Molecular Recognition of Nucleotides in Water by Scorpiand‐Type Receptors Based on Nucleobase Discrimination

Abstract

The detection of nucleotides is of crucial importance because they are the basic building blocks of nucleic acids. Scorpiand-based polyamine receptors functionalized with pyridine or anthracene units are able to form stable complexes with nucleotides in water, based on coulombic, π-π stacking, and hydrogen-bonding interactions. This behavior has been rationalized by means of an exploration with NMR spectroscopy and DFT calculations. Binding constants were determined by potentiometry. Fluorescence spectroscopy studies have revealed the potential of these receptors as sensors to effectively and selectively distinguish guanosine-5'-triphosphate (GTP) from adenosine-5'-triphosphate (ATP).

Anion selectivity of Zn–salophen receptors: Influence of ligand substituents

“…They are ubiquitous in both the organic and mineral worlds, play different key roles in biology [3][4][5][6], and cause dramatic effects as environmental pollutants [7]. For these reasons, the supramolecular recognition of anions is a topic of constant interest that is witnessed by the rich literature focused on the design and preparation of new receptors addressing this target [8][9][10][11][12][13].…”

Aryl-bis-(scorpiand)-aza receptors differentiate between nucleotide monophosphates by a combination of aromatic, hydrogen bond and electrostatic interactions

“…The addition of the nucleotides to a solution of PHENPOD at pH = 5 leads to a decrease in fluorescence which was particularly noticeable for AMP ( Figure 2). Such 15 quenching processes can be attributed to hydrogen bonding and charge interactions between the anionic phosphate moiety and the polyammonium chain of the protonated receptor, which could lead to an intra-complex proton transfer from one ammonium group to a phosphate making an amine lone pair 20 available for the quenching process. 6b The effective constants calculated by processing the fluorimetric data with the HypSpec program collected in Table 1 are in reasonable agreement with the values derived from the pH-metric titrations and confirm the selective recognition of AMP by 25 PHENPOD.…”

“…Nucleotides are amongst the most targeted anionic substrates 20 due to the key roles that they play in biology such as nucleic acid synthesis, transport across membranes, energy and electron-transfer events. Other relevant functions of nucleotides are related to cell-signalling processes.…”

“…19 Recently, some of us have designed a series of scorpiand-like receptors with different appended motifs in the tail able to discriminate certain nucleobases due to a predominant 10 hydrogen bonding or π-π stacking interaction. 20 A further development of the scorpiand-like receptors just mentioned are the double bis-scorpiand receptors PYPOD or PHENPOD, built up by connecting two macrocyclic units containing pyridine moieties with pyridine or phenanthroline 15 linkers, respectively (Scheme 1). 21 These compounds, which in particular for PYPOD, had shown RNA over DNA selectivity, 22 are examined in this work for their capability to achieve base-pair discrimination in the recognition of NMPs.…”

DNA Triplexes That Bind Several Cofactor Molecules

“…However, when as econd base pairing interaction is allowed to takep lace, by leaving ag ap as binding site in the center of at riple helix, dissociation constants for complexesw ithn ucleotidesr each the nanomolar range. [14][15][16][17][18][19] With such ac ombination of Watson-Crick and Hoogsteen base pairing (Figure 1b), nucleoside phosphates can be bound with affinitiesh igher than those found for non-DNA binding motifs, such as pyridinium tripods, [20] artificial tweezers, [21] scorpiandr eceptors, [22] or copperc omplexes. [23] Further,g ood binding selectivities can be achieved, [15] and intracellularl evels of purine nucleotides can be affected.…”