Resonance Rayleigh scattering method for the recognition and determination of double-stranded DNA using amikacin

In weakly acidic buffer medium, the interaction of amikacin with calf thymus DNA, yeast RNA and denatured DNA has been investigated by using resonance Rayleigh scattering (RRS) technique. The result shows that calf thymus DNA is capable of enhancing the RRS intensity of the amikacin, while yeast RNA and denatured DNA have very little enhancement effect. Based on the characteristics, a sensitive assay for detecting double-stranded DNA in the presence of denatured DNA and yeast RNA has been developed. The enhancement of the RRS signal is directly proportional to the concentration of double-stranded DNA in the range 0.02-12.0 μg ml⁻¹ for calf thymus DNA and its detection limit (3σ) is 2.5 ng ml⁻¹. The method shows a wide linear range and high sensitivity, and almost no interference can be observed from RNA, denatured DNA, amino acid and most of the metal ions. The trace amounts of nucleic acid in synthetic samples and practical samples are determined with satisfactory results. Therefore, the proposed method is promising for as an effect means for recognition in vivo and determination in situ of double-stranded DNA.     

抗癌药物的电化学研究(Ⅱ)道诺霉素在DNA修饰石墨粉末微电极上的电化学行为及分析应用

研究了道诺霉素 ( DNM)在石墨粉末微电极和 DNA修饰石墨粉末微电极上的电化学行为 ,并分析了产生差别的原因。在此基础上 ,提出了测定微量 DNM的方法 ,DNM浓度在 1 .0× 1 0 - 7～ 1 .0× 1 0 - 5mol/L之间其微分脉冲伏安 ( DPV)峰电流与浓度有良好的线性关系 ,检出限为 5 .0× 1 0 - 8mol/L。采用标准加入法测定了模拟样品中的 DNM,回收率在 94%～ 1 0 8%之间 ,结果令人满意     

Optical sensors based on hybrid DNA/conjugated polymer complexes

Single-stranded DNA (ss-DNA) can specifically bind to various targets, including a complementary ss-DNA, ions, proteins, drugs, and so forth. When binding takes place, the oligonucleotide probe often undergoes a conformational transition. This conformational change of the negatively charged ss-DNA can be detected by using a water-soluble, cationic polythiophene derivative, which transduces the complex formation into an optical (colorimetric or fluorometric) signal without any labeling of the probe or the target. This simple and rapid methodology has enabled the specific and sensitive detection of nucleic acids and human thrombin. This new biophotonic tool can easily be applied to the detection of various other biomolecules and is also useful in the high-throughput screening of new drugs.     

Specific surface of two hydrated cements differing in strength

Specific surface, S, of CSH-gel particles of disordered layered structure, was studied by water sorption/retention in two cement pastes differing in strength, i.e. C-33 (weaker) and C-43 (stronger), w/c=0.4. Hydration time in liquid phase was t _h=1 and 6 months, followed by hydration in water vapour either on increasing stepwise the relative humidity, RH=0.5→0.95→1.0 (WS) or on its lowering in an inverse order (WR). Specific surface was estimated from evaporable (sorbed) water content, EV (110°C), assuming a bi- and three-molecular sorbed water layer at RH=0.5 or 0.95, respectively (WS). On WR it was three- and three- to four-molecular (50 to 75%), respectively, causing a hysteresis of sorption isotherm. At RH=0.5 the S increased with cement strength from 146 m² g^-1 (C-33, 1 m) to 166 m² g^-1 (C-43, 1 m) and with hydration time to 163 (C-33, 6 m) and to 204 m² g^-1 (C-43, 6 m). At RH=1.0 (and 0.95), higher S-value were measured but these differences were smaller: S amounted to 190-200 m² g^-1 in C-33 (1 and 6 m) and 198-210 m² g-1 in C-43 (1 and 6 m). Thus no collapse occurred on air drying of paste C-43 (6 m). This revised version was published online in July 2006 with corrections to the Cover Date.     

Structural and dynamic variations in DNA hexamers containing T-T and F-F single and tandem internal mispairs

Molecular dynamics simulations of double-helical DNA oligomers have been performed to investigate differences in the structure, dynamics, and hydration of F-F and T-T mispairs. Hexamers containing F-F pairs were found to be more dynamic, especially in the region of the mispair itself. This dynamic variability derives from greater flexibility of F-F pairs. The T-T mispairs, on the other hand, were found to be comparatively tightly bound as wobble pairs. The major and minor groove edges of the T-T pairs were observed to be solvated at exposed carbonyl positions by at least one water molecule, while F-F pairs lacked solvating waters. Stacking interactions were nearly identical for T-T and F-F pairs, leading to similar average structures, even though F stacking was more dynamically variable. Solvation differences between F-F and T-T therefore support the steric exclusion model for nucleotide incorporation in DNA replication. Large differences in the orientation of minor groove functional groups, in addition to differences in solvation, further rationalize why F bases present during DNA extension events induce stalls. Two novel nucleotides are proposed to further elucidate minor groove interactions of DNA with polymerase molecules.Electronic Supplementary Material This Material consists of equilibration protocol, plots of center-of-mass stacking, water radial distribution functions, helical parameter dynamics, and dynamics data for a control AT sequence. Supplementary material is available in the online version of this article at Contribution to the Jacopo Tomasi Honorary Issue     

Targeting of Single‐Stranded Oligonucleotides through Metal‐Induced Cyclization of Short Complementary Strands

A new strategy to cyclize short synthetic oligonucleotides on DNA or RNA target strands is described. The approach is based on metal‐templated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2′ : 6′,2′′‐terpyridine (Tpy) moieties at their 3′‐ and 5′‐ends. Cyclization after metal addition (Zn²⁺, Fe²⁺) was demonstrated by means of thermal‐denaturation experiments, MALDI‐Q‐TOF‐MS, and gel electrophoresis (PAGE). 1D‐ and 2D‐NMR Experiments were performed to analyze the association of complementary strands after metal‐mediated cyclization. Our protocol allows the efficient circularization of synthetic oligonucleotides. Thereby, the hybridization on a complementary strand was more efficient with an RNA target strand and a 2′‐O‐methylated circularized oligomer.     

5-氟尿嘧啶-1-乙酸合铜(Ⅱ)的合成及其与DNA的作用

The 5-fluorouracil-1-acetic acid (5FuAA) and its Cu(Ⅱ) complex (5FuAACu) were synthesized and the date for the crystal complex was obtained. The interaction of 5-fluorouracil-1-acetic acid (5FuAA) and its Cu(Ⅱ) complex (5FuAACu) with DNA was also investigated by using spectral, viscometric, electrochemical and agarose gel electrophoresis methods. The results of interaction with DNA suggest that both 5FuAA and 5FuAACu can bind to DNA in a static electricity attraction mode. But the attraction of 5FuAACu is greater than that of 5FuAA.     

Synthesis, antitumor and DNA photocleaving activities of novel naphthalene carboxamides: effects of different thio-heterocyclic rings and aminoalkyl side chains

Two kinds of thio-heterocyclic fused naphthalene carboxamides, 3a-b, 4a-b, were designed, synthesized and quantitatively evaluated as efficient antitumor and DNA photocleaving agents. Compound 3a or 3b, having the thiophene ring, intercalated into DNA more strongly than compound 4a or 4b, having the thioxanthene ring. Compound 4a or 4b, photocleaved DNA more efficiently than 3a or 3b via superoxide anion. Compound 4a was the strongest inhibitor for P388 (murine leukemia cell), while 3a was the most cytotoxic one against A549 (human lung cancer cell). Each new compound showed stronger DNA photocleaving activity than corresponding naphthalimide.     

二维DNA晶体的程序化设计与自组装的研究进展

按照Watson-Crick的碱基配对原则，在理论上能够人工设计与合成DNA碱基序列并自组装成任何一维和二维结构的DNA晶体。DNA分子这种底端向上(bottom-up)的自组装模式为我们提供了一种精确合成纳米材料的方法。本文将从程序化设计、合成刚性的DNA分子瓦(DNA tile)、分子瓦自组装成二维DNA晶体以及二维DNA晶体作为模板在纳米技术中的应用等方面展开，简述这一新奇的并且有着潜在应用前景的研究领域的最新进展。     

Adsorption of the fluoride ion on the surface of various faces of a single crystal of silver: a quantum-chemical study

The fluoride ion adsorption from a gas phase on various faces of a single crystal of silver is studied by a density functional method within a cluster model for metal. The adsorption bond energy is found to increase in the series Ag(100) < Ag(111) < Ag(311) < Ag(110). A substantial structural and energetic heterogeneity of various adsorption sites is revealed. The results are utilized to simulate the electrochemical interface between individual faces of a single crystal of silver and aqueous solutions containing the fluoride ion. It is assumed that the adsorption potential may be represented as the sum of two contributions, one of which describes the metal–ion interaction and the other, the ion solvation energy. The plotted adsorption terms take into account partial degradation of the fluoride ion when adsorbed from an aqueous solution. Estimates of discreteness of the electrical double layer are presented. A conclusion on the maximum manifestation of specific adsorption of the fluoride ion for the Ag(100) face is made.Translated from Elektrokhimiya, Vol. 41, No. 2, 2005, pp. 232–238.Original Russian Text Copyright © 2005 by Nazmutdinov, Zinkicheva.This revised version was published online in April 2005 with corrections to the article note and article title and cover date.