A fluorescent molecular switch for room temperature operation based on oligonucleotide hybridization without labeling of probes or targets

A molecular switch was prepared by self-assembly. Neutravidin served as a template that allowed for a biotinylated probe oligonucleotide to be placed adjacent to a biotinylated long-chain linker that was terminated with thiazole orange (TO). Hybridization of probe oligonucleotide with target to form double-stranded DNA resulted in intercalation of the adjacent TO probe. This was a reversible process that could be tracked by fluorescence intensity changes. Formamide was used as a denaturant for double-stranded DNA, and could be used to depress thermal denaturation temperatures. In this work formamide had a dual function, providing for control of hybridization selectivity at room temperature, while concurrently ameliorating non-specific adsorption to improve signal-to-noise when using thiazole orange as a fluorescence signalling agent to determine oligonucleotide hybridization. Room temperature single nucleotide polymorphism (SNP) discrimination for oligonucleotide targets was achieved both in solution and for molecular switches that were immobilized onto optical fibers. In solution, a concentration of 18.5% formamide provided greater than 40-fold signal difference between single-stranded DNA and double-stranded DNA, in contrast to only a 2-fold difference in the absence of formamide. Selectivity for SNP determination in solution was demonstrated using targets of varying lengths including a 141-base PCR amplicon. The improved signal-to-noise achieved by use of formamide is likely due to preferential displacement of dye molecules that are otherwise electrostatically bound to the polyanionic nucleic acid backbone.     

Thermochemical Study of Solvation of Aliphatic Carboxamides in Aqueous Formamide Solutions

The entahlpies of solution of formamide, acetamide, and propionamide in aqueous formamide solutions (formamide concentration 8 mol kg^-1) at 298.15 K were measured. The entahlpies of transfer of amides from water to the mixed aqueous-organic solvent were calculated and compared with published data on the enthalpies of transfer of amides into aqueous urea solutions. The opposite trend in variation of the enthalpies of transfer of amides in these systems with increasing concentration of the nonaqueous component is due to different proton-donor power of formamide and urea relative to water. The enthalpy coefficients of pair interaction of amides with formamide in ternary aqueous solutions were calculated. Their positive values are due to endothermic interaction with formamide of the alkyl groups of amide molecules. The relative hydrophobicity of amides with different degrees of substitution of the amide group was estimated.     

Enthalpic Interaction Coefficients of Formamide in Aqueous Methanol and Ethanol Solutions at 298.15 K

The dilution enthalpies of formamide in aqueous methanol and ethanol solutions have been determined using a CSC-4400 isothermal calorimeter at 298.15 K. The homogeneous solution enthalpic interaction coefficients have been calculated over a range of alcohol concentrations according to the excess enthalpy concept. The results show that the enthalpic pair interaction coefficients h ₂ of formamide are negative in aqueous alcohol solutions and pass through a minimum in mixed solvents, whereas the h ₂ coefficients of formamide in aqueous ethanol solutions are more negative than those in aqueous methanol solutions. The results are discussed in terms of solute-solute and solute-solvent interactions.     

Synthesis and degradation of nucleic acid components by formamide and iron sulfur minerals

We describe the one-pot synthesis of a large panel of nucleic bases and related compounds from formamide in the presence of iron sulfur and iron-copper sulfur minerals as catalysts. The major products observed are purine, 1H-pyrimidinone, isocytosine, adenine, 2-aminopurine, carbodiimide, urea, and oxalic acid. Isocytosine and 2-aminopurine may recognize natural nucleobases by Watson-Crick and reverse Watson-Crick interactions, thus suggesting novel scenarios for the origin of primordial nucleic acids. Since the major problem in the origin of informational polymers is the instability of their precursors, we also investigate the effects of iron sulfur and iron-copper sulfur minerals on the stability of ribooligonucleotides in formamide and in water. All of the iron sulfur and iron-copper sulfur minerals stimulated degradation of RNA. The relevance of these findings with respect to the origin of informational polymers is discussed.     

Thermodynamics of bolaform electrolytes. V. Enthalpies and heat capacities in aqueous urea solutions

The partial molal heats of solution at infinite dilution of 1,4-bis(triethylammonium)butane dibromide and 1,10-bis(triethylammonium)decane dibromide in aqueous urea (up to 8m urea) have been determined calorimetrically in the temperature range 18–33°C. These data have been used to derive the partial molal heat capacities at infinite dilution, the enthalpies of transfer, and heat capacities of transfer at infinite dilution from water to urea-water solutions. The results show that the enthalpies of transfer are negative and decrease with increasing urea concentrations. The heat capacities of transfer are negative at low urea concentrations and increase in magnitude at higher urea concentrations. In the case of the smaller cation the partial molal heat capacity in 8m aqueous urea solution is greater than in pure water. The results are discussed in terms of structural changes in the solvents on dissolution.     

Preferential solvation in urea solutions at different concentrations: properties from simulation studies

We performed molecular dynamics simulations of urea solutions at different concentrations with two urea models (OPLS and KBFF) to examine the structures responsible for the thermodynamic solution properties. Our simulation results showed that hydrogen-bonding properties such as the average number of hydrogen bonds and their lifetime distributions were nearly constant at all concentrations between infinite dilution and the solubility limit. This implies that the characterization of urea-water solutions in the molarity concentration scale as nearly ideal is a result of facile local hydrogen bonding rather than a global property. Thus, urea concentration does not influence the local propensity for hydrogen bonds, only how they are satisfied. By comparison, the KBFF model of urea donated fewer hydrogen bonds than OPLS. We found that the KBFF urea model in TIP3P water better reproduced the experimental density and diffusion constant data. Preferential solvation analysis showed that there were weak urea-urea and water-water associations in OPLS solution at short distances, but there were no strong associations. We divided urea molecules into large, medium, and small clusters to examine fluctuation properties and found that any particular urea molecule did not stay in the same cluster for a long time. We found neither persistent nor large clusters.     

甘氨酸从水到有机物水溶液的迁移焓研究

蛋白质是各种生物形态结构和生命活动所依赖的物质基础,在水溶液中蛋白质天然结构的稳定性归结于氨基酸残基之间以及与溶液中其它组分的相互作用．天然环境中存在的众多物质对蛋白质的溶解度、变性行为和解缔等都有很大的影响．为深入了解蛋白质折叠与解折叠过程中的物理化学现象,以氨基酸、肽、酰胺及其衍生物作为蛋白质模型分子的热力学研究引起了广泛重视．     

Thermochemical parameters of Ni(NO3)2 solutions in water + formamide + α-alanine mixtures at 298 K

The enthalpies of mixing of aqueous solutions of nickel(II) nitrate in water + formamide + α-alanine mixtures in the range of existing amide concentrations have been measured calorimetrically. From these data the standard enthalpies of electrolyte transfer from water into ternary mixtures have been calculated. The type and character of electrolyte transfer isotherms are discussed on the basis of the heats of transfer of individual ions that were studied earlier, as well as the contributions into these values that characterize structural changes in the solution and chemical ion-solvent interactions.     

Thermodynamics of solvation and solvophobic effect in formamide

Using semi-adiabatic calorimetry, we measured the enthalpies of solution for various low-polar compounds including alkanes, aromatic hydrocarbons and their halogenated derivatives in formamide at temperature of 298 K. For the same compounds, the values of limiting activity coefficients in formamide were determined using GC headspace analysis at 298 K, and Gibbs free energies of solution and solvation were calculated. Based on these data and the available literature values of the Gibbs free energy of solvation in formamide for a number of other low-polar solutes, a study of the solvophobic effect in this solvent is performed, and its resemblance to the hydrophobic effect in aqueous solutions is demonstrated. It is shown that the contribution of the solvophobic effect into the solvation Gibbs free energy in formamide is much higher than that in aliphatic alcohols, but lower than that in water. Like in water, the magnitude of this contribution for different solutes linearly increases with the solute molecular volume. Solvophobic effect also significantly affects the enthalpies of dissolution in formamide, causing them to be more negative in the case of alkanes and more positive in the case of arenes.     

Voltammetry of osmium-modified DNA at a mercury film electrode: application in detecting DNA hybridization

Mercury film electrodes (MFE) have recently been used in nucleic acid electrochemical analysis as alternatives to the classical mercury drop ones. DNA modified with osmium tetroxide, 2,2'-bipyridine (Os,bipy) can be detected with a high sensitivity at mercury electrodes via measurements of a catalytic osmium signal. In this paper we show that mercury film on a glassy carbon electrode can be used in voltammetric analysis of Os,bipy-modified DNA. Application of the MFE as a detection electrode in double-surface electrochemical DNA hybridization assay involving osmium labeling of target DNA is demonstrated.     

An electronic signature of hydrolysation in the X-ray absorption spectrum of aqueous formaldehyde

Formaldehyde in aqueous solution is hydrolysed and forms methanediol. Using X-ray absorption spectroscopy we show that the hydrolysation product can be identified by a distinct electronic signature in the spectra. This is manifested by the disappearance of the oxygen 1s → π* absorption line. The X-ray absorption spectrum of aqueous formaldehyde is compared with those of the structurally similar formamide and urea, which are in contrast not hydrolysed in aqueous solution. We thereby demonstrate the exceptional sensitivity and simplicity of the technique to monitor this fundamental process in the aqueous phase.     

Analysis of internucleosomal DNA fragmentation in apoptotic thymocytes by dynamic sieving capillary electrophoresis

The analysis, by slab gel electrophoresis, of internucleosomal DNA cleavage or laddering, characteristic of apoptosis in many cell systems, is labour intensive, difficult to automate and best only semi-quantitative. In this report we show that CE, using dilute solutions of hydroxyethylcellulose as a replaceable sieving matrix, can be applied to the relatively rapid analysis of DNA laddering in whole digests of apoptotic rat thymocytes. Also, using the sensitivity of laser-induced fluorescence detection and the highly sensitive nucleic acid stain YO-PRO-1, the CE method reported here can use 1000–2000 fold fewer cells than needed for traditional slab gel methods.     

Sequential determination of urea and HMTA in the process solution of sol-gel route of advanced nuclear fuel fabrication

Determinations of hexamethylene tetramine (HMTA) and urea in the process solutions are required to optimize their concentrations for obtaining high quality ceramic oxide microspheres, for monitoring the washing procedure and for their subsequent recovery, recycling or waste disposal. Determination of urea in the feed solution by conventional procedures is difficult as it contains HMTA. It is more so in the effluent as it contains hydrolytic products like formaldehyde, methylol derivatives of urea, ammonium nitrate and ammonium hydroxide used for washing the gel microspheres. This work describes a derivative potentiometric method using a microprocessor-based autotitrator. Peaks on the first derivative of the titration plot corresponded to constituents of different basicities. Urea was selectively hydrolyzed at room temperature by the catalytic action of urease enzyme leaving HMTA unaffected. Ammonium hydroxide and ammonium bicarbonate produced from urea and HMTA were sequentially titrated for the analysis of the feed solution to obtain the three corresponding peaks respectively. Two separate titrations were required for the analysis of the effluent solution, which contained free ammonia also. One aliquot was first titrated directly without adding urease (for free ammonia and HMTA) and another aliquot was titrated after treatment with urease. The end points due to the ammonia used for washing and that from urea hydrolysis merged resulting in the appearance of three peaks again. Using this sequential method the relative standard deviations were found to be 0.81% and 1.38% for urea and HMTA, respectively, in eight determinations when the aliquots contained 50 to 75 mg of urea and 75 to 125 mg of HMTA. Feed and effluent solutions of the process stream were analyzed.     

Enthalpies of transfer of amino acids from water to aqueous solutions of formamide

Enthalpies of solution of glycine, l-alanine, l-serine in water and aqueous solutions of formamide were measured at 298.15 K. Transfer enthalpies of amino acids from water to aqueous solutions of formamide were derived and interpreted qualitatively with hydration co-sphere overlap model. The results show that the structure interaction between formamide and zwitterionic head-group and hydrophilic side chain of amino acids make a negative contribution to transfer enthalpy, while that with the hydrophobic side chain is positive. In the solvent composition range studied, transfer enthalpies decrease overall with the increasing concentration of formamide, with the relative order of l-serine < glycine < l-alanine.     

尿素和甲酰胺塑化热塑性淀粉

用甲酰胺和尿素作为塑化剂制备了热塑性淀粉 (TPS) .扫描电镜显示甲酰胺和尿素混合物可以使淀粉塑化 ,形成均一的连续相 ;根据FT IR谱图可以确定 ,与甘油相比 ,甲酰胺可以使热塑性淀粉体系在保存时更稳定 ,各基团的化学环境变化更小 ,这是由于甲酰胺可以和淀粉羟基形成更稳定的氢键 .X ray衍射说明甲酰胺和尿素 (重量比为 10 % 2 0 % )作为混合塑化剂可以有效抑制淀粉的回生 ,同时防止尿素结晶析出 .在RH=33%的湿度环境保存 1周 ,这种热塑性淀粉有良好的拉伸强度、伸长率和断裂能 ,分别达到 4 83MPa ,10 4 6 %和 2 17N·m .水含量对热塑性淀粉的力学性能的影响也被研究 .另外 ,热失重实验和吸水实验说明这种热塑性淀粉的热稳定性和耐水性也要优于常用的甘油塑化热塑性淀粉     

甲酰胺溶剂中溶质间的过量Gibbs自由能相互作用参数

利用气液色谱方法测定了２９８．１５Ｋ时若干非电解质溶质在甲酰胺－乙酰胺、甲酰胺－尿素、甲酰胺－高氯酸钠固定液中的保留参数，采用ＭｃＭｉｌａａｎ－Ｍａｙｅｒ理论，将溶液热力学过量性质与溶液中粒子的对相互作用，参相互作用参数相联系，利用热力学方法求得了溶质的保留参数与Ｇｉｂｌｓ自由能相互作用参数的关系，并就溶质－溶质间的相互作用及溶剂性质的影响进行了讨论。     

丙烯酰胺型阴离子表面活性单体与丙烯酰胺共聚物水溶液的流变特性

以丙烯酰胺型阴离子表面活性单体2-丙烯酰胺基十四烷基磺酸钠(NaAMC14S)为共单体,与丙烯酰胺(AM)的水溶液均相共聚合,使NaAMC14S的浓度分别处于临界胶束浓度上下,分别制备了具有无规结构与微嵌段结构的两类共聚物;用红外光谱法对共聚物的结构进行了表征,使用乌氏粘度法测定了特性粘数,相对表示出了共聚物的分子量;采用荧光探针法与表观粘度法重点研究了两类共聚物的疏水缔合性与水溶液的流变特性.研究结果表明,具有微嵌段结构的共聚物具有很强的疏水缔合性,当其水溶液的浓度达0.2wt%后,表观粘度迅速提高;其水溶液的切力变稀行为具有明显的可逆性,表现出强的抗剪切性能.本研究中特别发现,具有微嵌段结构的共聚物其盐水溶液的表观粘度远高于纯水溶液的表观粘度,当共聚物浓度为0.3wt%、CaCl2浓度为2wt%时,溶液的表观粘度竟然提高了3个数量级,表现出独特的正性盐敏性(即遇盐变稠).     

Hydrogel formation via hybridization of oligonucleotides derivatized in water-soluble vinyl polymers

Succinimido-copolymers, poly(N,N-dimethylacrylamide-co-N-acryloyloxysuccinimide)s, were coupled with 5′-terminal-amino-modified oligodeoxyribonucleotides (ODNs) to produce water-soluble copolymers partially derivatized with ODNs in their side chains. The mixing and thermal melting measurements of dilute mixed aqueous solutions of an ODN-derivatized copolymer and their complementary ODN and mixed solutions of complementary ODN-derivatized copolymers were monitored by ultraviolet spectroscopy. The results showed that hybrids were formed with their complementary ODNs at room temperature, but dissociated at high temperature. Based on the hybridization between complementary base pairs of nucleic acids and its thermal dissociation characteristics, two types of thermoresponsive hydrogels were prepared: (1) a hydrogel formed via hybridization between an oligodeoxythymidylate (oligoT)-derivatized copolymer and an oligodeoxyadenylate (oligoA), and (2) a hydrogel formed by hybridization between complementary oligoT- and oligoA-derivatized copolymers. Thus, selfassociation due to specific intermolecular hydrogen bonding between nucleic acid base pairs enabled the preparation of a novel thermoresponsive hydrogel.     

Detection of Tumor Necrosis Factor Gene by Piezoelectric Nucleic Acid Senosr

A piezoelectric nucleic acid sensor was constructed ofr detection of tumor necrosis factor gene.Two methods were employed for immobilization of nucleic acid probe on gold electrode of piezoelectric crystal.The results show that polyethyleneimine adbesion and glutaraldehyde cross-linking method has higher sensitivity,stability and selectivity than protein A method.The solid-phase nucleic acid hybridization of oligo unclecotides and tumor necrosis factor target gene sequence were monitorde using this sensor.Tumor necrosis factor gene sequence(580bp) was detected by this nucleic acid sensor for the first time.     

Detection of Tumor Necrosis Factor Gene by Piezoelectric Nucleic Acid Sensor

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