Pseudoknot preorganization of the preQ1 class I riboswitch

To explore folding and ligand recognition of metabolite-responsive RNAs is of major importance to comprehend gene regulation by riboswitches. Here, we demonstrate, using NMR spectroscopy, that the free aptamer of a preQ(1) class I riboswitch preorganizes into a pseudoknot fold in a temperature- and Mg(2+)-dependent manner. The preformed pseudoknot represents a structure that is close to the ligand-bound state and that likely represents the conformation selected by the ligand. Importantly, a defined base pair mutation within the pseudoknot interaction stipulates whether, in the absence of ligand, dimer formation of the aptamer competes with intramolecular pseudoknot formation. This study pinpoints how RNA preorganization is a crucial determinant for the adaptive recognition process of RNA and ligand.     

Microcalorimetrics studies of the thermodynamics and binding mechanism between L-tyrosinamide and aptamer

In recent years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complex interactions. In some cases, however, the aptamer complex binding behavior and mechanism are not clearly understood, especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC) and circular dichroism (CD) were useful tools for studying the fundamental binding mechanism between a DNA aptamer and L-tyrosinamide (L-TyrNH2). To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value, analogue of L-TyrNH2, and metal ion were carried out. The thermodynamic signature along with the coupled CD spectral change suggest that this binding behavior is an enthalpy-driven process, and the aptamer has a conformational change from B-form to A-form. The results showed that the interaction is an induced fit binding, and the driving forces in this binding behavior may include electrostatic interactions, hydrophobic effects, hydrogen bonding, and the binding-linked protonation process. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg(2+) not only improves binding affinity but also helps change the structure of the DNA aptamer.     

Cooperative and directional folding of the preQ1 riboswitch aptamer domain

Riboswitches are cis-acting RNA fragments that regulate gene expression by sensing cellular levels of the associated small metabolites. In bacteria, the class I preQ(1) riboswitch allows the fine-tuning of queuosine biosynthesis in response to the intracellular concentration of the queuosine anabolic intermediate preQ(1). When binding preQ(1), the aptamer domain undergoes a significant degree of secondary and tertiary structural rearrangement and folds into an H-type pseudoknot. Conformational "switching" of the riboswitch aptamer domain upon recognizing its cognate metabolite plays a key role in the regulatory mechanism of the preQ(1) riboswitch. We investigate the folding mechanism of the preQ(1) riboswitch aptamer domain using all-atom Go?-model simulations. The folding pathway of such a single domain is found to be cooperative and sequentially coordinated, as the folding proceeds in the 5' → 3' direction. This kinetically efficient folding mechanism suggests a fast ligand-binding response in competition with RNA elongation.     

Experimental and computational studies of selective recognition of Hg2+ by amide linked lower rim 1,3-dibenzimidazole derivative of calix[4]arene: species characterization in solution and that in the isolated complex, including the delineation of the nanostructures

Amide linked lower rim 1,3-dibenzimidazole derivative of calix[4]arene, L has been shown to be sensitive and selective to Hg(2+) in aqueous acetonitrile solution based on fluorescence spectroscopy, and the stoichiometry of the complexed species has been found to be 1:1. The selectivity of L toward Hg(2+) has been shown among 11 M(2+) ions, viz., Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Hg(2+), Pb(2+), Ca(2+), and Mg(2+) studied, including those of the mercury group and none of these ions impede the recognition of Hg(2+) by L. Role of the solvent on the recognition of Hg(2+) has been demonstrated. The role of calix[4]arene platform and the benzimidazole moieties in the recognition of Hg(2+) by L has been delineated upon performing such studies with five different molecules of relevance as reference molecular systems. The binding cores formed by the receptor L and the reference compounds have been established based on the single crystal XRD structures, and the preferential metal ion binding cores have been discussed. The binding of Hg(2+) with L has been further established based on (1)H and (13)C NMR, ESI MS, absorption, and fluorescence lifetime measurements. Some of these techniques have been used to establish the stoichiometry of the species formed. The complex species formed between L and Hg(2+) have been isolated and characterized and found to be 1:1 species even in the isolated complex. Whereas transmission electron microscopy (TEM), atomic force microscopy (AFM), and scanning electron microscopy (SEM) provided the nanostructural behavior of L, the TEM and SEM demonstrated that the mercury complex has different characteristics when compared to L. The TEM, SEM, and powder XRD studies revealed that whereas L is crystalline, that of the mercury complex is not, perhaps a reason for not being able to obtain single crystals of the complex. Binding characteristics of Hg(2+) toward L have been established based on the DFT computational calculations.     

Designing sequence to control protein function in an EF-hand protein

The extent of conformational change that calcium binding induces in EF-hand proteins is a key biochemical property specifying Ca(2+) sensor versus signal modulator function. To understand how differences in amino acid sequence lead to differences in the response to Ca(2+) binding, comparative analyses of sequence and structures, combined with model building, were used to develop hypotheses about which amino acid residues control Ca(2+)-induced conformational changes. These results were used to generate a first design of calbindomodulin (CBM-1), a calbindin D(9k) re-engineered with 15 mutations to respond to Ca(2+) binding with a conformational change similar to that of calmodulin. The gene for CBM-1 was synthesized, and the protein was expressed and purified. Remarkably, this protein did not exhibit any non-native-like molten globule properties despite the large number of mutations and the nonconservative nature of some of them. Ca(2+)-induced changes in CD intensity and in the binding of the hydrophobic probe, ANS, implied that CBM-1 does undergo Ca(2+) sensorlike conformational changes. The X-ray crystal structure of Ca(2+)-CBM-1 determined at 1.44 A resolution reveals the anticipated increase in hydrophobic surface area relative to the wild-type protein. A nascent calmodulin-like hydrophobic docking surface was also found, though it is occluded by the inter-EF-hand loop. The results from this first calbindomodulin design are discussed in terms of progress toward understanding the relationships between amino acid sequence, protein structure, and protein function for EF-hand CaBPs, as well as the additional mutations for the next CBM design.     

Probing the structure of DNA aptamers with a classic heterocycle

DNA aptamers are synthetic, single-stranded DNA oligonucleotides selected by SELEX methods for their binding with specific ligands. Here we present ethidium binding results for three related DNA aptamers (PDB code: 1OLD, 1DB6, and 2ARG)that bind L-argininamide (L-Arm). The ligand bound form of each aptamer's structure has been reported and each are found to be composed primarily of two domains consisting of a stem helical region and a loop domain that forms a binding pocket for the cognate ligand. Previous thermodynamic experiments demonstrated that the DNA aptamer 1OLD undergoes a large conformational ordering upon binding to L-Arm. Here we extend those linkage binding studies by examining the binding of the heterocyclic intercalator ethidium to each of the three aptamers by fluorescence and absorption spectrophotometric titrations. Our results reveal that ethidium binds to each aptamer with DeltaG degree's in the range of -8.7 to -9.4 kcal/mol. The stoichiometry of binding is 2:1 for each aptamer and is quantitatively diminished in the presence of L-Arm as is the overall fluorescence intensity of ethidium. Together, these results demonstrate that a portion of the bound ethidium is excluded from the aptamer in the presence of a saturating amount of L-Arm. These results demonstrate the utility of ethidium and related compounds for the probing of non-conventional DNA structures and reveal an interesting fundamental thermodynamic linkage in DNA aptamers. Results are discussed in the context of the thermodynamic stability and structure of each of the aptamers examined.     

The characterization for the binding of calcium and terbium to Euplotes octocarinatus centrin

Centrin is a member of the EF-hand superfamily that plays critical role in the centrosome duplication and separation. In the present paper, we characterized properties of metal ions binding to Euplotes octocarinatus centrin (EoCen) by fluorescence spectra and circular dichroism (CD) spectra. Changes of fluorescence spectra and alpha-helix contents of EoCen proved that Tb(3+) and Ca(2+) induced great conformational changes of EoCen resulting in exposing hydrophobic surfaces. At pH 7.4, Ca(2+) (and Tb(3+)) bond with EoCen at the ratio of 4:1. Equilibrium experiment indicated that Ca(2+) and Tb(3+) exhibited different binding capabilities for C- and N-terminal domains of protein. C-terminal domain bond with Ca(2+) or Tb(3+) approximately 100-fold more strongly than N-terminal. Aromatic residue-sensitized Tb(3+) energy transfer suggested that site IV bond to Tb(3+) or Ca(2+) more strongly than site III. Based on fluorescence titration curves, we reckoned the conditional binding constants of EoCen site IV quantitatively to be K(IV)=(1.23+/-0.51)x10(8)M(-1) and K(IV)=(6.82+/-0.33)x10(5)M(-1) with Tb(3+) and Ca(2+), respectively. Metal ions bond to EoCen in the order of IV>III>II, I.     

Synthesis and spectroscopic and structural characterization of two novel photoactivatable Ca2+ compounds

Two novel photoactivatable Ca(2+) compounds were synthesized to achieve a fast concentration jump of calcium ions in solution; this is of paramount importance for investigating the physiological cellular response. The light-sensitive ligands 4-(2-nitrophenyl)-3,6-dioxaoctane dioic acid (H2L1) and 4-(4,5-dimethoxy-2-nitrophenyl)-3,6-dioxaoctane dioic acid (H2L2) were generated by multistep syntheses, and the corresponding calcium complexes, Ca1 and Ca2, were isolated and characterized. The solution equilibria of H2L1 and H2L2 with Ca2+ were investigated; for both ligands, the formation of a 1:2 Ca2+/ligand species is detected and the complete characterization is presented. The crystal structures of Ca1 and Ca2 were determined. In Ca1 the solid state assembly is attained by a polymeric association of [(CaL1(H2O))2(mu-OH2)] dimeric units. Each calcium ion coordinates four oxygen atoms of one ligand (two ethereal, one carboxylic, and one bridging carboxylic oxygen atom), one water molecule, one bridging water molecule, and a carboxylate group of the other ligand within the dimer. The octacoordination of the metal is completed by an interaction with the adjacent dimeric unit. The crystal structure of the complex Ca2 does not show a polymeric nature, but it is a centrosymmetric dimer. The coordination number of the metal ion is still 8:4 oxygen atoms of the ligand; 3 water molecules; 1 bridging carboxylate group. A preliminary study of the photochemical features of the complexes Ca1 and Ca2 is reported: photoexcitation by a nanosecond pulsed UV laser induces the cleavage of the ligand. This drastically reduces the affinity of the ligand toward Ca2+, which is then released in solution.     

Salt effects on the conformational behavior of 5-carboxy- and 5-hydroxy-1,3-dioxane

The varied and essential involvement of metal ions and inorganic salts in biological and chemical processes motivated the present study where 5-carboxy- and 5-hydroxy-1,3-dioxanes are used as model frameworks for the evaluation of the conformational behavior of oxygen-containing receptors in the presence of Li(+), Na(+), K(+), Ag(+), Mg(2+), Ca(2+), Ba(2+), and Zn(2+). Thus, the position of equilibria, established by means of BF(3), between diastereomeric cis- and trans-5-substituted-2-phenyl-1,3-dioxanes, in solvent THF and in the presence of 0, 1, and 5 equiv of salt, has been determined. The observed Delta G(o) degrees values for the conformational equilibria of 5-carboxy-1,3-dioxane show that Ag(+), Li(+), and Ca(2+) complexation leads to increased stability of the axial isomer. In the case of the 5-hydroxy-1,3-dioxane, Mg(2+), Ag(+), and Zn(2+) are the metal ions that stabilize the axial conformer of the heterocycle upon association. Interpretation of the experimental observations was based on DFT molecular modeling studies at the Becke3LYP/6-31G* and Becke3LYP/6-31+G** levels of theory. Although gas-phase calculations give Delta E values that are too large when modeling equilibria involving ionic species in polar solution, the computational results confirm the structural and energetic consequences of metal cation coordination to the oxygen atom in carbonyls or ethers. The results derived from the present study contribute to our understanding of the chemical processes involved in molecular recognition and physiological events.     

Aptamer-oligonucleotide binding studied by capillary electrophoresis: cation effect and separation efficiency

Novel features of DNA structure, recognition and discrimination have been recently elucidated through the solution structural characterization of DNA aptamers that bind cofactors, amino acids and peptides with high affinity and specificity. Multidimensional nuclear magnetic resonance methodologies have been successfully applied to solve the solution structures. In this work, it was demonstrated that capillary electrophoresis was a powerful tool allowing the fundamental study of the binding mechanism between a DNA aptamer and three ligands, adenosine and adenylate compounds, i.e., adenosine diphosphate (ADP) and adenosine triphosphate (ATP). In order to gain further insight into this binding, thermodynamic measurements under different values of parameters (such as salt nature and its concentration (x) in the run buffer) were carried out. The results showed that dehydration at the binding interface, van der Waals interactions, H-bonding and adjustment of the aptamer recognition surface were implied in the aptamer-ligand association. As well, it was demonstrated that the addition in the medium of the sodium monovalent cation Na(+) or the nickel divalent cation Ni(2+) decreased the complex formation. Separation efficiency and peak shape can also be improved by Mg(2+) divalent cation, which increased the mass transfer kinetics during the ligand-aptamer binding process. A significant separation for the worst separated pair of peaks on the electropherogram ((ADP, ATP) peak pair) was thus achieved.     

A terpyridyl-imidazole (tpy-HImzPh3) based bifunctional receptor for multichannel detection of Fe2+ and F- ions

The X-ray crystal structures of the tridentate ligand, 4'-[4-(4,5-diphenyl-1H-imidazol-2-yl)-phenyl]-[2,2':6',2']terpyridine (tpy-HImzPh(3)) and its bis-homoleptic iron(ii) complex of composition [Fe(tpy-HImzPh(3))(2)](2+) have been determined, showing that the ligand crystallized in a monoclinic form with the space group P2(1)/c while its Fe(II) complex crystallizes in an orthorhombic form with space group Fddd. Both the anion and cation binding properties of the receptor were thoroughly investigated in dimethylformamide-acetonitrile (1?:?9) solution using absorption, emission, and (1)H NMR spectral studies which revealed that the receptor acts as a sensor for both F(-) and Fe(2+). In the presence of excess F(-) ion, deprotonation of the imidazole N-H fragment of the receptor occurs, an event which is signaled by the development of a yellow color visible with the naked eye. The estimated value of the equilibrium constant of the receptor with F(-) is 1.9 × 10(4) M(-1). Deprotonation is also observed in the presence of hydroxide. The receptor also shows colorimetric and fluorimetric sensing ability towards Fe(2+) ions. The binding site for the metal ion in the system has been unambiguously established by single-crystal X-ray diffraction studies of the Fe(II) complex of the receptor. The influence of solvents on the absorption and fluorescence spectra of the receptor has been investigated in detail. Cyclic voltammetric (CV) and square wave voltammetric (SWV) measurements carried out in dimethylformamide-acetonitrile (2?:?3) provided evidence in favor of cation (Fe(2+)) and anion (F(-)) concentration dependent electrochemical responses, enabling the ligand to act as a suitable electrochemical sensor for F(-) and Fe(2+) ions.     

钙(Ⅱ)对尖吻蝮蛇毒抗凝血因子Ⅰ的抗凝血活性的影响

皖南尖吻蝮蛇毒抗凝血因子Ⅰ(ACFⅠ)不具有酶的活性,通过与活化凝血因子X(FXa)结合成1l的复合物来延长凝血时间。用高效液相色谱分析方法,发现ACFⅠ与FXa的结合反应依赖于Ca     

Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): stability, heat, and hydration.

It has been shown that the DNA aptamer d(G(2)T(2)G(2)TGTG(2)T(2)G(2)) adopts an intramolecular G-quadruplex structure in the presence of K+. Its affinity for trombin has been associated with the inhibition of thrombin-catalyzed fibrin clot formation. In this work, we used a combination of spectroscopy, calorimetry, density, and ultrasound techniques to determine the spectral characteristics, thermodynamics, and hydration effects for the formation of G-quadruplexes with a variety of monovalent and divalent metal ions. The formation of cation-aptamer complexes is relatively fast and highly reproducible. The comparison of their CD spectra and melting profiles as a function of strand concentration shows that K+, Rb+, NH(4)+, Sr(2+), and Ba(2+) form intramolecular cation-aptamer complexes with transition temperatures above 25 degrees C. However, the cations Li+, Na+, Cs+, Mg(2+), and Ca(2+) form weaker complexes at very low temperatures. This is consistent with the observation that metal ions with ionic radii in the range 1.3-1.5 A fit well within the two G-quartets of the complex, while the other cations cannot. The comparison of thermodynamic unfolding profiles of the Sr(2+)-aptamer and K+ -aptamer complexes shows that the Sr(2+)-aptamer complex is more stable, by approximately 18 degrees C, and unfolds with a lower endothermic heat of 8.3 kcal/mol. This is in excellent agreement with the exothermic heats of -16.8 kcal/mol and -25.7 kcal/mol for the binding of Sr(2+) and K+ to the aptamer, respectively. Furthermore, volume and compressibility parameters of cation binding show hydration effects resulting mainly from two contributions: the dehydration of both cation and guanine atomic groups and water uptake upon the folding of a single-strand into a G- quadruplex structure.     

A new chiral, poly-imidazole N8-ligand and the related di- and tri-copper(II) complexes: synthesis, theoretical modelling, spectroscopic properties, and biomimetic stereoselective oxidations

The new poly-imidazole N(8) ligand (S)-2-piperazinemethanamine-1,4-bis[2-((N-(1-acetoxy-3-(1-methyl-1H-imidazol-4-yl))-2-(S)-propyl)-(N-(1-methyl-1H-imidazol-2-ylmethyl)))ethyl]-N-(phenylmethyl)-N-(acetoxy), also named (S)-Pz-(C2-(HisIm))(2) (L), containing three chiral (S) centers, was obtained by a multi-step synthesis and used to prepare dinuclear [Cu(2)(L)](4+) and trinuclear [Cu(3)(L)](6+) copper(II) complexes. Low-temperature EPR experiments performed on [Cu(2)(L)](4+) demonstrated that the two S = ? centers behaved as independent paramagnetic units, while the EPR spectra used to study the trinuclear copper complex, [Cu(3)(L)](6+), were consistent with a weakly coupled three-spin ? system. Theoretical models for the two complexes were obtained by DFT/RI-BP86/TZVP geometry optimization, where the structural and electronic characteristics nicely supported the EPR experimental findings. In addition, the theoretical analysis unveiled that the conformational flexibility encoded in both [Cu(2)(L)](4+) and [Cu(3)(L)](6+) arises not only from the presence of several σ-bonds and the bulky residues attached to the (S)-Pz-(C2-(HisIm))(2) ligand scaffold, but also from the poor coordination ability of the tertiary amino groups located in the ligand side-chains containing the imidazole units towards the copper(II) ions. Both the dinuclear and trinuclear complexes are efficient catalysts in the stereoselective oxidation of several catechols and flavonoid compounds, yielding the corresponding quinones. The structural features of the substrate-catalyst adduct intermediates were assessed by searching the conformational space of the molecule through MMFF94/Monte Carlo (MMFF94/MC) methods. The conformational flexibility of the bound ligand in the complexes proves to be beneficial for substrate binding and recognition. For the dinuclear complex, chiral recognition of the optically active substrates derives from weak electrostatic interactions between bound substrates and folded regions of the ligand scaffold. For the trinuclear complex, in the case of L/D-Dopa, the chiral recognition has a remarkable stereoselectivity index of 75%, the highest so far reported for this type of reaction. Here the dominant contribution to stereoselectivity arises from the direct interaction between a donor group (the Dopa carboxylate) far from the substrate reaction site (the catechol ring) with the additional (third) copper center not involved in the oxidative catalysis. On the other hand, in the case of bulky substrates, such as L/D-catechin, the observed poor substrate recognition is associated with much weaker interactions between the chiral regions of the complex and the chiral part of the substrate.     

Mechanistic studies of a calcium-dependent MRI contrast agent

Intracellular Ca(2+) plays an important role in signal transduction, and we are developing new MRI techniques to study its regulation in living animals. We have reported on an MRI contrast agent (DOPTA-Gd) where the relaxivity of the complex is controlled by the presence or absence of the divalent ion Ca(2+). By structurally modulating inner-sphere access of water to a chelated Gd(3+) ion, we observe a substantial and reversible change in T(1) upon the addition of Ca(2+) and not other divalent ions. Luminescence lifetime and NMRD measurements of the complex have been acquired, and several parameters contribute to the Ca(2+) dependent relaxivity change of DOPTA-Gd. The number of inner-sphere water molecules is more than doubled after the Ca(2+) concentration is increased. This finding strongly supports the proposed conformational change of DOPTA-Gd when Ca(2+) is bound. Relaxometric measurements confirm these results and provide an indication that second-sphere water molecules are probably responsible for paramagnetic relaxation enhancement in the absence of Ca(2+). After Ca(2+) is bound to DOPTA-Gd, the molecule undergoes a substantial conformational change that opens up the hydrophilic face of the tetraazacyclododecane macrocycle. This change dramatically increases the accessibility of chelated Gd(3+) ion to bulk solvent. The design of this class of calcium-activated MR contrast agent was based primarily on the assumption that the number of coordinated inner-sphere water molecules would be the dominating factor in observed relaxivity measurements. This result has been confirmed; however, careful mechanistic studies reveal that additional factors are involved in this process.     

Dioxadiaza- and trioxadiaza-macrocycles containing one dibenzofuran unit selective for cadmium

The binding properties of dioxadiaza- ([17](DBF)N2O2) and trioxadiaza- ([22](DBF)N2O3), macrocyclic ligands containing a rigid dibenzofuran group (DBF), to metal cations and structural studies of their metal complexes have been carried out. The protonation constants of these two ligands and the stability constants of their complexes with Ca2+, Ba2+, and Mn2+, Co2+, Ni2+, Cu2+, Zn2+ and Cd2+, were determined at 298.2 K in methanol-water (1:1, v/v), and at ionic strength 0.10 mol dm-3 in KNO3. The values of the protonation constants of both ligands are similar, indicating that no cavity size effect is observed. Only mononuclear complexes of these ligands with the divalent metal ions studied were found, and their stability constants are lower than expected, especially for the complexes of the macrocycle with smaller cavity size. However, the Cd2+ complex with [17](DBF)N2O2 exhibits the highest value of stability constant for the whole series of metal ions studied, indicating that this ligand reveals a remarkable selectivity for cadmium(II) in the presence of all the metal ions studied, except copper(II), indicating that this ligand reveals a remarkable selectivity for cadmium(II) in the presence of the mentioned metal ions. The crystal structures of H2[17](DBF)N2O3(2+) (diprotonated form of the ligand) and of its cadmium complex were determined by X-ray diffraction. The Cd2+ ion fits exactly inside the macrocyclic cavity exhibiting coordination number eight by coordination to all the donor atoms of the ligand, and additionally to two oxygen atoms from one nitrate anion and one oxygen atom from a water molecule. The nickel(II) and copper(II) complexes with the two ligands were further studied by UV-vis-NIR and the copper(II) complexes also by EPR spectroscopic techniques in solution indicating square-pyramidal structures and suggesting that only one nitrogen and oxygen donors of the ligands are bound to the metal. However an additional weak interaction of the second nitrogen cannot be ruled out.     

Label Free Determination of Potassium Ions Using Crystal Violet and Thrombin-Binding Aptamer

A label-free method for sensitive determination of potassium ions was developed. The most commonly studied thrombin-binding aptamer was used as the molecular probe and crystal violet was chosen as a fluorescence signal reporter. The fluorescence of crystal violet was significantly enhanced when the crystal violet solution was mixed with the single-stranded thrombin-binding aptamer. However, in the presence of potassium ions, due to the formation of potassium induced G-quadruplex structures, the fluorescence decreased. Potassium ions were determined using the change in fluorescence. The conformational transformation was investigated by circular dichroism, and interferences caused by sodium ions were studied. This label-free method offers a simple procedure that induces minimum effects on the G-quadruplex formation. Under the optimized conditions, the method exhibited a linear range from 30–420 µM for potassium ions with a detection limit of 6 µM.     

Deliberate design of ligand architecture yields dramatic enhancement of metal ion affinity

Evaluation of the malonamide substructure with respect to binding site preorganization and complementarity for lanthanide metal ions suggests a new ligand architecture specifically designed to enhance lanthanide ion affinity. Consideration of conformational reorganization, restricted bond rotation, and donor group orientation suggests that typical malonamide structures, for example, N,N,N'N'-tetrahexylpropane-1,3-diamide (1), N,N'-dibutyl-N,N'-dimethyl-2-tetradecylpropane-1,3-diamide (2), or N,N,N'N'-tetramethylpropane-1,3-diamide (6), are poorly organized for metal ion complexation. Molecular mechanics analyses show that the unfavorable enthalpic and entropic terms are eliminated by the use of the novel bicyclic architecture found in 3,9-diaza-3,9-dimethylbicyclo[4.4.0]decane-2,10-dione (7). Diamide 7 was prepared, and the X-ray crystal structure of the complex [Eu(7)(2)(NO(3))(3)] exhibits the same chelate conformation predicted by the molecular mechanics model. A hydrophobic derivative, 3,9-diaza-3,9-dioctylbicyclo[4.4.0]decane-2,10-dione (8), was prepared, and solvent extraction studies reveal that the preorganized architecture of 8 gives a dramatic enhancement in binding affinity, exhibiting Eu(3+) distribution coefficients that are 7 orders of magnitude larger than a typical malonamide ligand, 1.     

Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity

Molecular recognition of small molecule ligands by the nucleic acid aptamers for tobramycin, ATP, and FMN has been examined using electrospray ionization mass spectrometry (ESI-MS). Mass spectrometric data for binding stoichiometry and relative binding affinity correlated well with solution data for tobramycin aptamer complexes, in which aptamer/ligand interactions are mediated by hydrogen bonds. For the ATP and FMN aptamers, where ligand interactions involve both hydrogen bonding and significant pi-stacking, the relative binding affinities determined by MS did not fully correlate with results obtained from solution experiments. Some high-affinity aptamer/ligand complexes appeared to be destabilized in the gas phase by internal Coulombic repulsion. In CAD experiments, complexes with a greater number of intermolecular hydrogen bonds exhibited greater gas-phase stability even in cases when solution binding affinities were equivalent. These results indicate that in at least some cases, mass spectrometric data on aptamer/ligand binding affinities should be used in conjunction with complementary techniques to fully assess aptamer molecular recognition properties.     

The role of conformational changes in the signal enhancement of a selective chemosensor of Pb2+

In this work, the complexes formed by a fluoroionophore with three dications (M(2+) = Ca(2+), Hg(2+) and Pb(2+)) were studied theoretically, by applying both Density Functional Theory and its Time Dependent version (TDDFT). The experimental information concerning this fluoroionophore-Pb(2+) complex indicates a large increment in the absorption and emission signals. From a theoretical point of view, by using the structure with minimum energy of the fluoroionophore free as reference; distortions in the structure are observed when the complexes are formed and consequently important changes in terms of certain properties occur. Although there are increments in signal intensity in the case of the three ions considered here, TDDFT predicts that the Pb(2+) complex will manifest the most pronounced response and this conforms to experimental observations. Thus, we can associate the experimentally observed behavior with conformational changes. In order to corroborate this hypothesis we have analyzed the fluoroionophore-M(2+) structure complexes, both with ions, without ions and without the ionophore (which binds the ions); it is evident that if the ligand manifests geometric distortions, then the absorption signal will increase. The inert pair effect induces the particular conformation of the complex, when the Pb(2+) is present, acting as a lone pair, which is revealed when the electron localization function is analyzed. If structural distortions are present then the charge distribution and consequently the dipolar moment also present significant changes.