An unexpected highly selective mononuclear zinc complex for adenosine diphosphate (ADP)

Boron-Salphen Conjugate based Molecular Probe Exhibiting Fluorescence On-Off-On Response in Detection of Cu2+ and ATP through Displacement Approach

Synthesis and photophysical properties of a fluorescent probe HBD is described. Probe upon interaction with metal ions, anions and nucleoside pyrophosphates (NPPs) showed fluorescence quenching with Cu2+ due to chelation enhanced quenching effect (CHEQ). Moreover, interaction of ensemble HBD.Cu2+ with anions and NPPs showed fluorescence "turn-On" response with ATP selectively. "On-Off-On" responses observed with Cu2+ and ATP is attributed to an interplay between ESIPT and TICT processes. Cyclic voltammogram of probe exhibited quasi-reversible redox behaviour with three oxidation and two reduction potentials and the change in band gaps of probe suggested the interaction with Cu2+ and ATP. The 2 : 1 and 1 : 1 binding stoichiometry for an interaction between probe and Cu2+ (LOD, 62 nM) and ensemble, HBD.Cu2+ with ATP (LOD, 0.4 μM) respectively are realised by Job's plot and HRMS data. Cell imaging studies carried out to detect Cu2+ and ATP in HeLa cells. Also, the output emission observed with Cu2+ and ATP is utilized to construct an implication (IMP) logic gate. Test paper strips showed naked-eye visible color responses to detect Cu2+ and ATP. In real water samples probe successfully detected copper (0.03 μM) between 5-6.5 ppb level (ICP-MS method).

Azulene-based fluorescent chemosensor for adenosine diphosphate

AzuFluor® 435-DPA-Zn, an azulene fluorophore bearing two zinc(II)-dipicolylamine receptor motifs, exhibits fluorescence enhancement in the presence of adenosine diphosphate. Selectivity for ADP over ATP, AMP and PPi results from appropriate positioning of the receptor motifs, since an isomeric sensor cannot discriminate between ADP and ATP.

TICT fluorescent probe for Al3+: Sequential detection of PPi, ATP and ADP in semi-aqueous medium and real-life applications

A ditopic Schiff base ligand, H₂L has been synthesized and characterized by all spectroscopic techniques. It is highly selective and specific towards Al³⁺ in semi aqueous medium (DMF/H₂O mixture) by exhibiting a drastic increase in the fluorescence intensity. The emission studies, spectroscopic data, life time and quantum yield results have been used to understand its binding mode, explore its specificity and establish its efficacy. The intensity difference is remarkable in physiological pH range. Due to its reversible behavior this ditopic fluorescent chemosensor can be used multiple times to make it cost effective. Detection limit for this chemosensor was found to be 0.65 μM. Experiments with TLC plates show that it can be used as a practical and portable sensor for studying environmental samples in real life. The L-Al³⁺ complex generated in the solution acts as a sensor to sequentially detect pyrophosphate groups present in inorganic pyrophosphates, ATP and ADP among other anions by turning off the fluorescence. Inhibit logic gate and its corresponding truth table has been developed to aid in further exploiting its multidimensional applications.

A Quinoline-Appended Cyclodextrin Derivative as a Highly Selective Receptor and Colorimetric Probe for Nucleotides

The design and development of specific recognition and sensing systems for biologically important anionic species has received growing attention in recent years, as they play significant roles in biology, pharmacy, and environmental sciences. Herein, a new supramolecular sensing probe L1 was developed for highly selective differentiation of nucleotides. L1 displayed extremely marked absorption and emission differentiation upon binding with nucleotide homologs of AMP, ADP, and ATP, due to the divergent spatial orientations of guests upon binding, which allowed for a naked-eye colorimetric differentiation for nucleotides. A differentiating mechanism was unambiguously rationalized by using various spectroscopic studies and theoretical calculations. Furthermore, we successfully demonstrated that L1 can be applied to the real-time monitoring of the enzyme-catalyzed phosphorylation/dephosphorylation processes and thus demonstrated an unprecedented visualizable strategy for selectively differentiating the structurally similar nucleotides and real-time monitoring of biological processes via fluorescent and colorimetric changes.

Selective sensing of ATP by hydroxide-bridged dizinc(ii) complexes offering a hydrogen bonding cavity

This work illustrates the highly selective fluorescence detection of ATP in the presence of other competing anions, such as AMP, ADP, PPi and other phosphates by using a set of hydroxide-bridged dizinc(ii) complexes offering a cavity lined with hydrogen bonds and other interactive forces. ATP, as a whole, was recognized by the synergic combination of Zn-phosphate bonding, ππ stacking between the adenine ring of ATP and the pyridine ring of the dizinc complex and hydrogen bonding interactions that modulate the cavity structure of the dizinc complexes.

Molecular Receptors for Recognition and Sensing of Nucleotides

Nucleotides are constituents of nucleic acids and they have a variety of functions in cellular metabolism. Synthetic receptors and sensors are required to reveal the role of nucleotides in living organisms and mechanisms of signal transduction events. In recent years, a large number of nucleotide-selective synthetic receptors have been devised, which utilize different molecular designs and sensing mechanisms. This Minireview presents recent progress in the design of synthetic molecular receptors for selective recognition of nucleotides in aqueous solution. The binding properties of receptors and the origins of their selectivity for a particular nucleotide are discussed.

Supramolecular Assembly of Uridine Monophosphate (UMP) and Thymidine Monophosphate (TMP) with a Dinuclear Copper(II) Receptor

Understanding the intermolecular interactions between nucleotides and artificial receptors is crucial to understanding the role of nucleic acids in living systems. However, direct structural evidence showing precise interactions and bonding features of a nucleoside monophosphate (NMP) with a macrocycle-based synthetic molecule has not been provided so far. Herein, we present two novel crystal structures of uridine monophosphate (UMP) and thymidine monophosphate (TMP) complexes with a macrocycle-based dinuclear receptor. Structural characterization of these complexes reveals that the receptor recognizes UMP through coordinate-covalent interactions with phosphates and π-π stackings with nucleobases and TMP through coordinate-covalent interactions with phosphate groups. Furthermore, the receptor has been shown to effectively bind nucleoside monophosphates in the order of GMP > AMP > UMP > TMP > CMP in water at physiological pH, as investigated by an indicator displacement assay.

Understanding Stacking Interactions between an Aromatic Ring and Nucleobases in Aqueous Solution: Experimental and Theoretical Study

Stacking interactions between aromatic compounds and nucleobases are crucial in recognition of nucleotides and nucleic acids, but a comprehensive understanding of the strength and selectivity of these interactions in aqueous solution has been elusive. To this end, model complexes have been designed and analyzed by experiment and theory. For the first time, stacking free energies between five nucleobases and anthracene were determined experimentally from thermodynamic double mutant cycles. Three different experimental methods were proposed and evaluated. The dye prefers to bind nucleobases in the order (kcal/mol): G (1.3) > T (0.9) > U (0.8) > C (0.5) > A (0.3). The respective trend of interaction free energies extracted from DFT calculations correlates to that obtained experimentally. Analysis of the data suggests that stacking interactions dominate over hydrophobic effects in an aqueous solution and can be predicted with DFT calculations.

Fluorescence sensing of ADP over ATP and PPi in 100% aqueous solution

An anthracene-bridged dinuclear zinc(ii)-dipicolylamine complex was found to show high selectivity for ADP with a significant fluorescence enhancement over ATP, PPi and other common analytes in 100% aqueous solution. This complex can be used for fluorescence detection of ADP in living cells and for monitoring the activity of kinases.

Complexation of phosphates by 1,3-bis(3-(2-pyridylureido)propyl)-1,1,3,3-tetramethyldisiloxane

RATIONALE

Compounds containing a urea or thiourea moiety form complexes with anions thanks to the ability to form quite strong hydrogen bonds. We have synthesized 1,3-bis(3-(2-pyridylureido)propyl)-1,1,3,3-tetramethyldisiloxane (1). Compound 1 contains two urea moieties connected by a long flexible linker; thus, it should be able to adopt a structure suitable for formation of quite stable complexes with anions.

METHODS

The ability to form complexes of compound 1 with phosphates was tested by electrospray ionization mass spectrometry (ESI-MS). Full scan ESI mass spectra and collision-induced dissociation tandem mass (CID-MS/MS) spectra of the ions of interest were obtained on a quadrupole time-of-flight (QTOF) mass spectrometer.

RESULTS

It has been found that compound 1 is not only much more prone to form complexes with the phosphate anion than with other inorganic anions, but it is also able to form complexes with organic phosphates, namely nucleotides and phospholipids. However, compound 1 is not able to form complexes with organic compounds not containing a phosphate group (e.g. nucleosides, sugars, glycerolipids).

CONCLUSIONS

Compound 1 can be regarded as selective towards phosphate-containing organic compounds. Formation of such complexes may have some interesting applications for identification of organic phosphates in crude extracts from biological materials.

Self-assembled copper(II) metallacycles derived from asymmetric Schiff base ligands: efficient hosts for ADP/ATP in phosphate buffer

Novel asymmetric Schiff base ligands 2-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-phenol (H2L(1)) and 1-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-naphthalen-2-ol (H2L(2)) possessing dissimilar N,O-chelating sites and copper(ii) metallacycles (CuL(1))4 (1) and (CuL(2))4 (2) based on these ligands have been described. The ligands and complexes have been thoroughly characterized by satisfactory elemental analyses, and spectral (IR, (1)H, (13)C NMR, ESI-MS, UV/vis) and electrochemical studies. Structures of H2L(2) and 1 have been unambiguously determined by X-ray single crystal analyses. The crystal structure of H2L(2) revealed the presence of two distinct N,O-chelating sites on dissimilar cores (naphthalene and β-ketoaminato groups) offering a diverse coordination environment. Metallacycles 1 and 2 having a cavity created by four Cu(ii) centres coordinated in a homo- and heteroleptic fashion with respective ligands act as efficient hosts for adenosine-5'-diphosphate (ADP) and adenosine-5'-triphosphate (ATP) respectively, over other nucleoside polyphosphates (NPPs). The disparate sensitivity of these metallacycles toward ADP and ATP has been attributed to the size of the ligands assuming diverse dimensions and spatial orientations. These are attuned for π-π stacking and electrostatic interactions suitable for different guest molecules under analogous conditions, metallacycle 1 offers better orientation for ADP, while 2 for ATP. The mechanism of the host-guest interaction has been investigated by spectral and electrochemical studies and supported by molecular docking studies.

A fluorescent probe for estimation of adenosine diphosphate and monitoring of glucose metabolism

An ADP selective fluorescent probe working in aqueous medium was identified and the change in fluorescence as a function of ADP concentration was standardized. Using this probe, all the steps of glycolysis coupled with ATP/ADP inter-conversion and oxidative breakdown of pyruvate in the mitochondria were monitored and the consumption/production of ATP/ADP at each step was quantified. The quantity of ADP present in the mitochondria, taken from different body parts of a pig, was also determined. It is hypothesized that an appropriate modification of the technique may provide a diagnostic tool for monitoring biochemical pathways as well as for quick estimation of ADP in the mitochondria and other cell organelles.

A ratiometric fluorescent probe with unexpected high selectivity for ATP and its application in cell imaging

Naphthalimide-rhodamine compound (NR) is developed as a ratiometric fluorescent probe for ATP detection based on the FRET mechanism. It shows an unexpected high selectivity for ATP over other anions, especially organic phosphate anions, due to simultaneous interactions of two recognition sites, which benefits fluorescence imaging in living cells.

A Ga(3+)self-assembled fluorescent probe for ATP imaging in vivo

Adenosine 5'-triphosphate (ATP) is a functional molecule associated with many important biological processes. Fluorescent detection methods for ATP with facile performance and high selectivity are in demand. One of the possible multi-membered arrays assembled between DHBO and Ga(3+) ions was conducted in aqueous solution, which can selectively recognize ATP with fluorescence enhancement from ADP, AMP and other structurally similar nucleoside triphosphates in vitro and in vivo. ATP facilitates the interaction between DHBO and Ga(3+) ions, resulting in the fluorescence increase. The detection limit for ATP was calculated to be 5.49×10(-7)M, which is much lower than that of intracellular concentrations (1-10mM). In addition, DHBO-Ga(3+) can be applied to detect ATP-relevant enzyme activity.

Discrimination of adenine nucleotides and pyrophosphate in water by a zinc complex of an anthracene-based cyclophane

Combining metal-anion coordination and π-π stacking interactions, a zinc complex of a novel anthracene-based cyclophane was designed to recognise adenine nucleoside polyphosphates. This complex was found to show selective fluorescence enhancement for ATP, ADP, AMP and PPi in neutral aqueous solution. Among them, ADP induced the largest fluorescence change to the complex, while ATP showed the strongest binding affinity to the complex. This property was used to sense ATP in the presence of excess amounts of other phosphates such as ADP, AMP, PPi and Pi.

A Mononuclear Zinc Complex for Selective Detection of Diphosphate via Fluorescence ESIPT Turn-On

A mononuclear zinc complex has been found to exhibit unexpected selectivity for biologically important diphosphate anions (PPi and ADP). The diphosphate binding could turn-on the ESIPT, whose study reveals mechanistic insight to aid the future design of new sensors.