Zinc-cyclen coordination to UTP, TTP or pyrophosphate induces pyrene excimer emission

Argentivorous Molecules with Chromophores in Side Arms: Silver Ion-Induced Turn On and Turn Off of Fluorescence

The synthesis of argentivorous molecules (L¹ and L²) having two chromophores (4-(anthracen-9-yl)benzyl or 4-(pyren-1-yl)benzyl groups) and two benzyl groups and the fluorescence properties of their silver complexes in a solution and the solid state are reported. A crystallographic approach for the Ag⁺ complexes with L¹ and L² revealed that the observed fluorescence changes stem from the excimer formation and extinction of fluorescent. Furthermore, binding stabilities of L¹ and L² toward Ag⁺ ions were estimated by the Ag⁺-induced UV-vis and PL spectral changes.

Interaction of Nucleotides with a Trinuclear Terbium(III)-Dizinc(II) Complex: Efficient Sensitization of Terbium Luminescence by Guanosine Monophosphate and Application to Real-Time Monitoring of Phosphodiesterase Activity

An in-depth study of the interaction of a trinuclear terbium(III)-dizinc(II) complex with an array of nucleotides differing in the type of nucleobase and number of phosphate groups, as well as cyclic versus acyclic variants, is presented. The study examined the nature of the interaction and the efficiency at which guanine was able to sensitize terbium(III) luminescence. Competitive binding and titration studies were performed to help establish the nature/mode of the interactions. These established that (1) interaction occurs by the coordination of phosphate groups to zinc(II) (in addition to uridine in the case of uridine monophosphate), (2) acyclic nucleotides bind more strongly than cyclic counterparts because of their higher negative charge, (3) guanine-containing nucleotides are able to sensitize terbium(III) luminescence with the efficiency of sensitization following the order guanosine monophosphate (GMP) > guanosine diphosphate > guanosine triphosphate because of the mode of binding, and (4) nucleoside monophosphates bind to a single zinc(II) ion, whereas di- and triphosphates appear to bind in a bridging mode between two host molecules. Furthermore, it has been shown that guanine is a sensitizer of terbium(III) luminescence. On the basis of the ability of GMP to effectively sensitize terbium(III)-based luminescence while cyclic GMP (cGMP) does not, the complex has been utilized to monitor the catalytic conversion of cGMP to GMP by a phosphodiesterase enzyme in real time using time-gated luminescence on a benchtop fluorimeter. The complex has the potential to find broad application in monitoring the activity of enzymes that process nucleotides (co)substrates, including high-throughput drug-screening programs.

Structure-activity relationship study of ProxyPhos chemosensors for the detection of proximal phosphorylation and other phosphate species

Chemosensors for the detection of phosphate-containing biological species are in high need. Detection of proximally phosphorylated sites of PP_i and those found in peptides and proteins has been demonstrated using chemosensors containing pyrene, as a fluorescent reporter, and a Zn²⁺-chelate, as a phosphate-binding group. Using these sensors, detection of proximal phosphate groups is afforded by binding of at least two of the sensor molecules to the adjacent phosphates, via the Zn²⁺ centres, leading to excimer formation between the pyrene groups and the corresponding shift in emission from 376 to 476 nm. Although several reports of this chemosensor class have been made, no detailed studies of selectivity of these sensors among major phosphate targets have been reported. In this study, a library of this class of chemosensors, termed ProxyPhos, which contained various linkers and Zn²⁺-chelating groups (i.e. DPA, cyclen and cyclam), was prepared and the effects of structural variation on the sensing efficiency and selectivity were evaluated among proximally phosphorylated peptides, proteins, nucleotides, P_i and PP_i. As a result of this study, we have identified ProxyPhos library members that are most suitable for the detection of proximally phosphorylated peptides, PP_i, UTP, and a DpYD peptide motif, and have generally provided a foundation for the selection of ProxyPhos chemosensors for further development of specific biologically relevant assays. The broad utility of ProxyPhos is further supported by the demonstrated lack of these sensors' cytotoxicity, ability to rapidly permeate into live and fixed cells and compatibility with gel staining methods.

An AIE-based metallo-supramolecular assembly enabling an indicator displacement assay inside living cells

We report a novel metallo-supramolecular assembly (Z/E-TPE2CyZn-PV), which consists of a tetraphenylethene (TPE)-based dinuclear Zn2+-cyclen complex and pyrocatechol violet (PV). The assembly is developed for indicator-displacement assays (IDAs) inside living cells.

Synthetic receptor molecules for selective fluorescence detection of 8-oxo-dGTP in aqueous media

A series of 9-hydroxy-1,3-diazaphenoxazine-2-one derivatives were synthesized as fluorescent receptor molecules for 8-oxo-dGTP, which attach the cyclen-zinc complex at the 3-N position as the binding site for the triphosphate and the (2-aryloxycarbonylamino)ethyl group at the 9-O position as the hydrogen bonding site for 8-oxoguanine. Among these molecules, the receptor molecule 5a-Zn constructed of the ethyl linker at 3-N and the (2-benzyloxycarbonyl amino)ethyl group at 9-O displayed the best recognition ability for 8-oxoguanosine triphosphate (8-oxo-dGTP) in aqueous media. The receptor 5a-Zn was also shown to selectively detect 8-oxo-dGTP in a cell lysate solution.

Di- and Triphosphate Recognition and Sensing with Mono- and Dinuclear Fluorescent Zinc(II) Complexes: Clues for the Design of Selective Chemosensors for Anions in Aqueous Media

The synthesis of a new ligand (L1) containing two 1,4,7-triazacyclononane ([9]aneN₃ ) moieties linked by a 4,5-dimethylenacridine unit is reported. The binding and fluorescence sensing properties toward Cu²⁺ , Zn²⁺ , Cd²⁺ , and Pb²⁺ of L1 and receptor L2, composed of two [9]aneN₃ macrocycles bridged by a 6,6''-dimethylen-2,2':6',2''-terpyridine unit, have been studied by coupling potentiometric, UV/Vis absorption, and emission measurements in aqueous media. Both receptors can selectively detect Zn²⁺ thanks to fluorescence emission enhancement upon metal binding. The analysis of the binding and sensing properties of the Zn²⁺ complexes toward inorganic anions revealed that the dinuclear Zn²⁺ complex of L1 selectively binds and senses the triphosphate anion (TP), whereas the mononuclear Zn²⁺ complex of L2 displays selective recognition of diphosphate (DP). Binding of TP or DP induces emission quenching of the Zn²⁺ complexes with L1 and L2, respectively. These results are exploited to discuss the role played by pH, number of coordinated metal cations, and binding ability of the bridging units in metal and/or anion coordination and sensing.

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

Bis-polyaza pyridinophane scorpiands bind nucleotides in aqueous medium with 10-100 micromolar affinity, predominantly by electrostatic interactions between nucleotide phosphates and protonated aliphatic amines and assisted by aromatic stacking interactions. The pyridine-scorpiand receptor showed rare selectivity toward CMP with respect to other nucleotides, whereby two orders of magnitude affinity difference between CMP and UMP was the most appealing. The phenanthroline-scorpiand receptor revealed at pH 5 strong selectivity toward AMP with respect to other NMPs, based on the protonation of adenine heterocyclic N1. The results stress that the efficient recognition of small biomolecules within scorpiand-like receptors relies mostly on the electrostatic and H-bonding interactions despite the competitive interactions in the bulk solvent, thus supporting further optimisation of this versatile artificial moiety.

Dipeptide interactions with Zn(II)-cyclen artificial model for molecular recognition

The Zn(II)-cyclen-dipeptide ternary systems (where cyclen is abbreviated as L and dipeptide is glycylglycine (HL(1)) or glycyl-(S)-alanine (HL(2))) were investigated by potentiometry applying both "out-of-cell" and direct titrations and by (1) H NMR spectroscopy. Especially, the (1)H NMR study was found to be very efficient to estimate speciation in the systems. The results obtained under full equilibria indicated two main species, [Zn(L)(HL(1,2))](2+) and [Zn(L)(L(1,2))](+), in both the systems. In the [Zn(L)(HL(1,2))](2+) complex, presence of carbonyl-carboxylate chelate was confirmed, and in the [Zn(L)(L(1,2))](+) species, the peptide coordination is re-organized to carbonyl-amine chelate or only terminal amino group is coordinated. Equilibrium constants describing [Zn(L)](2+)-dipeptide interaction are relatively low, log K = 3.4 for Gly-Gly and 4.1 for Gly-(S)-Ala, respectively. Nevertheless, the values are slightly higher than stability constants for interaction of Zn(II) with the dipeptides (i.e. [Zn(L(1,2))](+) species) where a chelate formation is expected. It indicates that interaction between Zn(II) ion in [Zn(L)](2+) and the dipeptides should be supported by some additional interactions. Potentiometry carried out under non-equilibrum condition showed different species where these additional stabilizing forces play more important role.

Syntheses of polypyridyl metal complexes and studies of their interaction with quadruplex DNA

A series of metal complexes with substituted terpyridines show high affinity towards quadruplex DNA, particularly bimetallic (trpy)Pt/M(cyclen) complexes.

Focused fluorescent probe library for metal cations and biological anions

A focused fluorescent probe library for metal cations was developed by combining metal chelators and picolinium/quinolinium moieties as combinatorial blocks connected through a styryl group. Furthermore, metal complexes derived from metal chelators having high binding affinities for metal cations were used to construct a focused probe library for phosphorylated biomolecules. More than 250 fluorescent probes were screened for identifying an ultraselective probe for dTTP.

Chromogenic and fluorogenic chemosensors and reagents for anions. A comprehensive review of the years 2010-2011

This review focuses on examples reported in the years 2010-2011 dealing with the design of chromogenic and fluorogenic chemosensors or reagents for anions.

Pyrophosphate selective fluorescent probe and molecular flip-flop

Highly selective detection of pyrophosphate in the presence of inorganic phosphates, halides, acetate, ATP, other nucleotides in neutral aqueous solutions is achieved by a fluorescent Zn-ensemble based system. The implementation of the first molecule based JK-latch sequential logic function is also described.

Fluorescence detection of adenosine triphosphate in an aqueous solution using a combination of copper(II) complexes

Fluorescent ligands have been designed to form ternary complexes with a Cu(II) cation and phosphates in a buffer solution at physiological pH 7.4. It has been shown that a combination of two different ligands and CuCl(2) allows one to achieve high adenosine triphosphate/adenosine diphosphate, adenosine 5'-monophosphate selectivity, and ratiometric fluorescence sensing, while separately each ligand complex does not have such properties.

Structural basis for bifunctional zinc(II) macrocyclic complex recognition of thymine bulges in DNA

The zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane (cy4q) binds selectively to thymine bulges in DNA and to a uracil bulge in RNA. Binding constants are in the low-micromolar range for thymine bulges in the stems of hairpins, for a thymine bulge in a DNA duplex, and for a uracil bulge in an RNA hairpin. Binding studies of Zn(cy4q) to a series of hairpins containing thymine bulges with different flanking bases showed that the complex had a moderate selectivity for thymine bulges with neighboring purines. The dissociation constants of the most strongly bound Zn(cy4q)-DNA thymine bulge adducts were 100-fold tighter than similar sequences with fully complementary stems or than bulges containing cytosine, guanine, or adenine. In order to probe the role of the pendent group, three additional zinc(II) complexes containing 1,4,7,10-tetraazacyclododecane (cyclen) with aromatic pendent groups were studied for binding to DNA including 1-(2-quinolyl)methyl-1,4,7,10-tetraazacyclododecane (cy2q), 1-(4-biphenyl)methyl-1,4,7,10-tetraazacyclododecane (cybp), and 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-N,N-dimethylnaphthalen-1-amine (dsc). The Zn(cybp) complex binds with moderate affinity but little selectivity to DNA hairpins with thymine bulges and to DNA lacking bulges. Similarly, Zn(dsc) binds weakly both to thymine bulges and hairpins with fully complementary stems. The zinc(II) complex of cy2q has the 2-quinolyl moiety bound to the Zn(II) center, as shown by (1)H NMR spectroscopy and pH-potentiometric titrations. As a consequence, only weak (500 μM) binding is observed to DNA with no appreciable selectivity. An NMR structure of a thymine-bulge-containing hairpin shows that the thymine is extrahelical but rotated toward the major groove. NMR data for Zn(cy4q) bound to DNA containing a thymine bulge is consistent with binding of the zinc(II) complex to the thymine N3(-) and stacking of the quinoline on top of the thymine. The thymine-bulge bound zinc(II) complex is pointed into the major groove, and there are interactions with the guanine positioned 5' to the thymine bulge.

Probing solution behaviour of metallosupramolecular complexes using pyrene fluorescence

A new method for assessing the topology of metallosupramolecular assemblies using pyrene-appended ligands is reported. Two potentially tetradentate ligands containing one (L(1)) and two (L(2)) terminal pyrene moieties were synthesised and their complexes with Cu(+) and Cd(2+) were characterised. Photophysical measurements demonstrate that in [Cu(2)(L(1))(2)](2+), [CdL(1)](2+) and [Cu(2)(L(2))(2)](2+) the emission spectra are dominated by monomeric emission but in the cadmium complex of L(2) (where the pyrene units are in close proximity) a quenching of the luminescence coupled with weak emission at 540 nm is indicative of excimer formation.

A novel NIR fluorescent turn-on sensor for the detection of pyrophosphate anion in complete water system

A novel fluorescent sensor DCAA-Cu(2+) was developed, showing turn-on fluorescence in NIR region with high selectivity to pyrophosphate anion in 100% aqueous solution.

Fluorescent sensing and discrimination of ATP and ADP based on a unique sandwich assembly of pyrene-adenine-pyrene

It is still a challenging task to discriminate adenosine-5'-triphosphate (ATP) from various nucleoside triphosphates, such as GTP, CTP, UTP, and TTP. The ability to distinguish ATP from adenosine diphosphate (ADP) by fluorescent signals is also urgently desired. Herein, we report two pyrene-based zinc complexes as nucleoside polyphosphate receptors with high selectivity for ATP and ADP based on fluorescence and NMR studies. A unique pyrene-adenine-pyrene sandwich assembly was observed in the case of compound 1 with ATP or ADP, resulting in the increase of monomer fluorescence intensity; whereas the other bases of nucleoside triphosphates, such as GTP, CTP, UTP, and TTP were not sandwiched, resulting in a switch in the monomer-excimer fluorescence of pyrene. The different binding patterns of various nucleobases with a pyrene-pyrene assembly make 1 a highly selective fluorescent sensor for ANP (N=di, tri). In the case of compound 2, the first 0.5 equivalents of ATP induced a strong excimer emission, whilst ADP induced a large enhancement in the monomeric fluorescent peak. This fluorescence change makes 2 an efficient sensor to discriminate ATP from ADP.

Zn(II)-cyclam based chromogenic sensors for recognition of ATP in aqueous solution under physiological conditions and their application as viable staining agents for microorganism

Two chromogenic complexes, L.Zn (where L is (E)-4-((4-(1,4,8,11-tetraazacyclotetradecan-1-ylsulfonyl)phenyl)diazenyl)-N,N-dimethylaniline) and its [2]pseudorotaxane form (α-CD.L.Zn), were found to bind preferentially to adenosine triphosphate (ATP), among all other common anions and biologically important phosphate (AMP, ADP, pyrophosphate, and phosphate) ions in aqueous HEPES buffer medium of pH 7.2. Studies with live cell cultures of prokaryotic microbes revealed that binding of these two reagents to intercellular ATP, produced in situ, could be used in delineating the gram-positive and the gram-negative bacteria. More importantly, these dyes were found to be nontoxic to living microbes (eukaryotes and prokaryotes) and could be used for studying the cell growth dynamics. Binding to these two viable staining agents to intercellular ATP was also confirmed by spectroscopic studies on cell growth in the presence of different respiratory inhibitors that influence the intercellular ATP generation.

Fluorescent and colorimetric chemosensors for detection of nucleotides, FAD and NADH: highlighted research during 2004-2010

Due to the biological importance of nucleotides and related species, such as XNP (where X = adenosine (A), uridine (U), cytidine (C), guanosine (G), and N = mono, di, tri), FAD and NADH, the development of optical probes for these molecules has recently been an active area of research. This tutorial review focuses on the contributions between 2004-2010 concerning the fluorescent or colorimetric sensors for these biomolecules, and is organized according to their target molecule's structural classification.

DNA staining in agarose gels with Zn²+-cyclen-pyrene

A pyrene-labeled Zn²+-cyclen complex for the staining of DNA in agarose gels is reported. The metal chelate coordinates reversibly to the DNA phosphate backbone, which induces the formation of pyrene excimers. The typical pyrene excimer emission is used for the detection of the DNA. Staining is limited to agarose gels and is less sensitive than ethidium bromide, but DNA amounts as low as 10 ng and short DNA strands (∼300 b.p.) are detectable. Gel extraction as a standard technique in molecular biology was successfully performed after staining with Zn²+-cyclen-pyrene. Cytotoxicity tests on HeLa and V-79 cells reveal that the zinc-cyclen pyrene probe is significant less toxic compared to ethidium bromide.