Investigation of formation,recognition, stabilization,and conversion of dimeric G-quadruplexes of HIV-1 integrase inhibitors by electrospray ionization mass spectrometry

The dimeric G-quadruplex structures of d(GGGTGGGTGGGTGGGT) (S1) and d(GTGGTGGGTGGGTGGGT) (S2), the potent nanomolar HIV-1 integrase inhibitors, were detected by electrospray ionization mass spectrometry (ESI-MS) for the first time. The formation and conversion of the dimers were induced by NH(4)(+), DNA concentration, pH, and the binding molecules. We directly observed the specific binding of a perylene derivative (Tel03) and ImImImbetaDp in one system consisting of the intramolecular and the dimeric G-quadruplexes of the HIV-1 integrase inhibitor, which suggested that Tel03 could shift the equilibrium to the dimeric G-quadruplex formation, while ImImImbetaDp induces preferentially a structural change from the dimer to the intramolecular G-quadruplex. The results of this study indicated that Tel03 and ImImImbetaDp favor the stabilization of the dimeric G-quadruplex structures.     

A comparative study of assembly and disassembly process of dimeric and monomeric cyanine dyes with DNA templates

H-aggregates of dimeric cyanine dyes (TC-P4) formed in PBS could be disassembled by G-quadruplex into dimer and/or monomer, resulting in higher fluorescent selectivity than its corresponding monomer (TC).     

Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics

We demonstrate by NMR that the two-repeat human telomeric sequence d(TAGGGTTAGGGT) can form both parallel and antiparallel G-quadruplex structures in K(+)-containing solution. Both structures are dimeric G-quadruplexes involving three stacked G-tetrads. The sequence d(TAGGGUTAGGGT), containing a single thymine-to-uracil substitution at position 6, formed a predominantly parallel dimeric G-quadruplex with double-chain-reversal loops; the structure was symmetric, and all guanines were anti. Another modified sequence, d(UAGGGT(Br)UAGGGT), formed a predominantly antiparallel dimeric G-quadruplex with edgewise loops; the structure was asymmetric with six syn guanines and six anti guanines. The two structures can coexist and interconvert in solution. For the latter sequence, the antiparallel form is more favorable at low temperatures (<50 degrees C), while the parallel form is more favorable at higher temperatures; at temperatures lower than 40 degrees C, the antiparallel G-quadruplex folds faster but unfolds slower than the parallel G-quadruplex.     

A spectroscopic study of dyes: mechanism of detection of nonabsorbing analytes in reverse-phase chromatography with the aid of chromophores

In order to understand the mechanism by which dyes assist chromatographic detection in reverse-phase systems, absorption spectra of brilliant green and methylene blue were investigated. It is shown that dye-assisted chromatographic detection depends on the ability of the analyte to shift the monomer-dimer equilibrium of the dyes toward greater monomer concentrations. Monomers have higher molar absorptivities than dimers. Equilibrium constants and molar absorptivities for monomeric and dimeric forms of the dyes are reported.     

Monomer–Dimer Control and Crystal Engineering in TASPs

We have reported a template assembled synthetic protein (cavitein Q4) as an unexpected dimer in the solid state and as a monomer–dimer equilibrium in solution. We have since reported an ability to bias a cavitein’s monomer–dimer equilibrium in solution by sequence design involving histidine metal chelation or disulfide incorporation. However, little remains known about the forces contributing to dimeric cavitein crystal nucleation and lattice stabilization. We, therefore, designed glutamine variants to probe factors involved in dimeric cavitein crystallization. It was found that a key glutamate hydrogen-bonding interaction between dimers is integral to crystal formation and stabilization. Additionally, we obtained a crystal structure of a cavitein (Q4-E3H) designed to bias the dimeric structure via histidine metal coordination. The resolved structure indicates a histidine cluster interaction that likely accounts for the biased dimeric form observed in solution.     

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.     

Intermolecular association of tetrahydrofuran-2-carboxylic acid in solution: a vibrational circular dichroism study

Carboxylic acids are known for their strong intermolecular associations. With chiral carboxylic acids, this behavior can be studied using vibrational circular dichroism (VCD). Tetrahydrofuran-2-carboxylic acid 1, a chiral building block for beta-lactam antibiotics, is studied by emphasizing the effect of the dimerization. Experimental results indicate that for solutions of 1 in CDCl3 and CS2, a complex equilibrium exists between the monomers and dimers. B3LYP/aug-cc-pVTZ calculations are performed on both monomer and dimer structures. To simulate IR and VCD spectra, populations for monomer and dimers were approximated using a semiquantitative model. A good agreement between experimental and simulated spectra is obtained by taking into account both the monomeric and the dimeric structures, weighted using the experimentally determined populations.     

Synthesis and Structural Characterization of Stable Branched DNA G-Quadruplexes Using the Trebler Phosphoramidite

Guanine (G)-rich sequences can form a noncanonical four-stranded structure known as the G-quadruplex. G-quadruplex structures are interesting because of their potential biological properties and use in nanosciences. Here, we describe a method to prepare highly stable G-quadruplexes by linking four G-rich DNA strands to form a monomolecular G-quadruplex. In this method, one strand is synthesized first, and then a trebler molecule is added to simultaneously assemble the remaining three strands. This approach allows the introduction of specific modifications in only one of the strands. As a proof of concept, we prepared a quadruplex where one of the chains includes a change in polarity. A hybrid quadruplex is observed in ammonium acetate solutions, whereas in the presence of sodium or potassium, a parallel G-quadruplex structure is formed. In addition to the expected monomolecular quadruplexes, we observed the presence of dimeric G-quadruplex structures. We also applied the method to prepare G-quadruplexes containing a single 8-aminoguanine substitution and found that this single base stabilizes the G-quadruplex structure when located at an internal position.     

Design of a High-Sensitivity Dimeric G-Quadruplex/Hemin DNAzyme Biosensor for Norovirus Detection

G-quadruplexes can bind with hemin to form peroxidase-like DNAzymes that are widely used in the design of biosensors. However, the catalytic activity of G-quadruplex/hemin DNAzyme is relatively low compared with natural peroxidase, which hampers its sensitivity and, thus, its application in the detection of nucleic acids. In this study, we developed a high-sensitivity biosensor targeting norovirus nucleic acids through rationally introducing a dimeric G-quadruplex structure into the DNAzyme. In this strategy, two separate molecular beacons each having a G-quadruplex-forming sequence embedded in the stem structure are brought together through hybridization with a target DNA strand, and thus forms a three-way junction architecture and allows a dimeric G-quadruplex to form, which, upon binding with hemin, has a synergistic enhancement of catalytic activities. This provides a high-sensitivity colorimetric readout by the catalyzing H₂O₂-mediated oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline -6-sulfonic acid) diammonium salt (ABTS). Up to 10 nM of target DNA can be detected through colorimetric observation with the naked eye using our strategy. Hence, our approach provides a non-amplifying, non-labeling, simple-operating, cost-effective colorimetric biosensing method for target nucleic acids, such as norovirus-conserved sequence detection, and highlights the further implication of higher-order multimerized G-quadruplex structures in the design of high-sensitivity biosensors.     

Analysis of the unbinding force between telomestatin derivatives and human telomeric G-quadruplex by atomic force microscopy

The force analysis between a macrocyclic hexazole (6OTD) monomer/dimer and telomeric DNA using atomic force microscopy revealed the difference in their binding modes. The 6OTD dimer bound to the G-quadruplex more strongly than the monomer by sandwiching the G-quadruplex.     

Proton transfer reactions of matrix-assisted laser desorption/ionization matrix monomers and dimers

The gas-phase basicities of monomeric and dimeric deprotonated ferulic and sinapic acids, common matrix-assisted laser desorption/ionization (MALDI) matrices, were determined. A new bracketing method based on structure-reactivity correlations was developed for deriving gas-phase basicities from reaction efficiencies. The matrix dimer anions were found to be significantly less basic than the monomer anions, by about 115 kJ/mol. The low basicity of the dimer anion can qualitatively be explained by resonance stabilization. The energies for proton transfer from dimers to monomers are therefore about 1.2 eV lower than for proton transfer between monomers. For the MALDI process, proton transfer reactions involving matrix dimers provide a low energy pathway for matrix and analyte ion formation.     

A conformationally constrained nucleotide analogue controls the folding topology of a DNA g-quadruplex

Guanine-rich DNA and RNA sequences can fold into unique structures known as G-quadruplexes. The structures of G-quadruplexes can be divided into several classes, depending on the parallel or antiparallel nature of the strands and the number of G-rich tracts present in an oligonucleotide. Oligonucleotides with single tracts of guanines form intermolecular parallel tetrameric G-quadruplexes. Oligonucleotides with two tracts of guanosines separated by two or more bases can form both intermolecular antiparallel fold-back dimeric and parallel tetrameric G-quadruplexes, and those with four tracts of guanosines can form both intramolecular parallel and antiparallel structures. Intramolecular G-qaudruplexes can fold into several folding topologies including antiparallel crossover basket, antiparallel chair, and parallel propeller. The ability to control the folding of G-quadruplexes would allow the physical, biochemical, and biological properties of these various folding topologies to be studied. Previously, the known methods to control the folding topology of G-quadruplexes included changing the buffer by varying the mono- and divalent cations that are present, and by changing the DNA sequence. Because the glycosidic bonds in the G-quartets of G-quadruplexes with parallel strands are in the anti conformation, we reasoned that incorporation of nucleoside analogues that prefer the anti conformation of the glycosidic bond into G-rich sequences would increase the preference for parallel G-quadruplex formation. As predicted, by positioning the conformationally constrained nucleotide analogue 2'-O-4'-C-methylene-linked ribonucleotide into specific positions of a DNA G-quadruplex we were able to shift the thermodynamically favored structure of a G-quadruplex from an antiparallel to a parallel structure.     

Hydrogen‐bonding Structures and Energetics of Acrylamide Isomers,Tautomers, and Dimers: An ab initio Study and Spectral Analysis

Hydrogen‐bonding patterns and energetic profiles of acrylamide isomers (syn‐ and skew‐), tautomers (amide and imidic acid forms) and 13 stable dimers have been studied using the second‐order Møller–Plesset perturbation theory with basis sets up to aug‐cc‐pVTZ. Syn‐acrylamide is the most stable monomer with a reaction barrier of 4.15 kcal/mol for the syn–skew isomerization reaction. The direct amide–imidic acid tautomerization reaction is separated by too high a barrier to surpass. The most stable dimer corresponds to the planar double‐hydrogen‐bonded configuration, indicating its crucial role in determining the stability of the formed complex. Moreover, hydrogen bonds have significant effects on the infrared spectral features, which can be consistently explained solely based on the acrylamide dimeric structures and energetics without monomeric and dimeric tautomer forms. The results are useful for studying the stability of the acrylamide clusters in condensed‐phase samples such as those in food chemistry studies.     

Methods for investigating G-quadruplex DNA/ligand interactions

DNA is considered an important target for drug design and development. Until recently, the focus was on double-stranded (duplex) DNA structures. However, it has now been shown that single stranded DNA can fold into hairpin, triplex, i-motif and G-quadruplex structures. The more interesting G-quadruplex DNA structures comprise four strands of stacked guanine (G)-tetrads formed by the coplanar arrangement of four guanines, held together by Hoogsteen bonds. The DNA sequences with potential to form G-quadruplex structures are found at the chromosomal extremities (i.e. the telomeres) and also at the intra-chromosomal region (i.e. oncogenic promoters) in several important oncogenes. The formation of G-quadruplex structures is considered to have important consequences at the cellular level and such structures have been evoked in the control of expression of certain genes involved in carcinogenesis (c-myc, c-kit, K-ras etc.) as well as in the perturbation of telomeric organization. It has been shown that the formation of quadruplexes inhibits the telomere extension by the telomerase enzyme, which is up-regulated in cancer cells. Therefore, G-quadruplex structures are an important target for drug design and development and there is a huge interest in design and development of small molecules (ligands) to target these structures. A large number of so-called G-quadruplex ligands, displaying varying degrees of affinity and more importantly selectivity (i.e. the ability to interact only with quadruplex-DNA and not duplex-DNA), have been reported. Access to efficient and robust in vitro assays is needed to effectively monitor and quantify the G-quadruplex DNA/ligand interactions. This tutorial review provides an overview of G-quadruplex ligands and biophysical techniques available to monitor such interactions.     

Synthesis of the pivalamidate-bridged pentanuclear platinum(II,III) linear complexes with Pt...Pt interactions

Pentanuclear linear chain Pt(II,III) complexes [[Pt2(NH3)2X2((CH3)3CCONH)2(CH2COCH3)]2[PtX'4]].nCH3COCH3 (X = X' = Cl, n = 2 (1a), X = Cl, X' = Br, n = 1 (1b), X = Br, X' = Cl, n = 2 (1c), X = X' = Br, n = 1 (1d)) composed of a monomeric Pt(II) complex sandwiched by two amidate-bridged Pt dimers were synthesized from the reaction of the acetonyl dinuclear Pt(III) complexes having equatorial halide ligands [Pt2(NH3)2X2((CH3)3CCONH)2(CH2COCH3)]X' ' (X = Cl (2a), Br (2b), X' ' = NO3-, CH3C6H4SO3-, BF4-, PF6-, ClO4-), with K2[PtX'4] (X' = Cl, Br). The X-ray structures of 1a-1d show that the complexes have metal-metal bonded linear Pt5 structures, and the oxidation state of the metals is approximately Pt(III)-Pt(III)...Pt(II)...Pt(III)-Pt(III). The Pt...Pt interactions between the dimer units and the monomer are due to the induced Pt(II)-Pt(IV) polarization of the Pt(III) dimeric unit caused by the electron withdrawal of the equatorial halide ligands. The density functional theory calculation clearly shows that the Pt...Pt interactions between the dimers and the monomer are made by the electron transfer from the monomer to the dimers. The pentanuclear complexes have flexible Pt backbones with the Pt chain adopting either arch or sigmoid structures depending on the crystal packing.     

Structures of heterogeneous proton-bond dimers with a high dipole moment monomer: covalent vs electrostatic interactions

A number of calculated structures of heterogeneous proton-bound dimers containing monomers such as acetonitrile, cyanamide, vinylene carbonate, and propiolactone, which have high dipole moments, are presented. These proton-bound dimers are predicted to have a structural anomaly pertaining to the bond distances between the central proton and the basic sites on each of the monomers. The monomers with the high dipole moments also have the larger proton affinity and, on the basis of difference in proton affinities, it would be expected that the proton would be closer to this monomer than the one with the lower proton affinity. However, the proton is found to lie substantially closer to the monomer with the lower proton affinity in most cases, unless the difference in proton affinity is too large. Simply stated, the difference in proton affinities is smaller than the difference in the affinity to form an ion-dipole complex for the two monomers and it is the larger affinity for the high dipole moment monomer (which also has the higher proton affinity) to form an ion-dipole complex that is responsible for the proton lying closer to the low proton affinity monomer. The bond distances between the central proton and the monomers are found to be related to the difference in proton affinity. It is found, though, that the proton-bound dimers can be grouped into two separate groups, one where the proton-bound dimer contains a high dipole moment monomer and one group where the proton-bound dimer does not contain a high dipole moment monomer. From these plots it has been determined that a high dipole moment monomer is one that has a dipole moment greater than 2.9 D.     

Gas-phase H/D exchange and collision cross sections of hemoglobin monomers, dimers, and tetramers

The conformations of gas-phase ions of hemoglobin, and its dimer and monomer subunits have been studied with H/D exchange and cross section measurements. During the H/D exchange measurements, tetramers undergo slow dissociation to dimers, and dimers to monomers, but this did not prevent drawing conclusions about the relative exchange levels of monomers, dimers, and tetramers. Assembly of the monomers into tetramers, hexamers, and octamers causes the monomers to exchange a greater fraction of their hydrogens. Dimer ions, however, exchange a lower fraction of their hydrogens than monomers or tetramers. Solvation of tetramers affects the exchange kinetics. Solvation molecules do not appear to exchange, and solvation lowers the overall exchange level of the tetramers. Cross section measurements show that monomer ions in low charge states, and tetramer ions have compact structures, comparable in size to the native conformations in solution. Dimers have remarkably compact structures, considerably smaller than the native conformation in solution and smaller than might be expected from the monomer or tetramer cross sections. This is consistent with the relatively low level of exchange of the dimers.     

三种金属硫蛋白动力学稳定性的理论研究

对三类金属硫蛋白（大鼠金属硫蛋白亚型Ⅱ,兔肝金属硫蛋白亚型Ⅰ和兔肝金属硫蛋白亚型Ⅱ）的单体和二聚体进行了水溶液条件下的分子动力学模拟。其中大鼠金属硫蛋白亚型Ⅱ的结构直接来自于晶体数据,兔肝金属硫蛋白亚型Ⅰ和Ⅱ的结构则通过同源蛋白模型搭建。动力学模拟的结果显示,这三种单体在水溶液中都具有相当大的柔性,柔性主要来源于柔性区的氨基酸残基。三类金属硫蛋白单体的动力学模拟均表明α结构域的动力学稳定性都要优于     

Amine-chelated aryllithium reagents--structure and dynamics

Multinuclear NMR studies of five-membered-ring amine chelated aryllithium reagents 2-lithio-N,N-dimethylbenzylamine (1), the diethylamine and diisopropylamino analogues (2, 3), and the o-methoxy analogue (4), isotopically enriched in (6)Li and (15)N, have provided a detailed picture of the solution structures in ethereal solvents (usually in mixtures of THF and dimethyl ether, ether, and 2,5-dimethyltetrahydrofuran). The effect of cosolvents such as TMEDA, PMDTA, and HMPA has also been determined. All compounds are strongly chelated, and the chelation is not disrupted by these cosolvents. Reagents 1, 2, and 3 are dimeric in solvents containing a large fraction of THF. Below -120 degrees C, three chelation isomers of the dimers are detectable by NMR spectroscopy: one (A) with both nitrogens coordinated to one lithium of the dimer, and two (B and C) in which each lithium bears one chelating group. Dynamic NMR studies have provided rates and activation energies for the interconversion of the 1-A, 1-B, and 1-C isomers. They interconvert either by simple ring rotation, which interconverts B and C, or by amine decoordination (probably associative, DeltaG(++)(-93) = 8.5 kcal/mol), which can interconvert all of the isomers. The dimers of 1 are thermodynamically more stable than those of model systems such as phenyllithium, o-tolyllithium, or 2-isoamylphenyllithium (5, DeltaDeltaG > or = 3.3 kcal/mol). They are not detectably deaggregated by TMEDA or PMDTA, although HMPA causes partial deaggregation. The dimers are also more robust kinetically with rates of interaggregate exchange, measured by DNMR line shape analysis of the C-Li signal, orders of magnitude smaller than those of models (DeltaDeltaG(++) > or = 4.4 kcal/mol). Similarly, the mixed dimer of 1 and phenyllithium, 13, is kinetically more stable than the phenyllithium dimer by >2.2 kcal/mol. X-ray crystal structures of the TMEDA solvate of 1-A and the THF solvate of 3-B showed them to be dimeric and chelated in the solid state as well. Compound 4, which has a methoxy group ortho to the C-Li group, differs from the others in being only partially dimeric in THF, presumably for steric reasons. This compound is fully deaggregated by 1 equiv of HMPA. Excess HMPA leads to the formation of ca. 15% of a triple ion (4-T) in which both nitrogens appear to be chelated to the central lithium.     

Thermodynamics and kinetics of aggregation for the GNNQQNY peptide

The energy landscape of the monomer and dimer are explored for the amyloidogenic heptapeptide GNNQQNY from the N-terminal prion-determining domain of the yeast protein Sup35. The peptide is modeled by a united-atom potential and an implicit solvent representation. Replica exchange molecular dynamics is used to explore the conformational space, and discrete path sampling is employed to investigate the pathways that interconvert the most populated minima on the free energy surfaces. For the monomer, we find a rapid fluctuation between four different conformations, where a geometry intermediate between compact and extended structures is the most thermodynamically favorable. The GNNQQNY dimer forms three stable sheet structures, namely in-register parallel, off-register parallel, and antiparallel. The antiparallel dimer is stabilized by strong electrostatic interactions resulting from interpeptide hydrogen bonds, which restrict its conformational flexibility. The in-register parallel dimer, which is close to the amyloid beta-sheet structure, has fewer interpeptide hydrogen bonds, making hydrophobic interactions more important and increasing the conformational entropy compared to the antiparallel sheet. The estimated two-state rate constants indicate that the formation of dimers from monomers is fast and that the dimers are kinetically stable against dissociation at room temperature. Interconversions between the different dimers are feasible processes and are more likely than dissociation.