A dizinc complex for selective fluorescence sensing of uridine and uridine-containing dinucleotides

Selective Alkylation of C-Rich Bulge Motifs in Nucleic Acids by Quinone Methide Derivatives

A quinone methide precursor featuring a bis-cyclen anchoring moiety has been synthesized and its capacity to alkylate oligonucleotide targets quantified in the presence and absence of divalent metal ions (Zn(2+) , Ni(2+) and Cd(2+) ). The oligonucleotides were designed for testing the sequence and secondary structure specificity of the reaction. Gel electrophoretic analysis revealed predominant alkylation of C-rich bulges, regardless of the presence of divalent metal ions or even the bis-cyclen anchor. This C-selectivity appears to be an intrinsic property of the quinone methide electrophile as reflected by its reaction with an equimolar mixture of the 2'-deoxynucleosides. Only dA-N1 and dC-N3 alkylation products were detected initially and only the dC adduct persisted for detection under conditions of the gel electrophoretic analysis.

Exploring the binding ability of phenanthroline-based polyammonium receptors for anions: hints for design of selective chemosensors for nucleotides

The synthesis of receptor 2,6,10,14,18-pentaaza[20]-21,34-phenanthrolinophane (L1), containing a pentaamine chain linking the 2,9 positions of a phenanthroline unit, is reported. The protonation features of L1 and of receptor 2,6,10,14,18,22-hexaaza[23]-24,37-phenanthrolinophane (L2) have been studied by means of potentiometric, (1)H NMR, and spectrofluorimetric measurements; this study points out that the fluorescent emission of both receptors depends on the protonation state of the polyamine chain. In fact, the receptors are emissive only at neutral or acidic pH values, where all the aliphatic amine groups are protonated. Potentiometric titrations show that L2 is able to bind selectively ATP over TTP, CTP, and GTP. This selectivity is lost in the case of L1. (1)H and (31)P NMR measurements and molecular mechanics calculations show that the phosphate chains of nucleotides give strong electrostatic and hydrogen-bonding interactions with the ammonium groups of the protonated receptors, while the nucleobases interact either via pi-stacking with phenanthroline or via hydrogen bonding with the ammonium groups. Of note, MM calculations suggest that all nucleotides interact in an inclusive fashion. In fact, in all adducts the phosphate chain is enclosed within the receptor cavities. This structural feature is confirmed by the crystal structure of the [(H(6)L2)(2)(TTP)(2)(H(2)O)(2)](4+) adduct. Fluorescence emission measurements at different pH values show that L2 is also able to ratiometrically sense ATP in a narrow pH range, thanks to emission quenching due to a photoinduced electron transfer (PET) process from an amine group of the receptor to the excited phenanthroline.

Pattern-based sensing of nucleotides in aqueous solution with a multicomponent indicator displacement assay

A multicomponent indicator displacement assay (MIDA) based on an organometallic receptor and three dyes can be used for the identification and quantification of nucleotides in aqueous solution at neutral pH.