Direct NMR detection of alkali metal ions bound to G-quadruplex DNA

We describe a general multinuclear (1H, 23Na, 87Rb) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually "NMR visible" in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers: d(TG4T), d(G4T3G4), and d(G4T4G4). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine O6 atoms from the terminal G-quartet and one O2 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G4T4G4) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 micros at 15 degrees C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA.     

Small change in a G-rich sequence,a dramatic change in topology: new dimeric G-quadruplex folding motif with unique loop orientations

NMR study has shown that DNA oligonucleotide d(G(3)T(4)G(4)) adopts an asymmetric bimolecular G-quadruplex structure in solution. The structure of d(G(3)T(4)G(4))(2) is composed of three G-quartets, overhanging G11 residue and G3, which is part of the loop. Unique structural feature of d(G(3)T(4)G(4))(2) fold is the orientation of the two loops. Thymidine residues T4-T7 form a diagonal loop, whereas T15-T18 form an edge type loop. The G-quadruplex core of d(G(3)T(4)G(4))(2) consists of two stacked G-quartets with syn-anti-anti-anti alternation of dG residues and one G-quartet with syn-syn-anti-anti alternation. Another unusual structural feature of d(G(3)T(4)G(4))(2) is a leap between G19 and G20 over the middle G-quartet and chain reversal between G19 and G20 residues. The presence of one antiparallel and three parallel strands reveals the hitherto unknown G-quadruplex folding motif consisting of antiparallel/parallel strands and diagonal as well as edge type loops. Further examination of the influence of different monovalent cations on the folding of d(G(3)T(4)G(4)) showed that it forms a bimolecular G-quadruplex in the presence of K+, Na+, and NH4+ ions with the same general fold.     

Not all G-quadruplexes exhibit ion-channel-like properties: NMR study of ammonium ion (non)movement within the d(G(3)T(4)G(4))(2) quadruplex

A solution-state NMR study on 15NH4(+) ion movement within d(G(3)T(4)G(4))(2), a dimeric G-quadruplex consisting of three G-quartets and two T(4) loops, rather unexpectedly demonstrated the absence of 15NH4(+) ion movement between the binding sites U and L along the central axis of the G-quadruplex. Distinct temperature dependences of autocorrelation signals for U and L binding sites have been observed in 15N-1H NzExHSQC spectra which correlate with the local stiffness of the G-quadruplex. The volumes of the cross-peaks, which are the result of 15NH4(+) ion movement, have been interpreted in terms of rate constants, T(1) relaxation, and proton exchange. 15NH4(+) ion movements from the binding sites U and L into the bulk solution are characterized by lifetimes of 139 ms and 1.7 s at 298 K, respectively. The 12 times faster movement from the binding site U demonstrates that 15NH4(+) ion movement is controlled by the structure of T4 loop residues, which through diagonal- vs edge-type orientations impose distinct steric restraints for cations to leave or enter the G-quadruplex. Arrhenius-type analysis has afforded an activation energy of 66 kJ mol(-)1 for the UB process, while it could not be determined for the LB process due to slow rates at temperatures below 298 K. We further the use of the 15NH4(+) ion as an NMR probe to gain insight into the occupancy of binding sites by cations and kinetics of ion movement which are intrinsically correlated with the structural details, dynamic fluctuations, and local flexibility of the DNA structure.     

Cation exchange in lipophilic G-quadruplexes: not all ion binding sites are equal

Lipophilic guanosine derivatives that form G-quadruplexes are promising building blocks for ionophores and ion channels. Herein, cation exchange between solvated cations (K+ and NH4+) and bound cations in the G-quadruplex [G1]16.4Na+.4DNP- was studied by electrospray ionization mass spectrometry and solution 1H, 15N NMR spectroscopy. The ESI-MS and 1H NMR data provided evidence for the formation of mixed-cationic Na+, K+ G-quadruplexes. The use of 15NH4+ cations in NMR titrations, along with 15N-filtered 1H NMR and selective NOE experiments, identified two mixed-cationic intermediates in the cation exchange pathway from [G1]16.4Na+.4DNP- to [G1]16.4NH4+.4DNP-. The central Na+, bound between the two symmetry-related G8-Na+ octamers, exchanges with either K+ or NH4+ before the two outer Na+ ions situated within the C4 symmetric G8 octamers. A structural rationale, based on differences in the cations' octahedral coordination geometries, is proposed to explain the differences in site exchange for these lipophilic G-quadruplexes. Large cations such as Cs+ can be exchanged into the central cation binding site that holds the two symmetry-related C4 symmetric G8 octamer units together. The potential relevance of these findings to both supramolecular chemistry and DNA G-quadruplex structure are discussed.     

Stacking and not solely topology of T3 loops controls rigidity and ammonium ion movement within d(G4T3G4)2 G-quadruplex

A solution state NMR study has shown that d(G4T3G4) in the presence of (15)NH4(+) ions folds into a single bimolecular G-quadruplex structure in which its G-tracts are antiparallel and the two T3 loops span along the edges of the outer G-quartets on the opposite sides of the G-quadruplex core. This head-to-tail topology is in agreement with the topology of the G-quadruplex recently found in the X-ray crystal structure formed by d(G4T3G4) in the presence of K(+) ions [Neidle et al. J. Am. Chem. Soc. 2006, 128, 5480]. In contrast, the presence of K(+) ions in solution resulted in a complex ensemble of G-quadruplex structures. Molecular models based on NMR data demonstrate that thymine loop residues efficiently base-base stack on the outer G-quartets and in this way stabilize a single structure in the presence of (15)NH4(+) ions. The use of heteronuclear NMR enabled us to localize three (15)NH4(+) ion binding sites between pairs of adjacent G-quartets and study the kinetics of their movement. Interestingly, no (15)NH4(+) ion movement within the G-quadruplex was detected at 25 degrees C. At 35 degrees C we were able to observe slow movement of (15)NH4(+) ions from the outer binding sites to bulk solution with the characteristic residence lifetime of 1.2 s. The slow movement of (15)NH4(+) ions from the outer binding sites into bulk solution and the absence of movement from the inner binding site were attributed to steric hindrance imposed by the T3 loops and the rigidity of the G-quadruplex.     

Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure

The human telomeric sequence d[T(2)AG(3)](4) has been demonstrated to form different types of G-quadruplex structures, depending upon the incubation conditions. For example, in sodium (Na(+)), a basket-type G-quadruplex structure is formed. In this investigation, using circular dichroism (CD), biosensor-surface plasmon resonance (SPR), and a polymerase stop assay, we have examined how the addition of different G-quadruplex-binding ligands affects the conformation of the telomeric G-quadruplex found in solution. The results show that while telomestatin binds preferentially to the basket-type G-quadruplex structure with a 2:1 stoichiometry, 5,10,15,20-[tetra-(N-methyl-3-pyridyl)]-26-28-diselena sapphyrin chloride (Se2SAP) binds to a different form with a 1:1 stoichiometry in potassium (K(+)). CD studies suggest that Se2SAP binds to a hybrid G-quadruplex that has strong parallel and antiparallel characteristics, suggestive of a structure containing both propeller and lateral, or edgewise, loops. Telomestatin is unique in that it can induce the formation of the basket-type G-quadruplex from a random coil human telomeric oligonucleotide, even in the absence of added monovalent cations such as K(+) or Na(+). In contrast, in the presence of K(+), Se2SAP was found to convert the preformed basket G-quadruplex to the hybrid structure. The significance of these results is that the presence of different ligands can determine the type of telomeric G-quadruplex structures formed in solution. Thus, the biochemical and biological consequences of binding of ligands to G-quadruplex structures found in telomeres and promoter regions of certain important oncogenes go beyond mere stabilization of these structures.     

Label-free fluorescent probing of G-quadruplex formation and real-time monitoring of DNA folding by a quaternized tetraphenylethene salt with aggregation-induced emission characteristics

Biosensing processes such as molecular beacons require non-trivial effort to covalently label or mark biomolecules. We report here a label-free DNA assay system with a simple dye with aggregation-induced emission (AIE) characteristics as the fluorescent bioprobe. 1,1,2,2-Tetrakis[4-(2-bromoethoxy)phenyl]ethene is nonemissive in solution but becomes highly emissive when aggregated. This AIE effect is caused by restriction of intramolecular rotation, as verified by a large increase in the emission intensity by increasing viscosity and decreasing temperature of the aqueous buffer solution of 1,1,2,2-tetrakis[4-(2-triethylammonioethoxy)phenyl]ethene tetrabromide (TTAPE). When TTAPE is bound to a guanine-rich DNA strand (G1) via electrostatic attraction, its intramolecular rotation is restricted and its emission is turned on. When a competitive cation is added to the G1 solution, TTAPE is detached and its emission is turned off. TTAPE works as a sensitive poststaining agent for poly(acrylamide) gel electrophoresis (PAGE) visualization of G1. The dye is highly affinitive to a secondary structure of G1 called the G-quadruplex. The bathochromic shift involved in the G1 folding process allows spectral discrimination of the G-quadruplex from other DNA structures. The strong affinity of TTAPE dye to the G-quadruplex structure is associated with a geometric fit aided by the electrostatic attraction. The distinct AIE feature of TTAPE enables real-time monitoring of folding process of G1 in the absence of any pre-attached fluorogenic labels on the DNA strand. TTAPE can be used as a K+ ion biosensor because of its specificity to K+-induced and -stabilized quadruplex structure.     

Thallium pi-cation complexation by calix[4]tubes: (205)Tl NMR and x-ray evidence

Thallium cation complexation by calix[4]tubes has been investigated by a combination of (205)Tl, (1)H NMR and ES MS demonstrating the solution formation of a dithallium complex in which the cations are held in the calix[4]arene cavities. In addition, the structure of the complex has been determined in the solid state revealing the cations to be held exclusively by pi-cation interactions. Furthermore, this crystal structure has been used as the basis for molecular dynamics simulations to confirm that binding of the smaller K(+) cation in the calix[4]tube cryptand like array occurs via the axial route featuring a pi-cation intermediate.     

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.     

Syntheses; 77Se, 203Tl, and 205Tl NMR; and theoretical studies of the Tl2Se6(6-), Tl3Se6(5-), and Tl3Se7(5-) anions and the X-ray crystal structures of [2,2,2-crypt-Na]4[Tl4Se8].en and [2,2,2-crypt-Na]2[Tl2Se4](infinity)1.en

The 2,2,2-crypt salts of the Tl4Se8(4-) and [Tl2Se4(2-)]infinity1 anions have been obtained by extraction of the ternary alloy NaTl0.5Se in ethylenediamine (en) in the presence of 2,2,2-crypt and 18-crown-6 followed by vapor-phase diffusion of THF into the en extract. The [2,2,2-crypt-Na]4[Tl4Se8].en crystallizes in the monoclinic space group P2(1)/n, with Z = 2 and a = 14.768(3) angstroms, b = 16.635(3) angstroms, c = 21.254(4) angstroms, beta = 94.17(3) degrees at -123 degrees C, and the [2,2,2-crypt-Na]2[Tl2Se4]infinity1.en crystallizes in the monoclinic space group P2(1)/c, with Z = 4 and a = 14.246(2) angstroms, b = 14.360(3) angstroms, c = 26.673(8) angstroms, beta = 99.87(3) degrees at -123 degrees C. The TlIII anions, Tl2Se6(6-) and Tl3Se7(5-), and the mixed oxidation state TlI/TlIII anion, Tl3Se6(5-), have been obtained by extraction of NaTl0.5Se and NaTlSe in en, in the presence of 2,2,2-crypt and/or in liquid NH3, and have been characterized in solution by low-temperature 77Se, 203Tl, and 205Tl NMR spectroscopy. The 1J(203,205Tl-77Se) and 2J(203,205Tl-203,205Tl) couplings of the three anions have been used to arrive at their solution structures by detailed analyses and simulations of all spin multiplets that comprise the 205,203Tl NMR subspectra arising from natural abundance 205,203Tl and 77Se isotopomer distributions. The structure of Tl2Se6(6-) is based on a Tl2Se2 ring in which each thallium is bonded to two exo-selenium atoms so that these thalliums are four-coordinate and possess a formal oxidation state of +3. The Tl4Se8(4-) anion is formally derived from the Tl2Se6(6-) anion by coordination of each pair of terminal Se atoms to the TlIII atom of a TlSe+ cation. The structure of the [Tl2Se4(2-)]infinity1 anion is comprised of edge-sharing distorted TlSe4 tetrahedra that form infinite, one-dimensional [Tl2Se42-]infinity1 chains. The structures of Tl3Se6(5-) and Tl3Se7(5-) are derived from Tl4Se4-cubes in which one thallium atom has been removed and two and three exo-selenium atoms are bonded to thallium atoms, respectively, so that each is four-coordinate and possesses a formal oxidation state of +3 with the remaining three-coordinate thallium atom in the +1 oxidation state. Quantum mechanical calculations at the MP2 level of theory show that the Tl2Se6(6-), Tl3Se6(5-), Tl3Se7(5-), and Tl4Se8(4-) anions exhibit true minima and display geometries that are in agreement with their experimental structures. Natural bond orbital and electron localization function analyses were utilized in describing the bonding in the present and previously published Tl/Se anions, and showed that the Tl2Se6(6-), Tl3Se6(5-), Tl3Se7(5-), and Tl4Se8(4-) anions are electron-precise rings and cages.     

Pentavalent and tetravalent uranium selenides, Tl3Cu4USe6 and Tl2Ag2USe4: syntheses, characterization, and structural comparison to other layered actinide chalcogenide compounds

The compounds Tl(3)Cu(4)USe(6) and Tl(2)Ag(2)USe(4) were synthesized by the reaction of the elements in excess TlCl at 1123 K. Both compounds crystallize in new structure types, in space groups P2(1)/c and C2/m, respectively, of the monoclinic system. Each compound contains layers of USe(6) octahedra and MSe(4) (M = Cu, Ag) tetrahedra, separated by Tl(+) cations. The packing of the octahedra and the tetrahedra within the layers is compared to the packing arrangements found in other layered actinide chalcogenides. Tl(3)Cu(4)USe(6) displays peaks in its magnetic susceptibility at 5 and 70 K. It exhibits modified Curie-Weiss paramagnetic behavior with an effective magnetic moment of 1.58(1) μ(B) in the temperature range 72-300 K, whereas Tl(2)Ag(2)USe(4) exhibits modified Curie-Weiss paramagnetic behavior with μ(eff) = 3.4(1) μ(B) in the temperature range 100-300 K. X-ray absorption near-edge structure (XANES) results from scanning transmission X-ray spectromicroscopy confirm that Tl(3)Cu(4)USe(6) has Se bonding characteristic of discrete Se(2-) units, Cu bonding generally representative of Cu(+), and U bonding consistent with a U(4+) or U(5+) species. On the basis of these measurements, as well as bonding arguments, the formal oxidation states for U may be assigned as +5 in Tl(3)Cu(4)USe(6) and +4 in Tl(2)Ag(2)USe(4).     

15NH4+ ion movement inside d(G4T4G4)2 G-quadruplex is accelerated in the presence of smaller Na+ ions

2D NMR studies demonstrate that the residence lifetime of 15NH4+ ions within the bimolecular G-quadruplex adopted by d(G4T4G4) is reduced from 270 ms in the presence of ammonium ions alone to 36 ms in the presence of Na+ ions.     

Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking

It has been shown that DNA oligonucleotides composed, in part, of G repeat sequences can adopt G-quadruplex structures in the presence of specific metal ions. In this work, we use a combination of spectroscopic and calorimetric techniques to determine the spectral and thermodynamic characteristics of two DNA aptamers, d(G2T2G2TGTG2T2G2), G2, and d(G3T2G3TGTG3T2G3), G3; a sequence in the promoter region of the c-MYC oncogene, d(TG4AG3TG4AG3TG4A2G2), NHE-III; and the human telomere sequence d(AG3T2AG3T2AG3T2AG3), 22GG. The circular dichroism spectra of these oligonucleotides in the presence of K+ indicate that all form G-quadruplexes with G-quartets in an antiparallel arrangement (G2), in a parallel arrangement (NHE-III and 22GG), or in a mixed parallel and antiparallel G-quartet arrangement (G3). Melting profiles show transition temperatures, TM, above 45 degrees C that are independent of strand concentration, consistent with the formation of very stable intramolecular G-quadruplexes. We used differential scanning calorimetry to obtain complete thermodynamic profiles for the unfolding of each quadruplex. Subtracting the thermodynamic folding profiles of G2 from those of G3 yielded the following thermodynamic profile for the formation of a G-quartet stack: DeltaG degrees 20 = -2.2 kcal/mol, DeltaHcal = -14.6 kcal/mol, TDeltaScal = -12.4 kcal/mol, DeltanK+ = -0.3 mol of K+/mol, and DeltanW = 13 mol of H2O/mol. Furthermore, we used this profile to estimate the thermodynamic contributions of the loops and/or extra base sequences of each oligonucleotide in the G-quadruplex state. The average free energy contributions of the latter indicate that the incorporation of loops and base overhangs stabilizes quadruplex structures. This stabilization is enthalpy-driven and is due to base-stacking contributions.     

First examples of thallium chalcogenide cages. Syntheses, 77Se, 203Tl, and 205Tl NMR study of the Tl4Se5(4-) and Tl4Se6(4-) anions, the X-ray crystal structure of (2,2,2-crypt-K+)3Tl5Se5(3-), and theoretical studies

The Tl5Se5(3-) anion has been obtained by extracting KTlSe in ethylenediamine in the presence of 2,2,2-crypt. The salt, (2,2,2-crypt-K+)3Tl5Se5(3-), crystallizes in the triclinic system, space group P1, with Z = 2 and a = 11.676(2) A, b = 16.017(3) A, c = 25.421(5) A, alpha = 82.42(3) degrees, beta = 88.47(3) degrees, gamma = 69.03(3) degrees at -123 degrees C. Two other mixed oxidation state TlI/TlIII anions; Tl4Se5(4-) and Tl4Se6(4-), have been obtained by extracting KTlSe into liquid NH3 in the presence of 2,2,2-crypt and have been characterized in solution by low-temperature 77Se, 203Tl, and 205Tl NMR spectroscopy and were shown to exist as a 1:1 equilibrium mixture at -40 degrees C. The couplings, 1J(203,205Tl-77Se) and 2J(203,205Tl-203,205Tl), have been observed for Tl4Se5(4-) and Tl4Se6(4-) and have been used to arrive at the solution structures of both anions. Structural assignments were achieved by detailed analyses and simulations of all spin multiplets that comprise the 205,203Tl NMR spectra and that arise from natural abundance 205,203Tl and 77Se or enriched 77Se isotopomer distributions. The structures of all three anions are based on a Tl4Se4 cube in which Tl and Se atoms occupy alternate corners. There are one and two exo-selenium atoms bonded to thallium in Tl4Se5(4-) and Tl4Se6(4-), respectively, so that these thalliums are four-coordinate and possess a formal oxidation state of +3 and the remaining three-coordinate thallium atoms are in the +1 oxidation state. The structure of Tl5Se5(3-) may be formally regarded as an adduct in which Tl+ is coordinated to the unique exo-selenium and to two seleniums in a cube face containing the TlIII atom. The Tl4Se5(4-), Tl4Se6(4-), and Tl5Se5(3-) anions and the presently unknown, but structurally related, Tl4Se4(4-) anion can be described as electron-precise cages. Ab initio methods at the MP2 level of theory show that Tl4Se5(4-), Tl4Se6(4-), and Tl5Se5(3-) exhibit true minima and display geometrical parameters that are in excellent agreement with their experimental cubanoid structures, and that Tl4Se4(4-) is cube-shaped (Td point symmetry). The gas-phase energetics associated with plausible routes to the formation and interconversions of these anions have been determined by ab initio methods and assessed. It is proposed that all three cubanoid anions are derived from the known Tl2Se2(2-), TlSe3(3-), Se2(2-), and polyselenide anions that have been shown to be present in the solutions they are derived from.     

钾离子浓度依赖的铅离子稳定G-四链体构型转化

已有研究普遍认为铅离子(Pb²⁺)诱导富G适体链形成的G-四链体(Pb²⁺-G4)比钾离子(K⁺)诱导富G适体链形成的G-四链体(K⁺-G4)更为稳定,因而Pb²⁺可以置换K⁺-G4中的K⁺,而且K⁺的存在不影响Pb²⁺-G4的稳定性。有趣的是本研究发现K⁺ (20 μmol∙L⁻¹–1 mmol∙L⁻¹)不仅可以诱导10 µmol∙L⁻¹ Pb²⁺稳定的T2TT(Pb²⁺-T2TT,杂合G4结构)发生构型转换,甚至还可取代Pb²⁺-T2TT中的Pb²⁺,形成K⁺稳定的T2TT (K⁺-T2TT,平行G4结构),最终转化形成的K⁺-G4结构与单独K⁺诱导富G适体链形成K⁺-G4的构型基本一致。随后,进一步考察了另外7条富G适体链,发现这一转化过程具有一定的普适性。该研究结果为理解G4构型转化以及内嵌离子交换提供了新的视角,也为拓展G4在生化分析和生物领域的应用提供了新的理论基础。     

A computational investigation of HCN2+ isomeric structures: implications for the chemistry of Titan's atmosphere.

The structure and stability of various HCN2+ isomeric structures have been investigated at the complete active space SCF (CASSCF) and multireference-configuration interaction [MR-Cl-SD(Q)] levels of theory with the 6-31G(d) and 6-311G(d,p) basis sets. The investigated species include the singlet (S) and triplet (T) open-chain H-N-C-N+ ions 1S, 1S', and 1T, the open-chain H-C-N-N+ ions 2S, 2S', and 2T, the HC-N2+ cyclic structures 3S and 3T, and the HN-CN+ cyclic structures 4S and 4T. All these species have been identified as true energy minima on the CASSCF(8,7)/6-31G(d) potential energy surface, and their optimised geometries, refined at the CASSCF(8,8)/6-31G(d) level of theory, have been used to perform single point calculations at the [MR-Cl-SD(Q]/6-311G(d,p) computational level. The most stable structure was the H-N-C-N+ ion 1T, whose absolute enthalpy of formation at 298.15 K has been estimated as 333.9 +/- 2 kcalmol(-1) using the Gaussian-3 (G3) procedure. The two species closest in energy to 1T are the triplet H-C-N-N+ ion 2T and the singlet diazirinyl cation 3S, whose G3 enthalpies of formation at 298.15 K are 343.5 +/- 2 and 340.6 +/- 2 kcalmol(-1), respectively. Finally, we have discussed the implications of our calculations for the detailed structure of the HCN2+ ions formed in the reaction between N3+ and HCN, experimentally observed by flowing after-glow-selected ion flow/drift tube mass spectrometry and possibly occurring in Titan's atmosphere.     

Solubility, complex formation, and redox reactions in the Tl2O3-HCN/CN(-)-H2O system. Crystal structures of the cyano compounds Tl(CN)3.H2O, Na[Tl(CN)4].3H2O, K[Tl(CN)4], and Tl(I)[Tl(III)(CN)4] and of Tl(I)2C2O4

Thallium(III) oxide can be dissolved in water in the presence of strongly complexing cyanide ions. Tl(III) is leached from its oxide both by aqueous solutions of hydrogen cyanide and by alkali-metal cyanides. The dominating cyano complex of thallium(III) obtained by dissolution of Tl2O3 in HCN is [Tl(CN)3(aq)] as shown by 205Tl NMR. The Tl(CN)3 species has been selectively extracted into diethyl ether from aqueous solution with the ratio CN-/Tl(III) = 3. When aqueous solutions of the MCN (M = Na+, K+) salts are used to dissolve thallium(III) oxide, the equilibrium in liquid phase is fully shifted to the [Tl(CN)4]- complex. The Tl(CN)3 and Tl(CN)4- species have for the first time been synthesized in the solid state as Tl(CN)3.H2O (1), M[Tl(CN)4] (M = Tl (2) and K (3)), and Na[Tl(CN)4].3H2O (4) salts, and their structures have been determined by single-crystal X-ray diffraction. In the crystal structure of 1, the thallium(III) ion has a trigonal bipyramidal coordination with three cyanide ions in the equatorial plane, while an oxygen atom of the water molecule and a nitrogen atom from a cyanide ligand, attached to a neighboring thallium complex, form a linear O-Tl-N fragment. In the three compounds of the tetracyano-thallium(III) complex, 2-4, the [Tl(CN)4]- unit has a distorted tetrahedral geometry. Along with the acidic leaching (enhanced by Tl(III)-CN- complex formation), an effective reductive dissolution of the thallium(III) oxide can also take place in the Tl2O3-HCN-H2O system yielding thallium(I), while hydrogen cyanide is oxidized to cyanogen. The latter is hydrolyzed in aqueous solution giving rise to a number of products including (CONH2)2, NCO-, and NH4+ detected by 14N NMR. The crystalline compounds, Tl(I)[Tl(III)(CN)4], Tl(I)2C2O4, and (CONH2)2, have been obtained as products of the redox reactions in the system.     

Promoting the formation and stabilization of G-quadruplex by dinuclear RuII complex Ru2(obip)L4

The remarkable ability of a new dinuclear Ru (II) complex Ru 2(obip)L 4 [obip = 2-(2-pyridyl)imidazo[4,5- f][1,10]-phenanthroline; L = 2,2'-bipyridine] to promote the formation and stabilization of the human telomeric repeat AG3(T2AG3)3 quadruplex was reported. The experimental results indicated that Ru 2(obip)L 4 could induce the formation of an antiparallel G-quadruplex structure in the absence of metal cations. It could induce positive T m shifts of +9.4 and +5.8 degrees C in Na (+) and K (+) buffers, respectively, in which an increase in the melting temperature of the quadruplex indicated a stabilizing effect. Binding stoichiometry with the quadruplex was investigated through a luminescence-based Job plot. The major inflection point for Ru 2(obip)L 4 at x = 0.48 was observed. The data were consistent with a 1:1 [quadruplex]/[complex] binding mode, which was suggestive of a specific Ru 2(obip)L 4-quadruplex interaction with a single guanine tetrad.     

203,205Tl NMR studies of crystallographically characterized thallium alkoxides. X-ray Structures of [TI(OCH2CMe3)]4 and [TI(OAr)]infinity, where OAr = OC6H3(Me)2-2,6 and OC6H3(CHMe2)2-2,6

[Tl(OCH2Me)]4 (1) was reacted with excess HOR to prepare a series of [Tl(OR)]n, where OR = OCHMe2 (2, n = 4), OCMe3 (3, n = 4), OCH2CMe3 (4, n = 4), OC6H3(Me)2-2,6 (5, n = infinity), and OC6H3(CHMe2)2-2,6 (6, n = infinity). Single-crystal X-ray diffraction experiments revealed that in the solid state the alkoxide-ligated compound 4 adopts a cubane structure, whereas the aryloxide derivatives, 5 and 6, formed polymeric chains. Compounds 1-6 were also characterized by 203,205Tl solution and 205Tl solid-state NMR spectroscopy. In solution it was determined that 1-4 retained the [Tl-O]4 cube structure, whereas the polymeric species 5 and 6 appeared to be fluxional. Variations in the solution and solid-state structures for the [Tl(OR)]4 cubes and polymeric [Tl(OAr)]infinity are influenced by the steric hindrance of the ligand. The acidity of the parent alcohol influences the degree of covalency at the Tl metal center, which is reflected in the 203,205Tl chemical shifts for 1-6.     

Artificial G-wire switch with 2,2'-bipyridine units responsive to divalent metal ions

Development of a guanine nanowire (G-wire) that is controllable and can be switched by external signals is important for the creation of molecular electronic technologies. Here, we constructed a G-wire in which the thymines of the main chain of d(G4T4G4) were replaced with 2,2'-bipyridine units, which have two aromatic rings that rotate arbitrarily upon coordination with metal ions. Circular dichroism of the DNA oligonucleotides with or without the 2,2'-bipyridine unit showed that divalent metal ions induce the bipyridine-containing oligonucleotide to switch from an antiparallel to a parallel G-quadruplex. Native polyacrylamide gel electrophoresis showed that the parallel-stranded G-quadruplex DNA had a high-order structure. Circular dichroism and native gel electrophoresis analyses suggested that adding Na2EDTA causes a reverse structural transition from a parallel-stranded high-order structure to an antiparallel G-quadruplex. Moreover, atomic force microscopy showed a long nanowire ( approximately 200 nm) in the presence of Ni2+ but no significant image in the absence of Ni2+ or in the presence of both Ni2+ and Na2EDTA. These observations revealed that the parallel-stranded high-order structure is a G-wire containing numerous DNA oligonucleotide strands bound together via divalent metal ion-2,2'-bipyridine complexes. Finally, we found that alternating addition of Ni2+ and Na2EDTA can cycle the G-wire between the high-order and disorganized structures, with an average cycling efficiency of 0.95 (i.e., 5% loss per cycle). These results demonstrate that a DNA oligonucleotide incorporating the 2,2'-bipyridine unit acts as a G-wire switch that can be controlled by chemical input signals, namely, divalent metal ions.