Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance

Direct monitoring of single-molecule reactions has recently become a promising means of mechanistic investigation. However, the resolution of reaction pathways from single-molecule experiments remains elusive, primarily because of interference from extraneous processes such as bulk diffusion. Herein, we report a single-molecule kinetic investigation of DNA hybridization on a metal surface, as an example of a bimolecular association reaction. The tip of the scanning tunneling microscope (STM) was functionalized with single-stranded DNA (ssDNA), and hybridization with its complementary strand on an Au(111) surface was detected by the increase in the electrical conductance associated with the electron transport through the resulting DNA duplex. Kinetic analyses of the conductance changes successfully resolved the elementary processes, which involve not only the ssDNA strands and their duplex but also partially hybridized intermediate strands, and we found an increase in the hybridization efficiency with increasing the concentration of DNA in contrast to the knowledge obtained previously by conventional ensemble measurements. The rate constants derived from our single-molecule studies provide a rational explanation of these findings, such as the suppression of DNA melting on surfaces with higher DNA coverage. The present methodology, which relies on intermolecular conductance measurements, can be extended to a range of single-molecule reactions and to the exploration of novel chemical syntheses.

Hybridization of a single DNA molecule on a surface was investigated by electrical conductance measurements. The hybridization efficiency increases with increasing the DNA concentration, in contrast to preceding studies with ensemble studies.     

Physicochemical properties of quaternized poly(amidoamine) dendrimers with four octyl chains

A cationic dendrimer-type tetrameric surfactant (C(8)qbG0) with four octyl chains and four ammonium groups was synthesized by the reaction of poly(amidoamine) dendrimers with generation of zero and glycidyldimethyloctylammonium bromide. The physicochemical properties of C(8)qbG0 and of their mixtures with sodium dodecyl sulfate (SDS) were characterized by investigating surface tension, electrical conductivity, fluorescence of pyrene, and dynamic light-scattering. The critical micelle concentration (cmc) of C(8)qbG0 was 13 mmol dm(-3) at the concentration of one terminal group and the surface tension at the cmc attained 34 mN m(-1). The occupied area of C(8)qbG0 was 1.94 nm(2) molecule(-1), indicating that the tetrameric dendrimers adsorb widely at the air/water interface. The fluorescence intensity ratio of the first-to-third band in the emission spectra of pyrene for C(8)qbG0 decreased from around the cmc obtained by the surface tension measurement. The hydrodynamic radius of C(8)qbG0 determined by dynamic light-scattering was about 1.3 nm. The addition of SDS to the aqueous solutions of C(8)qbG0 enhanced the surface activities; the mixtures exhibited lower cmc, lower surface tension, and higher solubilization of pyrene than SDS alone. It was found that the mixtures of C(8)qbG0 and SDS form large aggregates due to the interactions between their alkyl chains as well as hydrophilic groups.     

Ion-exchanger phase spectrophotometry for trace cobalt

An ion-exchanger phase spectrophotometric method with disodium 1-nitroso-2-naphthol-3,6-disulphonate (Nitroso-R salt) has been developed for the determination of cobalt(II) at 0.1 mug/l. levels in sea-water. The sensitivity is about 1000 times that for conventional spectrophotometry.     

Determination of 6-methyladenine in DNA by high-performance liquid chromatography.

A method for the determination of 6-methyladenine (6MA) by high-performance liquid chromatography (HPLC) has been developed. DNA bases were separated by using the strong cation-exchange resin Zipax SCX. Purine bases were obtained by hydrolysis and dialysis of DNA and analysed by HPLC. 6MA in DNA from Escherichia coli was determined by the proposed method. It is suggested that the method could be applicable to analyses of 6MA from other biological sources.     

Synthesis of inherently dissymmetric polyamides,

The preparation of polyamides from derivatives of optically active biphenic acid is described. The diacid chlorides chosen were 2,2′-dinitro-6,6′-dimethylbiphenyl-4,4′-dicarbonyl chloride and 2,2′-dichloro-6,6′-dimethylbiphenyl-4,4′-dicarbonyl chloride, the diamines were phenyldiamines (o-, m-, p-) piperazine, trans-2,5-dimethylpiperazine, and 1,2-piperaazolidine. Polymerization was carried out by the method of interfacial polycondensation. The polymers of aromatic diamines were insoluble in common organic solvents but soluble in dimethylformamide containing 5% lithium chloride, triesters of phosphoric acid, and methanesulfonic acid. The polymers of aliphatic diamines were also insoluble in common organic solvents but soluble in trifluoroethanol. All polymers had melting points higher than 280°C.     

A new synthetic route to phomoidride B and its derivatives

We have developed a new synthetic route to phomoidride B, which could also be applied to the synthesis of phomoidride B derivatives using Pd-catalyzed coupling reaction of a thiolester with an organozinc reagent. In addition, direct construction of the maleic anhydride moiety has been achieved by a Pd-catalyzed carbonylation reaction.     

Structure-activity studies on triazolothienodiazepine derivatives as platelet-activating factor antagonists.

A series of triazolodiazepines was synthesized and evaluated for anti-platelet activating factor (PAF) activities. Structure-activity relationship (SAR) studies on this series revealed that the introduction of a methyl group into the 8-position of the thienodiazepine nucleus can lead to a lengthening of the duration of action. Introduction of a methyl group produced an asymmetric center and the enantiomers so formed were separated with an optical resolving column. In the in vitro assay system, the (+)-isomers displayed 50-200 times more potent anti-PAF activity than the (-)-isomers. After comparison of toxicology and pharmacokinetics, (+)-6-(2-chlorophenyl)-3- cyclopropanecarbonyl-8,11-dimethyl-2,3,4,5-tetrahydro-8H-pyrido[4' ,3':4,5]thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepine (35(+)-isomer, E6123) was selected from among the compounds synthesized as a candidate for clinical study.     

Copper-catalyzed oxidative cleavage of carbon-carbon double bond of enol ethers with molecular oxygen

A novel CC bond cleavage reaction of aromatic enol ethers (1) to give ketones (2) using molecular oxygen as oxidant is described. Among the examined catalysts (Cu(II), Pd(II), Ru(II), and H⁺), CuCl₂ exhibited the highest activity. The reaction proceeded smoothly with several kinds of substrates.