Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from the intron of the N-myc gene

A multidimensional heteronuclear NMR study has demonstrated that a guanine-rich DNA oligonucleotide originating from the N-myc gene folds into G-quadruplex structures in the presence of K(+), NH(4)(+), and Na(+) ions. A monomeric G-quadruplex formed in K(+) ion containing solution exhibits three G-quartets and flexible propeller-type loops. The 3D structure with three single nucleotide loops represents a missing element in structures of parallel G-quadruplexes. The structural features together with the high temperature stability are suggestive of the specific biological role of G-quadruplex formation within the intron of the N-myc gene. An increase in K(+) ion and oligonucleotide concentrations resulted in transformation of the monomeric G-quadruplex into a dimeric form. The dimeric G-quadruplex exhibits six stacked G-quartets, parallel strand orientations, and propeller-type loops. A link between the third and the fourth G-quartets consists of two adenine residues that are flipped out to facilitate consecutive stacking of six G-quartets.     

Electron-transfer chemistry of Ru-linker-(heme)-modified myoglobin: rapid intraprotein reduction of a photogenerated porphyrin cation radical

We report the synthesis and characterization of RuC7, a complex in which a heme is covalently attached to a [Ru(bpy)(3)](2+) complex through a -(CH(2))(7)- linker. Insertion of RuC7 into horse heart apomyoglobin gives RuC7Mb, a Ru(heme)-protein conjugate in which [Ru(bpy)(3)](2+) emission is highly quenched. The rate of photoinduced electron transfer (ET) from the resting (Ru(2+)/Fe(3+)) to the transient (Ru(3+)/Fe(2+)) state of RuC7Mb is >10(8) s(-1); the back ET rate (to regenerate Ru(2+)/Fe(3+)) is 1.4 x 10(7) s(-1). Irreversible oxidative quenching by [Co(NH(3))(5)Cl](2+) generates Ru(3+)/Fe(3+): the Ru(3+) complex then oxidizes the porphyrin to a cation radical (P*+); in a subsequent step, P*+ oxidizes both Fe(3+) (to give Fe(IV)=O) and an amino acid residue. The rate of intramolecular reduction of P*+ is 9.8 x 10(3) s(-1); the rate of ferryl formation is 2.9 x 10(3) s(-1). Strong EPR signals attributable to tyrosine and tryptophan radicals were recorded after RuC7MbM(3+) (M = Fe, Mn) was flash-quenched/frozen.     

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.     

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.     

Spectroscopic studies of interactions involving horseradish peroxidase and Tb3+

The spectroscopic properties of interactions involving horseradish peroxidase (HRP) and Tb(3+) in the simulated physiological solution was investigated with some electrochemical and spectroscopic methods, such as cyclic voltammetry (CV), circular dichroism (CD), X-ray photoelectron spectroscopy (XPS) and synchronous fluorescence (SF). It was found that Tb(3+) can coordinate with oxygen atoms in carbonyl groups in the peptide chain of HRP, form the complex of Tb(3+) and HRP (Tb-HRP), and then lead to the conformation change of HRP. The increase in the random coil content of HRP can disturb the microstructure of the heme active center of HRP, in which the planarity of the porphyrin cycle in the heme group is increased and then the exposure extent of the electrochemical active center is decreased. Thus Tb(3+) can inhibit the electrochemical reaction of HRP and its electrocatalytic activity for the reduction of H(2)O(2) at the Au/Cys/GC electrode. The changes in the microstructure of HRP obstructed the electron transfer of Fe(III) in the porphyrin cycle of the heme group, thus HRP catalytic activity is inhibited. The inhibition effect of Tb(3+) on HRP catalytic activity is increased with the increasing of Tb(3+) concentration. This study would provide some references for better understanding the rare earth elements and heavy metals on peroxidase toxicity in living organisms.     

Spin-orbit-induced anomalous pH-dependence in (1)H NMR spectra of Co(III) amine complexes: a diagnostic tool for structure elucidation

The pH-dependent (1)H NMR characteristics of a series of Co(III)-(polyamin)-aqua and Co(III)-(polyamin)-(polyalcohol) complexes, [Co(tach)(ino-kappa(3)-O(1,3,5))](3+) (1(3+)), [Co(tach)(ino-kappa(3)-Omicron(1,2,6))](3+) (2(3+)), [Co(tach)(taci-kappa-Nu(1)-kappa(2)-O(2,6))](3+) (3(3+)), [Co(ditame)(H(2)O)](3+) (4(3+)), and [Co(tren)(H(2)O)(2)](3+) (5(3+)), were studied in D(2)O by means of titration experiments (tach = all-cis-cyclohexane-1,3,5-triamine, ino = cis-inositol, taci = 1,3,5-triamino-1,3,5-trideoxy-cis-inositol, tren = tris(2-aminoethyl)amine, ditame = 2,2,6,6-tetrakis-(aminomethyl)-4-aza-heptane). A characteristic shift was observed for H(-C) hydrogen atoms in the alpha-position of a coordinated amino group upon deprotonation of a coordinated oxygen donor. For a cis-H-C-N-Co-O-H arrangement, deprotonation of the oxygen donor resulted in an additional shielding (shift to lower frequency) of the H(-C) proton, whereas for a trans-H-C-N-Co-O-H arrangement, deprotonation resulted in a deshielding (shift to higher frequency). The effect appears to be of rather general nature: it is observed for primary (1(3+)-5(3+)), secondary (4(3+)), and tertiary (5(3+)) amino groups, and for the deprotonation of an alcohol (1(3+)-3(3+)) or a water (4(3+), 5(3+)) ligand. Spin-orbit-corrected density functional calculations show that the high-frequency deprotonation shift for the trans-position is largely caused by a differential cobalt-centered spin-orbit effect on the hydrogen nuclear shielding. This effect is conformation dependent due to a Karplus-type behavior of the spin-orbit-induced Fermi-contact shift and thus only significant for an approximately antiperiplanar H-C-N-Co arrangement. The differential spin-orbit contribution to the deprotonation shift in the trans-position arises from the much larger spin-orbit shift for the protonated than for the deprotonated state. This is in turn due to a trans-effect of the deprotonated (hydroxo or alkoxo) ligand, which weakens the trans Co-N bond and thereby interrupts the Fermi-contact mechanism for transfer of the spin-orbit-induced spin polarization to the hydrogen nucleus in question. The unexpectedly large long-range spin-orbit effects found here for 3d metal complexes are traced back to small energy denominators in the perturbation theoretical expressions of the spin-orbit shifts.     

A comparative mechanistic study of the reversible binding of NO to a water-soluble octa-cationic Fe(III) porphyrin complex

The water-soluble, non-mu-oxo dimer-forming porphyrin, [5,10,15,20-tetrakis-4'-t-butylphenyl-2',6'-bis-(N-methylene-(4'-t-butylpyridinium))porphyrinato]iron(III) octabromide, (P(8+))Fe(III), with eight positively charged substituents in the ortho positions of the phenyl rings, was characterized by UV-vis and 1H NMR spectroscopy and 17O NMR water-exchange studies in aqueous solution. Spectrophotometric titrations of (P(8+))Fe(III) indicated a pKa1 value of 5.0 for coordinated water in (P(8+))Fe(III)(H2O)2. The monohydroxo-ligated (P(8+))Fe(III)(OH)(H2O) formed at 5 < pH < 12 has a weakly bound water molecule that undergoes an exchange reaction, k(ex) = 2.4 x 10(6) s(-1), significantly faster than water exchange on (P(8+))Fe(III)(H2O)2, viz. k(ex) = 5.5 x 10(4) s(-1) at 25 degrees C. The porphyrin complex reacts with nitric oxide to yield the nitrosyl adduct, (P(8+))Fe(II)(NO+)(L) (L = H2O or OH-). The diaqua-ligated (P(8+))Fe(III)(H2O)2 binds and releases NO according to a dissociatively activated mechanism, analogous to that reported earlier for other (P)Fe(III)(H2O)2 complexes. Coordination of NO to (P(8+))Fe(III)(OH)(H2O) at high pH follows an associative mode, as evidenced by negative deltaS(double dagger)(on) and deltaV(double dagger)(on) values measured for this reaction. The observed ca. 10-fold decrease in the NO binding rate on going from six-coordinate (P(8+))Fe(III)(H2O)2 (k(on) = 15.1 x 10(3) M(-1) s(-1)) to (P(8+))Fe(III)(OH)(H2O) (k(on) = 1.56 x 10(3) M(-1) s(-1) at 25 degrees C) is ascribed to the different nature of the rate-limiting step for NO binding at low and high pH, respectively. The results are compared with data reported for other water-soluble iron(III) porphyrins with positively and negatively charged meso substituents. Influence of the porphyrin periphery on the dynamics of reversible NO binding to these (P)Fe(III) complexes as a function of pH is discussed on the basis of available experimental data.     

Diamidodipyrrins: versatile bipyrrolic ligands with multiple metal binding modes

A straightforward, facile synthesis of diamidodipyrromethenes (diamidodipyrrins, DADP (R,R')) is presented. These tetradentate ligands readily form complexes with metal ions such as Ni (2+) and Cu (2+) and can adopt different binding modes with these metals. One version of the ligand (DADP (Ph, iPr )) has been structurally characterized in its "free base" form, as a HBr salt, and as the Ni (2+) and Cu (2+) complexes. A symmetric NNOO donor set is found for the Cu (2+) complex in the solid state, involving two carbonyl oxygen atoms and two dipyrrin nitrogen atoms, and this coordination mode has been confirmed in solution by electron paramagnetic resonance. An asymmetric NNNO binding mode found for the Ni (2+) complex in the solid state persists in solution as revealed by (1)H NMR. The HBr salt form of the ligand shows an intriguing hydrogen-bonded head-to-head dimer arrangement. Experiments show that Cu (2+), but not Ni (2+), can mediate the rapid oxidation of the diamidodipyrromethane precursors to the diamidodipyrromethene ligands in the presence of dioxygen. The work here shows that diamidodipyrrins are a versatile new class of ligands in the area of nonporphyrinic pyrrole-based compounds that merit further investigation.     

17O NMR and density functional theory study of the dynamics of the carboxylate groups in DOTA complexes of lanthanides in aqueous solution

The rotation of the carboxylate groups in DOTA (DOTA = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate) complexes of several lanthanide ions and Sc(3+) was investigated with density functional theory (DFT) calculations and with variable temperature (17)O NMR studies at 4.7-18.8 T. The data obtained show that the rotation is much slower than the other dynamic processes taking place in these complexes. The exchange between the bound and unbound carboxylate oxygen atoms for the largest Ln(3+) ions (La(3+)→Sm(3+)) follows a pathway via a transition state in which both oxygens of the carboxylate group are bound to the Ln(3+) ion, whereas for the smaller metal ions (Tm(3+), Lu(3+), Sc(3+)) the transition state has a fully decoordinated carboxylate group. The activation free energies show a steady increase from about 75 to 125-135 kJ·mol(-1) going from La(3+) to Lu(3+). This computed trend is consistent with the results of the (17)O NMR measurements. Fast exchange between bound and unbound carboxylate oxygen atoms was observed for the diamagnetic La-DOTA, whereas for Pr-, Sm-, Lu-, and Sc-DOTA the exchange was slow on the NMR time scale. The trends in the linewidths for the various metal ions as a function of the temperature agree with trends in the rates as predicted by the DFT calculations.     

Iron borohydride pincer complexes for the efficient hydrogenation of ketones under mild, base-free conditions: synthesis and mechanistic insight

The new, structurally characterized hydrido carbonyl tetrahydridoborate iron pincer complex [(iPr-PNP)Fe(H)(CO)(η(1)-BH(4))] (1) catalyzes the base-free hydrogenation of ketones to their corresponding alcohols employing only 4.1 atm hydrogen pressure. Turnover numbers up to 1980 at complete conversion of ketone were reached with this system. Treatment of 1 with aniline (as a BH(3) scavenger) resulted in a mixture of trans-[(iPr-PNP)Fe(H)(2)(CO)] (4a) and cis-[(iPr-PNP)Fe(H)(2)(CO)] (4b). The dihydrido complexes 4a and 4b do not react with acetophenone or benzaldehyde, indicating that these complexes are not intermediates in the catalytic reduction of ketones. NMR studies indicate that the tetrahydridoborate ligand in 1 dissociates prior to ketone reduction. DFT calculations show that the mechanism of the iron-catalyzed hydrogenation of ketones involves alcohol-assisted aromatization of the dearomatized complex [(iPr-PNP*)Fe(H)(CO)] (7) to initially give the Fe(0) complex [(iPr-PNP)Fe(CO)] (21) and subsequently [(iPr-PNP)Fe(CO)(EtOH)] (38). Concerted coordination of acetophenone and dual hydrogen-atom transfer from the PNP arm and the coordinated ethanol to, respectively, the carbonyl carbon and oxygen atoms, leads to the dearomatized complex [(iPr-PNP*)Fe(CO)(EtO)(MeCH(OH)Ph)] (32). The catalyst is regenerated by release of 1-phenylethanol, followed by dihydrogen coordination and proton transfer to the coordinated ethoxide ligand.     

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.     

稀土配合物{La［o-C6H4(NO2)(CO2)］3·(DMF)2}2的晶体结构及其荧光性能

合成了一种新的双核倒反中心的稀土镧配合物{La［o-C6H4(NO2)(CO2)］3·(DMF)2}2. 通过元素分析、 核磁共振谱和红外光谱对配合物的组成和结构进行了表征,  用热重分析研究了该配合物的热稳定性,  用X射线单晶衍射法测定了其晶体结构. 镧配合物{La［o-C6H4(NO2)(CO2)］3·(DMF)2}2晶体属三斜晶系, 空间群P1,  晶胞参数a=1.902(2) nm, b=1.245 0(2) nm, c=1.298 7(2) nm, α=64.555(2)°, β=66.348(2)°, γ=71.920(2)°, V=1.569 5(5) nm3, Dc=1.658 Mg/m3, Z=2, μ=1.437 mm-1, F(000)=784. 配合物中有2个La(Ⅲ)被4个邻硝基苯甲酸的羧酸根的负氧离子桥联, 每个La(Ⅲ)的中心离子配位数为9,  配位原子分别来自于7个邻硝基苯甲酸的羧酸根的负氧离子和2个DMF的羰基氧原子. 化合物中的氢键和π…π堆积作用使其成为三维立体结构. 同时发现了标题化合物固体具有光致发光现象, 发光性能测试表明， 配合物具有很好的荧光性质.     

Raman study of the coordination structure of a rare Earth-acetate complex in water

The Raman spectra of aqueous LnCl(3) x 20H(2)O x CH3(C)OOLi (LnCl(3), rare earth chloride) solutions have been measured in the liquid state. The change of the Raman symmetric Ln(3+)-OH(2) stretching band (v(w)) showed that the decrease in the ionic radius of rare earth (Ln(3+)) ions induces a change in coordination number of the Ln(3+) ion. The two peaks at 946 and 958 cm(-1) of the C-C stretching band (v(CC)) of the acetate ion are assigned to the bidentate ligand and the polymeric chain structure, respectively. The coordination structure of the acetate ion to Ln(3+) ion prefers the bidentate ligand to the polymeric chain structure throughout the rare earth series. The fraction of the bidentate ligand increases with decreasing ionic radius of the Ln(3+) ion. On the basis of the analyses of the v(w) and v(CC) bands, the change in the coordination number of the Ln(3+) ion is mainly due to the structural change (from the polymeric chain structure to the bidentate ligand) of the Ln(3+)-acetate complex rather than a elimination of one water molecule. Our results show that the Ln(3+) ions tend to form the bidentate ligand rather than the divalent (M(2+)) ions.     

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.     

Phthalocyanines: a new class of G-quadruplex-ligands with many potential applications

A G-quadruplex is a four-stranded DNA structure featuring stacked guanine tetrads, G-quartets. Formation of a G-quadruplex in telomere DNA can inhibit telomerase activity; therefore, development of G-quadruplex-ligands, which induce and/or stabilize G-quadruplexes, has become an area of great interest. Phthalocyanine derivatives have substantial potential as high-affinity G-quadruplex-ligands because these planar chromophores are similar in size and shape to the G-quartets. Here, we focus on the latest findings on phthalocyanine derivatives as G-quadruplex-ligands, and discuss the mechanisms by which phthalocyanines bind to G-quadruplexes with high affinity and selectivity. We also discuss potential biomedical and organic electronic applications of phthalocyanines that are dependent on their photophysical properties.     

Metal ion-dependent molecular inclusion chemistry: inclusion of aromatic anions by coordinated 1,4,7,10-tetrakis((S)-2-hydroxy-3-phenoxypropyl)-1,4,7,10-tetraazacyclododecane

The ability of the pendant donor macrocyclic ligand 1,4,7,10-tetrakis((S)-2-hydroxy-3-phenoxypropyl)-1,4,7,10-tetraaza- cyclododecane((S)-thphpc12) (or [Cd((S)-thphpc12)](2+)) to act as a metal ion-dependent receptor for aromatic anions has been investigated in solution and in the solid state. [Cd((S)-thphpc12)](2+) adopts a stable conical conformation with a large hydrophobic cavity, which has been shown to contain, via complementary multiple hydrogen bonding, p-nitrophenolate, aromatic carboxylates, p-toluenesulfonate, certain aromatic amino acid anions, phenoxyacetate, and acetate. In the case of p-nitrophenolate only, one or two anions can be contained within the receptor cavity. The crystal structure of [Cd((S)-thphpc12)(p-nitrophenolate)(2)] shows a coplanar arrangement of the p-nitrophenolates, where each is retained in the cavity by a pair of hydrogen bonds to cis hydroxyl groups. The crystal structure of the p-aminobenzoate inclusion complex indicates retention of the guest via a pair of hydrogen bonds to each oxygen atom of the carboxylate moiety. The crystal structure of the (L)-phenylalaninate inclusion complex indicates that the amino acid is retained by five hydrogen bonds, two involving the nitrogen atom and three to the oxygen atoms of the carboxylate moiety. Binding constants (10(3)-10(5) M(-1)) for the inclusion of some of the aforementioned anions in [Cd((S)-thphpc12)](2+) and related receptors were measured by (1)H NMR titration in DMSO-d(6) at 298 K.     

Dissecting the strand folding orientation and formation of G-quadruplexes in single- and double-stranded nucleic acids by ligand-induced photocleavage footprinting

The widespread of G-quadruplex-forming sequences in genomic DNA and their role in regulating gene expression has made G-quadruplex structures attractive therapeutic targets against a variety of diseases, such as cancer. Information on the structure of G-quadruplexes is crucial for understanding their physiological roles and designing effective drugs against them. Resolving the structures of G-quadruplexes, however, remains a challenge especially for those in double-stranded DNA. In this work, we developed a photocleavage footprinting technique to determine the folding orientation of each individual G-tract in intramolecular G-quadruplex formed in both single- and double-stranded nucleic acids. Based on the differential photocleavage induced by a ligand tetrakis(2-trimethylaminoethylethanol) phthalocyaninato zinc tetraiodine (Zn-TTAPc) to the guanines between the two terminal G-quartets in a G-quadruplex, this method identifies the guanines hosted in each terminal G-quartets to reveal G-tract orientation. The method is extremely intuitive, straightforward, and requires little expertise. Besides, it also detects G-quadruplex formation in long single- and double-stranded nucleic acids.     

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.     

Crystal violet as a G-quadruplex-selective probe for sensitive amperometric sensing of lead

A sensitive and selective amperometric sensing platform for lead (Pb(2+)) was developed based on a Pb(2+)-induced G-rich DNA conformational switch from a random-coil to G-quadruplex (G4) with crystal violet as the G4-binding indicator.     

Lanthanide(III) and group 13 metal ion complexes of tripodal amino phosphinate ligands

The tripodal amino-phosphinate ligands, tris(4-(phenylphosphinato)-3-benzyl-3-azabutyl)amine (H(3)ppba.2HCl.H(2)O) and tris(4-(phenylphosphinato)-3-azabutyl)amine (H(3)ppa.HCl.H(2)O) were synthesized and reacted with Al(3+), Ga(3+), In(3+) and the lanthanides (Ln(3+)). At 2 : 1 H(3)ppba to metal ratios, complexes of the type [M(H(3)ppba)(2)](3+)(M = Al(3+), Ga(3+), In(3+), Ho(3+)-Lu(3+)) were isolated. The bicapped [Ga(H(3)ppba)(2)](NO(3))(2)Cl.3CH(3)OH was structurally characterized and was shown indirectly by various techniques to be isostructural with the other [M(H(3)ppba)(2)](3+) complexes. Also, at 2 : 1 H(3)ppba to metal ratios, complexes of the type [M(H(4)ppba)(2)](5+)(M = La(3+)-Tb(3+)) were characterized, and the X-ray structure of [Gd(H(4)ppba)(2)](NO(3))(4)Cl.3CH(3)OH was determined. At 1 : 1 H(3)ppba to metal ratios, complexes of the type [M(H(4)ppba)](4+)(M = La(3+)-Er(3+)) were isolated and characterized. Elemental analysis and spectroscopic evidence supported the formation of a 1 : 1 monocapped complex. Reaction of 1 : 1 ratios of H(3)ppa with Ln(3+) and In(3+) yielded complexes of the type [M(H(3)ppa)](3+)(M = La(3+)-Yb(3+)) but with Ga(3+), complex of the type [Ga(ppa)].3H(2)O was obtained. Reaction of 1 : 1 ratios of H(3)ppa with Ln(3+) and In(3+) yielded complexes of the type [M(H(3)ppa)](3+)(M = La(3+)-Yb(3+)) but with Ga(3+) a neutral complex [Ga(ppa)].3H(2)O was obtained. The formation of an encapsulated 1 : 1 complex is supported by elemental analysis and spectroscopic evidence.