand exchange at Pd(II). The collected fractions were analyzed by ESI‐TOF‐MS and those showing addition of a single Pd(II) ion combined.…”

“…On the other hand, the metal ion employed in the very first artificial metal‐mediated base pair, [27] namely Pd(II), has proven challenging and elusive to the conventional experiments. Melting temperature measurements, for example, are complicated by the relatively slow ligand exchange at Pd(II), which manifests itself as multiphasicity and hysteresis between the denaturation and renaturation curves [28–30] . We have previously tried to address this problem by complementing melting temperature measurements with a FRET‐based strand displacement assay, with moderate success [30] .…”

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

“…In the case of Pd II , orthometallation of phenylpyridine led to the first palladacyclic nucleobase Phe Py Pd , which forms stable Pd II ‐mediated base pairs with the canonical nucleobases guanine, cytosine and thymine (see Figure i for the proposed Phe Py Pd ‐T pair) . A related monodentate organopalladium nucleobase has likewise been reported . Organometallic metal‐mediated base pairs have a few advantages over their traditional counterparts.…”

Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair

“…In addition, many synthetic nucleobase analogues have been devised, broadening the metal-ion scope of metal-mediated base pairing. As a result, metal-mediated base pairs are known involving Cu(II), [10][11][12][13] Cu(I), [14] Mn(III) [15], Ni(II) [16], Zn(II) [17], and other metal ions [18,19]. Nevertheless the most prominent metal ions used with artificial nucleobases remain Ag(I) and Hg(II), too [20][21][22][23][24][25][26][27].…”