Interaction of Pd2+ complexes of 2,6-disubstituted pyridines with nucleoside 5′-monophosphates

Fluorescent Oligonucleotide Probes for Screening High‐Affinity Nucleobase Surrogates

“…The present data, together with those obtained previously by NMR titrations allow comparison of the base pairing behavior of Pd II chelates 1 a –Pd, 1 b –Pd and 1 c –Pd at monomer level and within the base stack of a double‐helical oligonucleotide (Figure ). All of the Pd II ‐mediated base pairs studied were stabilized in the oligonucleotide environment, presumably by base stacking interactions.…”

“…On the other hand, the free ligands showed no affinity for the gap of the oligonucleotide probes, underlining the importance of the bridging metal ion for efficient binding. In all likelihood, the binding mode established for 1 a –Pd, 1 b –Pd and 1 c –Pd at the monomer level by NMR titrations is retained at the oligonucleotide level. Accordingly, the least bulky chelate 1 a –Pd would bind to N1 and the bulkier chelates 1 b –Pd and 1 c –Pd to N7 of purine residues (the pyrimidine binding site is always N3).…”

“…NMR titrations have identified a number of metal chelates exhibiting a high affinity for and, in some cases, a modest selectivity between nucleobases . Interpretation of these results is, however, complicated by the fact that studies carried out at monomer level fail to take into account the steric constraints imposed by the base stack of a double‐helical nucleic acid.…”

Metal‐Dependent Nucleobase Recognition by Picolinamide

“…We have previously studied Pd II ‐mediated pairing of dipicolinamide with canonical nucleobases, at monomer level as well as within glycol nucleic acid (GNA) oligonucleotides. At the monomer level, the Pd II chelate of dipicolinamide exhibited fairly high affinity for all of the canonical nucleoside‐5′‐monophosphates . At the oligonucleotide level, Pd II ‐mediated base pairing between dipicolinamide and thymine resulted in a dramatic increase in melting temperature but only when placed in a terminal position .…”

“…[2] We have previously studied Pd II -mediated pairing of dipicolinamide with canonical nucleobases, at monomer level as well as within glycol nucleic acid (GNA) oligonucleotides.A tt he monomer level, the Pd II chelate of dipicolinamide exhibited fairly high affinity for all of the canonical nucleoside-5'-monophosphates. [6] At the oligonucleotide level,P d II -mediated base pairing between dipicolinamide and thymine resulted in ad ramatic increase in meltingt emperature but only when placed in at erminal position. [7] The universally high affinity for all nucleobases at the monomer level and the contrasting behavior at at erminal and at an intrachain positionw ithin an oligonucleotide suggest that in Pd II -mediated base pairs, dipicolinamide and the canonical nucleobase prefer ap erpendicular, rather than ac oplanar,o rientation.…”