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.     

Enantioselective synthesis of near enantiopure compound by asymmetric autocatalysis triggered by asymmetric photolysis with circularly polarized light

Right- and left-handed circularly polarized light (CPL) has been proposed as one of the origins of homochirality of biomolecules. However, the enantiomeric excess induced by CPL has been only very low (<2% ee). We found the unprecedented example of asymmetric autocatalysis triggered directly by a chiral physical factor, that is, right- and left-handed CPL, leading to a near enantiopure compound. Asymmetric photolysis of racemic pyrimidyl alkanol by r-CPL irradiation followed by asymmetric autocatalysis affords (R)-pyrimidyl alkanol with >99.5% ee. On the other hand, irradiation with l-CPL affords (S)-pyrimidyl alkanol with >99.5% ee. Thus, chiral physical power, such as CPL, in conjunction with asymmetric autocatalysis, provides a highly enantioenriched compound.     

Catalytic cyclopropanation of alkenes via (2-furyl)carbene complexes from 1-benzoyl-cis-1-buten-3-yne with transition metal compounds

The reaction of alkenes with conjugated ene-yne-ketones, such as 1-benzoyl-2-ethynylcycloalkenes, with a catalytic amount of Cr(CO)(5)(THF) gave 5-phenyl-2-furylcyclopropane derivatives in good yields. The key intermediate of this cyclopropanation is a (2-furyl)carbene complex generated by a nucleophilic attack of carbonyl oxygen to an internal alkyne carbon in pi-alkyne complex or sigma-vinyl cationic complex. A wide range of late transition metal compounds, such as [RuCl(2)(CO)(3)](2), [RhCl(cod)](2), [Rh(OAc)(2)](2), PdCl(2), and PtCl(2), also catalyzes the cyclopropanation of alkenes with ene-yne-ketones effectively. When the reactions were carried out with dienes as a carbene acceptor, the more substituted or more electron-rich alkene moiety was selectively cyclopropanated with the (2-furyl)carbenoid intermediate.     

The stereoisomers of 3,7,11-trimethyldodeca-2,6,10-triene

Four geometrical steroisomers of 3,7,11-trimethyldodeca-2,6,10-triene have been synthesized. The PMR and ¹³C NMR spectra of these compounds provide important information on the geometry of Me substituted double bonds, while the mass spectra distinguish (E and Z,E)-isomers from (E and Z,Z)-isomers.     

Synthesis and antihypertensive activity of 3-acetoxy-2,3-dihydro-5-[2- (dimethylamino)ethyl]-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one (diltiazem) derivatives having substituents at the 8 position.

In order to improve the potency and duration of biological actions of diltiazem, a number of 1,5-benzothiazepine derivatives having the substituents at the 8 position were prepared and evaluated for their antihypertensive activity in spontaneously hypertensive rats. The introduction of methyl, ethyl, isopropyl, benzyl, methoxy, ethoxy, phenoxy, and methylthio groups increased the antihypertensive activity and prolonged duration of action, whereas cyclohexyl, cyclopentoxy, tolyloxy, p-methoxyphenoxy and phenylthio derivatives were less active than diltiazem. Among them, the 8-benzyl and phenoxy derivatives showed the most potent and long-lasting antihypertensive action.     

Absolute asymmetric photoreactions of aliphatic amino acids by circularly polarized synchrotron radiation: critically pH-dependent photobehavior

The absolute asymmetric photoreaction (AAP) of racemic aliphatic amino acids, such as alanine (Ala) and leucine (Leu), by left- and right-handed circularly polarized light (l- and r-CPL) irradiation was investigated in aqueous solutions at various pHs, by using the Onuki-type polarizing undulator installed in an electron storage ring. The magnitude of the optical purity (op) generated and the enantiomer-enriching mechanism operative in the AAP were found to be entirely dependent on the ionic state (and thus pH) of the amino/carboxylic acid moieties. At pH 1, the op of Ala and Leu determined by circular dichroism (CD) spectral measurement gradually developed with CPL irradiation, according to Kagan's equation. In contrast, irradiation at pH 7 gave op's much smaller than the theoretical values predicted by Kagan's equation. However, it turned out that the photodecomposition at pH 7 produces the corresponding alpha-hydroxycarboxylic acids stereoselectively, the CD sign of which is just opposite to that of the remaining amino acid, thus affording the apparently small op. It is concluded that, irrespective of solution pH, the AAP of amino acid proceeds upon CPL irradiation. At pH 1, the photodecomposition of valine, Leu, and isoleucine occurs via a Norrish type II mechanism, which is also applicable to other amino acids possessing a gamma-hydrogen. In the case of amino acids lacking a gamma-hydrogen, such as glycine and Ala, the photodecomposition mechanism is a photodeamination/hydroxylation and a Norrish type I reaction. At pH 7, the main photoproducts were ammonia and alpha-hydroxycarboxylic acids that were produced via photodeamination.     

Structures of euglobal-G1, -G2, and -G3 from Eucalyptus grandis, three new inhibitors of Epstein-Barr virus activation

Three new euglobals with acylphloroglucinol-monoterpene structures, named euglobal -G1 (1), -G2 (2), and -G3 (3) were isolated from the chloroform extract of the juvenile leaves of Eucalyptus grandis (Myrtaceae). The structures of these new compounds were determined on the basis of their spectral data. The compounds strongly inhibited the Epstein-Barr virus activation.     

PHOTOCYTOTOXICITY OF WATER-SOLUBLE METALLOPORPHYRIN DERIVATIVES

Abstract— A new water-soluble porphyrin derivative, 2,4-bis(1-decyloxyethyl)-deuteroporphyrinyl–6,7-bisaspartic acid(C–10-DP), and its metal complexes (Ga, In, Sn, Zn, Mn, Cu, Ni and Fe) were examined for their physicochemical properties (absorption, fluorescene, triplet lifetime and partition coefficient) and photocytotoxicity on HeLa cells. The five derivatives with longer(>1ms) triplet lifetimes (free base, Zn, Ga, In and Sn complexes) exhibited remarkable photocytotoxicity, and the other derivatives (Mn, Cu, Ni and Fe), which had or were deduced to have fairly short (<0.01 ms) triplet lifetimes, manifested no photocytotoxicity, indicating that the triplet lifetime of these derivatives played a significant role in their photocytotoxicity. Cellular fluorescence due to C10-DP and its gallium complex was observed mainly on the plasma membrane at the concentrations showing significant photocytotoxicity with low (<32.6%) cytotoxicity in the dark(2–10 μM).