Sequence dependence of Pd(II)-mediated base pairing by palladacyclic nucleobase surrogates

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.…”

“…[28][29][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] However, strand displacement and melting temperature experiments both fundamentally quantify the same property, namely hybridization affinity of an oligonucleotide as a whole. Failure of the stability of a metal-mediated base pair to translate into duplex stability of a corresponding oligonucleotide has been reported not only with Pd(II) [31,32] but also with Ag(I).…”

“…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] .…”

“…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][29][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] However, strand displacement and melting temperature experiments both fundamentally quantify the same property, namely hybridization affinity of an oligonucleotide as a whole.…”

Site-specific covalent metalation of DNA oligonucleotides with phosphorescent platinum(ii) complexes

“…20 Several organometallic metal-mediated base pairs have also been reported in the context of Hg(II) and Pd(II) complexes. [21][22][23][24][25][26][27][28] Their advantage over regular metal-mediated base pairs is the increased metal-ligand bond strength, so that they persist even at low concentrations.…”