Small-Molecule Selectively Recognizes Human Telomeric G-Quadruplex DNA and Regulates Its Conformational Switch

Structural complexity is an inherent feature of the human telomeric sequence, and it presents a major challenge for developing ligands of pharmaceutical interest. Recent studies have pointed out that the induction of a quadruplex or change of a quadruplex conformation on binding may be the most powerful method to exert the desired biological effect. In this study, we demonstrate a quadruplex ligand that binds selectively to different forms of the human telomeric G-quadruplex structure and regulates its conformational switch. The results show that not only can oxazine750 selectively induce parallel quadruplex formation from a random coil telomeric oligonucleotide, in the absence of added cations, it also can easily surpass the energy barrier between two structures and change the G-quadruplex conformation in Na+ or K+ solution. The combination of its unique properties, including the size and shape of the G-quadruplex and the small molecule, is proposed as the predominant force for regulating the special structural formation and transitions.

Enhanced catalytic DNAzyme for label-free colorimetric detection of DNA

A DNAzyme-based label-free method for the colorimetric detection of DNA is introduced, with a supramolecular hemin G-quartet complex as the sensing element and a 36-mer single-strand DNA as the analyte that is detected at 10 nM.

Submicrometre scale single-crystalline gold plates of nanometre thickness: synthesis through a nucleobase process and growth mechanism

Synthesis of submicrometre scale single-crystalline gold plates of nanometre thickness in the presence of nucleobase guanine through chemical reduction of HAuCl4 was investigated. The elemental composition of the as-prepared gold nanoplates was estimated using energy-dispersive x-ray spectroscopy. The as-prepared gold plates were composed of essentially (111) lattice planes, as revealed by both x-ray diffraction (XRD) and transmission electron microscopy (TEM) results. It was found that the molar ratio of HAuCl4 to guanine played a very important role in the formation of gold nanoplates. Gold nanoplates could be produced at a molar ratio of [HAuCl4]/[guanine] = 50: 1 while only smaller gold spherical nanoparticles were obtained at molar ratios of [HAuCl4]/[guanine] <= 20:1. A possible growth mechanism of the as-prepared gold nanoplates is proposed and discussed. The results and conclusion presented in this work may be valuable for our further understanding of the roles of precursor ligands in the control of nanoparticles aggregation states and the preparation of shape-controlled nanoparticles.

Aptamer-based label-free method for hemin recognition and DNA assay by capillary electrophoresis with chemiluminescence detection

An aptamer-based label-free approach to hemin recognition and DNA assay using capillary electrophoresis with chemiluminescence detection is introduced here. Two guanine-rich DNA aptamers were used as the recognition element and target DNA, respectively. In the presence of potassium ions, the two aptamers folded into the G-quartet structures, binding hemin with high specificity and affinity. Based on the G-quartet-hemin interactions, the ligand molecule was specifically recognized with a K (d)approximate to 73 nM, and the target DNA could be detected at 0.1 mu M. In phosphate buffer of pH 11.0, hemin catalyzed the H2O2-mediated oxidation of luminol to generate strong chemiluminescence signal; thus the target molecule itself served as an indicator for the molecule-aptamer interaction, which made the labeling and/or modification of aptamers or target molecules unnecessary. This label-free method for molecular recognition and DNA detection is therefore simple, easy, and effective.

Structural stability and electronic state of transition metal trimers

Ground state geometries were searched for transition metal trimers Sc-3, Y-3, La-3, Lu-3, Ti-3, Zr-3, and Hf-3 by density functional methods. For all the studied trimers, our calculation indicates that the ground state geometries are either equilateral triangle (Zr-3 and Hf-3) or near equilateral triangle (Ti-3, Sc-3, Y-3, La-3, and Lu-3). For rare earth trimers Sc-3, Y-3, La-3, and Lu-3, isosceles triangle (near equilateral triangle) at quartet state is the ground state. Isosceles triangle at doublet state is the competitive candidate for the ground state. For Zr-3 and Hf-3, equilateral triangle at singlet state is the most stable. For Ti-3, isosceles triangle (near equilateral triangle) at quintet state gives the ground state. For Sc-3, Zr-3, and Hf-3, where experimental results are available, the predicted geometries are in agreement with experiment in which the ground state is equilateral triangle (Zr-3) or fluxional (Sc-3 and Hf-3). For Y-3, the calculated geometry is in agreement with experimental observation and previous theoretical study that Y-3 is a bent molecule for the ground state.

Theoretical investigation of LaC2 and LaC2+ clusters

LaC2 (with doublet and quartet states) and LaC2+ (with singlet and triplet states) cluster have been studied by using the B3LYP (Becke three-parameter/Lee-Yang-Parr) density functional method and the HF (Hartree-Fock) method with LANLIDZ basis set. For each cluster, four possible isomers in C-2v, C-s, C-proportional to v and D-proportional to h symmetries have been investigated. The results indicate that structures in C-s symmetry are local minima in all cases and, in most cases (particularly for high spin states), our initial guess in C-s symmetry converges to structures in C-2v symmetry. For the isomers in C-2v, C-proportional to v and D-proportional to h symmetries, local minima were found to be dependent on the method and spin state. The two clusters may also exist as linear chains. The ordering of the binding energies for the isomers in all spin states is C-s similar to C-2v < C-proportional to v < D-proportional to h. The ionization potential of LaC2 is reported as well. (C) 1998 Elsevier Science B.V.

Theoretical investigation of LaC3n+ (n = 0, 1, 2) clusters by density functional theory

LaC3n+ (n = 0, 1, 2) clusters have been studied using B3LYP (Becke 3-parameter-Lee-Yang-Parr) density functional method. The basis set is Dunning/ Huzinaga valence double zeta for carbon and [2s2p2d] for lanthanum, denoted LANL1DZ. Four isomers are presented for each cluster; two of them are edge binding isomers with C-2 upsilon symmetry, the other two are Linear chains with C-infinity upsilon symmetry. Meanwhile, two spin states for each isomer, that is, singlet and triplet for LaC3+, doublet and quartet for LaC3 and LaC32+, respectively, are also considered. Geometries, vibrational frequencies, infrared intensities, and other quantities are reported and discussed. The results indicate that at some spin states; the C-2 upsilon symmetry isomers are the dominant structures, while for the other spin states, linear isomers are energetically favored. (C) 1998 John Wiley & Sons, Inc.

Theoretical investigation of small lathanum carbide clusters

LaC2+, LaC22+, LaC3 and LaC3- clusters have been studied using B3LYP density functional method. Four isomers with C-2v, C-s, C-infinity v and D-infinity h symmetry were presented for LaC2+ and LaC22+. Meanwhile, two spin states, namely, singlet and triplet for LaC2+, doublet and quartet for LaC22+ were considered The results indicated that ring isomers with C-2v and C-s symmetry are the most stable for La-C2(+) at both spin states and for LaC22+ at quartet state. Whereas for LaC22+ at doublet state, linear isomer with C-infinity v symmetry is energetically favored, For LaC3 and LaC3- clusters,, three isomers have been presented for each cluster, that is, two ring isomers with C-2v symmetry ( in one of them, La forms two single bonds with two carbons, and in another, La forms a double bond with carbon), and one linear isomer with C-infinity v symmetry. The results revealed that the ring isomer in which La forms two single bonds with carbons is the lowest in energy.