Study of cavity size and nature of bridging units on recognition of nucleotides by cyclophanes

We synthesized a few novel cyclophanes CP-1 to CP-4 containing anthracene units linked together through different bridging and spacer groups and have investigated their interactions with various nucleosides and nucleotides. Of these systems, CP-1 and CP-3 showed selectivity for 5'-GTP and 5'-ATP as compared to other nucleotides and nucleosides, whereas negligible selectivity was observed with CP-2 and CP-4. Interestingly, CP-1, CP-2 and CP-3 exhibited significant binding interactions with the fluorescent indicator, 8-hydroxy-1,3,6-pyrene trisulfonate (HPTS), resulting in the formation of non-fluorescent complexes. Titration of these complexes with nucleosides and nucleotides resulted in the displacement of HPTS, leading to the revival of its fluorescence intensity. It was observed that 5'-GTP induced the maximum displacement of HPTS from the complex [CP-1·HPTS] with an overall fluorescence enhancement of ca. 150-fold, while 5'-ATP induced ca. 45-fold. Although the displacement of HPTS from the complexes [CP-2·HPTS] and [CP-3·HPTS] was found to be similar to that of [CP-1·HPTS], these complexes showed lesser selectivity and sensitivity. In contrast, negligible displacement of HPTS was observed from the complex [CP-4·HPTS] under similar conditions. These results indicate that CP-1, having a well-defined cavity and good electron acceptor (viologen), is capable of forming selective and stable complexes. Though CP-2 and CP-3 retain the good electron acceptor (viologen), their reduced aromatic surface and larger cavity, respectively, resulted in lesser sensitivity. In contrast, CP-4 having a large cavity and a poor acceptor (1,2-bis(pyridin-4-yl)ethene) showed negligible selectivity, thereby indicating the importance of cavity size, bridging unit and aromatic surface on biomolecular recognition properties of cyclophanes.     

Supramolecular Complexation of Biological Phosphates with an Acyclic Triazolium‐Linked Anthracenyl‐1,3‐Diconjugate of Calix[4]Arene: Synthesis,Characterization, Spectroscopy,Microscopy, and Computational Studies

A triazolium‐anthracenyl calix[4]arene conjugate ( L ) was synthesized by methylating the precursor triazole derivative and then characterized. The potential of the cationic L to differentiate nucleoside triphosphates (NTPs) from their mono‐ and diphosphates was demonstrated. Due to its unique combination of arms with the calix‐platform, a fluorescence enhancement was observed for L with all the NTPs, whereas there is no report with such enhancement being exhibited in case of all the NTPs. This has been supported by the aggregation of L observed from microscopy. Selectivity of L towards NTPs over other phosphates was a result of specific weak interactions, namely, ion–ion, hydrogen bonding and π ??? π, present in the 1:2 complex of L and NTPs (based on ESI MS), which were absent in their congener‐phosphates as delineated by NMR and computational studies. Thus, L stands as a unique receptor for NTPs.     

Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing

The rational design of fluorescent nucleoside analogues is greatly hampered by the lack of a general method to predict their photophysics, a problem that is especially acute when base pairing and stacking change fluorescence. To better understand these effects, a series of tricyclic cytidine (tC and tC^O) analogues ranging from electron-rich to electron-deficient was designed and synthesized. They were then incorporated into oligonucleotides, and photophysical responses to base pairing and stacking were studied. When inserted into double-stranded DNA oligonucleotides, electron-rich analogues exhibit a fluorescence turn-on effect, in contrast with the electron-deficient compounds, which show diminished fluorescence. The magnitude of these fluorescence changes is correlated with the oxidation potential of nearest neighbor nucleobases. Moreover, matched base pairing enhances fluorescence turn-on for the electron-rich compounds, and it causes a fluorescence decrease for the electron-deficient compounds. For the tC^O compounds, the emergence of vibrational fine structure in the fluorescence spectra in response to base pairing and stacking was observed, offering a potential new tool for studying nucleic acid structure and dynamics. These results, supported by DFT calculations, help to rationalize fluorescence changes in the base stack and will be useful for selecting the best fluorescent nucleoside analogues for a desired application.     

Characterization of Protein Complexes Containing Nucleoside Diphosphate Kinase with Characteristics of Light Signal Transduction through Phytochrome in Etiolated Pea Seedlings

Abstract— At 5 days after sowing of pea seeds in darkness, intact seedlings were either irradiated with red light for 40 s at 50 μmol/m²/s at the third internode or with red light as above and then with far-red light for 180 s at 0.4 μmol/m²/s, and the stems were sectioned from below the hook (mainly the third internodes) and placed in liquid N₂ in a mortar. The samples were well ground, and after the addition of extraction buffer, homogenates were centrifuged to prepare the crude membrane and soluble fractions. Red-light irradiation increased the phosphorylation of an 18 kDa protein, while far-red-light irradiation decreased it. The 18 kDa protein (formerly 15 kDa protein) was identified as nucleoside diphosphate kinase (EC 2.4.6) (NDP kinase) by western blotting using an NDP kinase-specific antibody. The membrane and the soluble fractions of the red-light-irradiated samples were separated by native polyacrylamide gel electrophoresis. The protein complexes prepared from the membrane and soluble fractions differed in their mobilities, as determined by two-dimensional electrophoresis and nonequilibrium pH gradient electrophoresis. The major protein spots from both samples were cut out from the gel and tested for NDP kinase and protein kinase activity. Both protein preparations showed NDP kinase activity and changes from nucleoside diphosphates and deoxynucleoside diphosphates to nucleoside triphosphates and deoxynucleoside triphosphates in the presence of [γ-³²P]ATP. Both preparations showed protein kinase phosphorylation of myelin basic protein (MBP) rather than histone H1 as protein substrates, suggesting that NDP kinase possesses a function similar to that of MAP kinase.     

Tri- and tetraurea piperazine cyclophanes: synthesis and complexation studies of preorganized and folded receptor molecules

A series of symmetrical tri‐ and tetrameric N‐ethyl‐ and N‐phenylurea‐functionalized cyclophanes have been prepared in nearly quantitative yields (86–99 %) from the corresponding tri‐ and tetraamino‐functionalized piperazine cyclophanes and ethyl or phenyl isocyanates. Their conformational and complexation properties have been studied by single‐crystal X‐ray diffraction, variable‐temperature NMR spectroscopy, and ESI‐MS analysis. The rigid 27‐membered trimeric cyclophane skeleton assisted by a seam of intramolecular hydrogen bonds results in a preorganized ditopic recognition site with an all‐syn conformation of the urea moieties that, complemented by a lipophilic cavity of the cyclophane, binds molecular and ionic guests as well as ion pairs. The all‐syn conformation persists in acidic conditions and the triprotonated triurea cyclophane binds an unprecedented anion pair, H₂PO₄^????HPO₄^2?, in the solid state. The tetra‐N‐ethylurea cyclophane is less rigid and demonstrates an induced‐fit recognition of diisopropyl ether in the solid state. The guest was encapsulated within the lipophilic interior of a quasicapsule, formed by intramolecular hydrogen‐bond‐driven folding of the 36‐membered cyclophane skeleton. In the gas phase, the essential role of the urea moieties in the binding was demonstrated by the formation of monomeric 1:1 complexes with K⁺, TMA⁺, and TMP⁺ as well as the ion‐pair complexes [KI+K]⁺, [TMABr+TMA]⁺ and [TMPBr+TMP]⁺. In the positive‐mode ESI‐MS analysis, ion‐pair binding was found to be more pronounced with the larger tetraurea cyclophanes. In the negative mode, owing to the large size of the binding site, a general binding preference towards larger anions, such as the iodide, over smaller anions, such as the fluoride, was observed.     

Dimeric quinacridone cyclophanes: Synthesis,structures,and photophysical properties

Two novel quinacridone (QA) cyclophanes with intrinsic intramolecular dye-dye interactions have been designed and synthesized.X-ray crystal structures as well as detailed photophysical properties have been well demonstrated.These two dyes have a major advantage that efficient fluorescence quenching can be observed even in their dilute solutions.A comparison of photophysical properties between the dimeric QA cyclophane and its reference monomeric counterpart indicates that the dimerization is predominant for...     

Azolium-linked cyclophanes: effects of structure, solvent, and counteranions on solution conformation behavior

This paper describes the synthesis, structural characterization, and solution behavior of some xylyl-linked imidazolium and benzimidazolium cyclophanes decorated with alkyl or alkoxy groups. The addition of alkyl/alkoxy chains to the cyclophanes allows for studies in chlorinated solvents, whereas previous solution studies of azolium cyclophanes have generally required highly polar solvents. The azolium cyclophanes may exist in a syn/syn conformation (azolium rings mutually syn, arene rings mutually syn) or a syn/anti conformation (azolium rings mutually syn, arene rings mutually anti). The preferred conformation is significantly affected by (i) binding of bromide (ion pairing) to the protons on the imidazolium or benzimidazolium rings, which occurs in solutions of bromide salts of the cyclophanes in chlorinated solvents, and (ii) the addition of alkoxy groups to the benzimidazolium cyclophanes. These structural modifications have also led to cyclophanes that adopt conformations not previously identified for similar azolium cyclophane analogues. Detailed (1)H NMR studies for one cyclophane identified binding of bromide at two independent sites within the cyclophane.     

Synthesis, DNA polymerase incorporation, and enzymatic phosphate hydrolysis of formamidopyrimidine nucleoside triphosphates

The nucleoside triphosphates of N6-(2-deoxy-alpha,beta-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy.dGTP) and its C-nucleoside analogue (beta-C-Fapy.dGTP) were synthesized. The lability of the formamide group required that nucleoside triphosphate formation be carried out using an umpolung strategy in which pyrophosphate was activated toward nucleophilic attack. The Klenow fragment of DNA polymerase I from Escherichia coli accepted Fapy.dGTP and beta-C-Fapy.dGTP as substrates much less efficiently than it did dGTP. Subsequent extension of a primer containing either modified nucleotide was less affected compared to when the native nucleotide is present at the 3'-terminus. The specificity constants are sufficiently large that nucleoside triphosphate incorporation could account for the level of Fapy.dG observed in cells if 1% of the dGTP pool is converted to Fapy.dGTP. Similarly, polymerase-mediated introduction of beta-C-Fapy.dG could be useful for incorporating useful amounts of this nonhydrolyzable analogue for use as an inhibitor of base excision repair. The kinetic viability of these processes is enhanced by inefficient hydrolysis of Fapy.dGTP and beta-C-Fapy.dGTP by MutT, the E. coli enzyme that releases pyrophosphate and the corresponding nucleoside monophosphate upon reaction with structurally related nucleoside triphosphates.     

Preparation of a mixture of nucleoside triphosphates suitable for use in synthesis of nucleotide phosphate sugars from ribonucleic acid using nuclease P1, a mixture of nucleoside monophosphokinases and acetate kinase

This paper (1) describes the enzymatic synthesis of a mixture of adenosine, guanosine, cytidine, and uridine triphosphates (ATP, GTP, CTP, and UTP) from ribonucleic acid (RNA). RNA was hydrolyzed by nuclease P1 to a mixture of 5'-nucleoside monophosphates. This mixture was converted to the nucleoside triphosphates using a mixture of nucleoside monophosphate kinases and acetate kinase, with acetyl phosphate as the ultimate phosphoryl donor. The nucleoside monophosphokinases were extracted from brewer's yeast in a four-step procedure. The specific activity of the yeast enzyme preparation after gel permeation chromatography was sufficiently high that the yeast kinases could be immobilized in volumes that were practical for laboratory scale syntheses. Conversions from NMP to NTP in a mixture containing 0.34 mol of total nucleoside phosphates were: ATP, 90%; GTP, 90%; CTP, 60%; and UTP, 40%.     

Modular synthesis of pi-acceptor cyclophanes derived from 1,4,5,8-naphthalenetetracarboxylic diimide and 1,5-dinitronaphthalene

Three neutral cyclophanes were synthesized, and their association with indole, an aromatic pi-donor, was studied. The cyclophanes were designed to contain a rigid, hydrophobic binding cavity with 1,4,5,8-naphthalenetetracarboxylic diimide or 1,5-dinitronaphthalene as the pi-acceptor. Two of the cyclophanes also contain a (S)-(valine-leucine-alanine) tripeptide unit to provide chiral hydrogen bonding interactions with guest molecules. Despite the fact that these cyclophanes contain a hydrophobic binding cavity of appropriate dimensions, their association with indole is very weak. In the case of cyclophanes derived from 1,5-dinitronaphthalene, steric interactions force the nitro groups out of the plane of the naphthalene ring, diminishing their effectiveness as pi-acceptors. A simple UV--visible titrimetric method, using N,N,N',N'-tetramethyl-1,4-phenylenediamine (TMPD) as a pi-donor, was used to rank the pi-acceptor strength of these and other aromatic units. These titrations show that 1,4,5,8-naphthalenetetracarboxylic diimide and 1,5-dinitronaphthalene derivatives are weaker pi-acceptors than viologens, which make good pi-acceptor cyclophanes. Methyl viologen is in turn a weaker pi-acceptor than anthaquinone disulfonate, suggesting that the latter may serve as a useful building block for pi-accepting cyclophane hosts.     

Synthesis of [m.n]Cyclophanes: Regiochemistry Transfer from Vinyl Halides to Cyclophanes via Fischer Carbene Complexes

The double benzannulation of bis‐carbene complexes of chromium with α,ω‐diynes generates [m.n]cyclophanes in which all three rings are generated in a single reaction. This triple annulation process is very flexible allowing for the construction of symmetrical [n.n]cyclophanes and unsymmetrical [m.n]cyclophanes as well as isomers in which the two benzene rings are both meta bridged or both para bridged, and isomers that contain both meta and para bridges. The connectivity patterns of the bridges in the cyclophanes can be controlled by regioselectivity transfer from the bis‐vinyl carbene complexes in which the substitution pattern of the vinyl groups in the carbene complexes dictate the connectivity pattern in the [m.n]cyclophanes. This synthesis of [n.n]cyclophanes is quite flexible with regard to ring size and can be used with tether lengths ranging from n=2 to n=16 and thus to ring sizes with up to 40 member rings. The only limitation to regioselectivity transfer from the carbene complexes to the [m.n]cyclophanes was found in the synthesis of para,para‐cyclophanes with four carbon tethers for which the loss of fidelity occurred with the unexpected formation of meta,para‐cyclophanes.     

Novel probes showing specific fluorescence enhancement on binding to a hexahistidine tag

The introduction of hexahistidine (His tag) is widely used as a tool for affinity purification of recombinant proteins, since the His tag binds selectively to nickel-nitrilotriacetic acid (Ni(2+)-NTA) complex. To develop efficient "turn-on" fluorescent probes for His-tagged proteins, we adopted a fluorophore displacement strategy, that is, we designed probes in which a hydroxycoumarin fluorophore is joined via a linker to a metal-NTA moiety, with which it forms a weak intramolecular complex, thereby quenching the fluorescence. In the presence of a His tag, with which the metal-NTA moiety binds strongly, the fluorophore is displaced, which results in a dramatic enhancement of fluorescence. We synthesized a series of hydroxycoumarins that were modified by various linkers with NTA (NTAC ligands), and investigated the chemical and photophysical properties of the free ligands and their metal complexes. From the viewpoint of fluorescence quenching, Ni(2+) and Co(2+) were the best metals. Fluorescence spectroscopy revealed a 1:1 binding stoichiometry for the Ni(2+) and Co(2+) complexes of NTACs in pH 7.4 aqueous buffer. As anticipated, these complexes showed weak intrinsic fluorescence, but addition of a His-tagged peptide (H-(His)(6)-Tyr-NH(2); Tyr was included to allow convenient concentration measurement) in pH 7.4 aqueous buffer resulted in up to a 22-fold increase in the fluorescence quantum yield. We found that the Co(2+) complexes showed superior properties. No fluorescence enhancement was seen in the presence of angiotensin I, which contains two nonadjacent histidine residues; this suggests that the probes are selective for the polyhistidine peptide.     

Experimental and Computational Study of Complexes Between Quats and Naphthalenophanes

Abstract

A number of neutral cyclophanes incorporating either a 2,6- or a 2,7-dioxynaphthalene unit have been synthesised and their binding properties toward tetramethylammonium and N-methylpyridinium picrates assessed by means of a ¹H NMR spectroscopic technique. A parallel computational study based on molecular mechanics and molecular dynamics calculations has been carried out. There is at least a rough agreement between complexation phenomena based on cation - π interactions in solution and molecular mechanics calculations in the gas phase, in that the stability trend seen across the series of naphthalenophane/tetramethylammonium complexes is satisfactorily reproduced. Furthermore, there is a clear corre-spondence between the magnitude of the observed upfield shifts upon complexation and the calculated structures of host-guest complexes.     

Complexation of antibacterial quinolonic acid and cinolonic derivatives with Zn(II) and Al(III): application to their determination in human urine

Nalidixic acid, 7-hydroxymethylnalidixic acid, oxolinic acid, pipemidic acid and cinoxacine form complexes with zinc(II) in the presence of acetate buffer of pH 5.5 and oxolinic acid, pipemidic acid and cinoxacine form complexes with aluminium(III) in the presence of chloroacetate buffer of pH 3.0. In all cases, an enhancement of the fluorescence emission was observed. Fluorimetric studies on the spectral characteristics of the complexes were performed. A 1:1 stoichiometry for all the complexes was established. The association constants were calculated, by using the changes in the fluorescence of all antibacterials, that occurred when the complexes were formed. The fluorescence reactions were used to develop methods for the determination of all of the above compounds, showing a higher sensitivity than in the absence of the cationic ions. The methods were satisfactorily applied to the determination of these compounds in urine.     

Synthesis and photophysical properties of biaryl-substituted nucleos(t)ides. Polymerase synthesis of DNA probes bearing solvatochromic and pH-sensitive dual fluorescent and 19F NMR labels

The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.     

Molecular Recognition by Cyclophane/Guanidinium Supramolecular Receptor Embedded at the Air-Water Interface

In order to develop a supramolecular receptor through a self-assembling process, a site-specific host and an inclusion-type host were mixed as a Langmuir monolayer, and guest binding and pressure-induced fluorescence emission were investigated. A guanidinium amphiphile and several cyclophanes carrying hydrophobic moieties were used as the host molecules; molecular recognition of an aqueous fluorescent guest, 6-p-toluidino-2-naphthalenesulfonic acid (TNS) by binary mixed receptor monolayers was evaluated by a surface pressure-molecular area (π-A) isotherm and a surface fluorescence measurement. An apparent increase in fluorescence intensity was observed when the mixed monolayers of the guanidinium and cyclophane amphiphiles were compressed on an aqueous TNS solution. In contrast, single-component monolayers of the guanidinium or the cyclophane did not show a significant increase in fluorescence emission. In the mixed monolayers, the guest TNS would be bound to the interface by strong electrostatic interaction with the guanidinium, and inclusion of the formed complex probably suppresses the quenching effect in polar medium and/or self-quenching. Experiments with various mixing ratios of these components suggest selective formation of an equimolar cooperative receptor of the guanidinium and the cyclophane. Investigation of the cyclophane structures by fluorescence emission and a competitive binding experiment with another guest were also carried out.     

Binding and Sensing Properties of a Hybrid Naphthalimide–Pyrene Aza-Cyclophane towards Nucleotides in an Aqueous Solution

Selective recognition of nucleotides with synthetic receptors is an emerging direction to solve a series of nucleic acid-related challenges in biochemistry. Towards this goal, a new aza-cyclophane with two different dyes, naphthalimide and pyrene, connected through a triamine linker has been synthesized and studied for the ability to bind and detect nucleoside triphosphates in an aqueous solution. The receptor shows Foerster resonance energy transfer (FRET) in fluorescence spectra upon excitation in DMSO, which is diminished dramatically in the presence of water. According to binding studies, the receptor has a preference to bind ATP (adenosine triphosphate) and CTP (cytidine triphosphate) with a “turn-on” fluorescence response. Two separate emission bands of dyes allow one to detect nucleotides in a ratiometric manner in a broad concentration range of 10⁻⁵–10⁻³ M. Spectroscopic measurements and quantum chemical calculations suggest the formation of receptor–nucleotide complexes, which are stabilized by dispersion interactions between a nucleobase and dyes, while hydrogen bonding interactions of nucleobases with the amine linkers are responsible for selectivity.     

Fully validated assay for the quantification of endogenous nucleoside mono- and triphosphates using online extraction coupled with liquid chromatography–tandem mass spectrometry

An analytical method coupling online solid-phase extraction (SPE) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) was developed to quantify 16 endogenous nucleoside mono- and triphosphates in cellular samples. Separation was achieved on a porous graphitic carbon (PGC) column without ion-pairing agent in the mobile phase. Low levels of the ion-pairing agent diethylamine (DEA) added to the reconstitution solution were necessary to prevent peak tailing of nucleoside triphosphates. The mass spectrometer, a triple quadrupole with an electrospray ionisation source, was operated in positive mode. Two multiple reaction monitoring (MRM) segments were programmed, each an internal standard. Extraction and separation of nucleoside mono- and triphosphates were obtained within 20 min. The total duration of a single run was 37 min. Calibration curves, performed with labelled nucleotides added to the sample matrix, ranged from 0.29 to 18.8 pmol injected for deoxyribonucleotides and from 3.9 to 3,156 pmol for ribonucleotides. Accuracy did not deviate more than ?14.6 and 10.2 % from nominal values for all compounds at all levels. CV results were all lower than 17.0 % for the LLOQ level and 14.6 % for the other levels. Quality control (QC) samples were also in agreement with acceptance criteria, except for the lower QC of GMP. Ion suppression, matrix effect, extraction recoveries and stability were assessed. After validation, the method was applied to the evaluation of the effects of gemcitabine and hydroxyurea on nucleotide pools in Messa cells.     

A highly selective and sensitive fluorescence "turn-on" probe for Ag+ in aqueous solution and live cells

A naphthalimide-based fluorescent probe, NPQ, that contains a novel receptor was successfully developed. NPQ exhibited "turn-on" fluorescence and excellent selectivity toward Ag(+) in the presence of various other metal ions in aqueous solution. A series of control compounds were designed and synthesized in order to explore the photoinduced electron transfer (PET) quenching mechanism of NPQ and binding mode of NPQ with Ag(+). Moreover, with the NPQ-Ag(+) complex, I(-) was easily selectively recognized by a marked fluorescence quenching. The live cell imaging experiments demonstrate that NPQ can be used as a fluorescent probe for monitoring Ag(+) in living cells.     

Synthesis of alpha-L-threofuranosyl nucleoside triphosphates (tNTPs)

[structure: see text] The alpha-l-threofuranosyl nucleoside triphosphates of T, G, and D (tTTP, tGTP, and tDTP) were synthesized from the described 2'-O-DMT-protected derivatives using the Eckstein method, while the corresponding C derivative (tCTP) was prepared from the 2'-O-acetyl derivative. The prepared alpha-l-threofuranosyl nucleoside triphosphates, despite being one carbon shorter than the native 2'-deoxyfuranosyl nucleoside triphosphates, are effective substrates for selected DNA polymerases.