Direct observation of second-order atom tunnelling

Tunnelling of material particles through a classically impenetrable barrier constitutes one of the hallmark effects of quantum physics. When interactions between the particles compete with their mobility through a tunnel junction, intriguing dynamical behaviour can arise because the particles do not tunnel independently. In single-electron or Bloch transistors, for example, the tunnelling of an electron or Cooper pair can be enabled or suppressed by the presence of a second charge carrier due to Coulomb blockade. Here we report direct, time-resolved observations of the correlated tunnelling of two interacting ultracold atoms through a barrier in a double-well potential. For the regime in which the interactions between the atoms are weak and tunnel coupling dominates, individual atoms can tunnel independently, similar to the case of a normal Josephson junction. However, when strong repulsive interactions are present, two atoms located on one side of the barrier cannot separate, but are observed to tunnel together as a pair in a second-order co-tunnelling process. By recording both the atom position and phase coherence over time, we fully characterize the tunnelling process for a single atom as well as the correlated dynamics of a pair of atoms for weak and strong interactions. In addition, we identify a conditional tunnelling regime in which a single atom can only tunnel in the presence of a second particle, acting as a single atom switch. Such second-order tunnelling events, which are the dominating dynamical effect in the strongly interacting regime, have not been previously observed with ultracold atoms. Similar second-order processes form the basis of superexchange interactions between atoms on neighbouring lattice sites of a periodic potential, a central component of proposals for realizing quantum magnetism.     

Direct electrochemical detection of PCR product based on charge transfer through DNA

Human genome project and genetic identification for inherited diseases will definitely have a profound impact on the diagnosis of diseases[1], which calls for rapid and accurate assays of DNA. Among different types of sensors, electrochemical DNA biosensors offer a promising alter-native means[2,3]. Recent efforts to elucidate the mecha-nism of charge transfer in DNA have demonstrated that the charge transfer is sensitive to the perturbation in base stack[4,5]. Long-range charge transfer i…     

Direct measurement of hole transport dynamics in DNA

Our understanding of oxidative damage to double helical DNA and the design of DNA-based devices for molecular electronics is crucially dependent upon elucidation of the mechanism and dynamics of electron and hole transport in DNA. Electrons and holes can migrate from the locus of formation to trap sites, and such migration can occur through either a single-step "superexchange" mechanism or a multistep charge transport "hopping" mechanism. The rates of single-step charge separation and charge recombination processes are found to decrease rapidly with increasing transfer distances, whereas multistep hole transport processes are only weakly distance dependent. However, the dynamics of hole transport has not yet been directly determined. Here we report spectroscopic measurements of photoinduced electron transfer in synthetic DNA that yield rate constants of approximately 5 x 10(7) s(-1) and 5 x 10(6) s(-1), respectively, for the forward and return hole transport from a single guanine base to a double guanine base step across a single adenine. These rates are faster than processes leading to strand cleavage, such as the reaction of guanine cation radical with water, thus permitting holes to migrate over long distances in DNA. However, they are too slow to compete with charge recombination in contact ion pairs, a process which protects DNA from photochemical damage.     

Carcinogenesis switched on by DNA cross-link between complementary bases aroused by aflatoxin and N-nitroso compounds

The di-region theory put forward by Dai Qianhuan, a molecular mechanism of chemical carcinogenesis, concluded that the carcinogenesis induced by most of the environmental carcinogens is switched on by the cross-linking between DNA complementary bases aroused by the bifunctional alkylation of their metabolic intermediates. It was evidenced in this paper with DNA filter elution method that one carcinogenic mycotoxin, aflatoxin G1, four carcinogenic N-nitroso compounds, N-nitrosodiethyl-amine, N-nitrosodibutyl-amine, N-nitrosomorpholine and N-nitrosopyrrolidine, one carcinogenic diazo color, 4-dimethylaminodiazobenzene and one carcinogenic nitrogen-containing heterocyclic compound, quinoline, all induced DNA interstrands cross-linking with dosage correlation after metabolic activation. However, the non-carcinogens in corresponding series for control, aflatoxin B2, N-nitroso-diphenylamine, 4′-bromo-4-dimethylaminodiazobenzene and isoquinoline, cannot induce DNA interstrands cross-linking at all in the same condition. A method for the determination of cross-linking ratio between DNA complementary bases in total DNA interstrands cross-linking, which has no monitoring measure as yet, has been established for the first time based upon a 24 hour repairing experiment. The DNA complementary pair cross-linking ratio induced by a metabolized carcinogen is correlated with its carcinogenic potential. It may be concluded that the mutations including point and frameshift mutagenesis induced by aflatoxin and other carcinogens are switched on by their corresponding cross-linking base pair between complementary bases. Therefore, the di-region theory is a reasonable molecular mechanism for chemical, endogenous and physical carcinogenesis.     

Direct measurement of electrical transport through DNA molecules

Attempts to infer DNA electron transfer from fluorescence quenching measurements on DNA strands doped with donor and acceptor molecules have spurred intense debate over the question of whether or not this important biomolecule is able to conduct electrical charges. More recently, first electrical transport measurements on micrometre-long DNA 'ropes', and also on large numbers of DNA molecules in films, have indicated that DNA behaves as a good linear conductor. Here we present measurements of electrical transport through individual 10.4-nm-long, double-stranded poly(G)-poly(C) DNA molecules connected to two metal nanoelectrodes, that indicate, by contrast, large-bandgap semiconducting behaviour. We obtain nonlinear current-voltage curves that exhibit a voltage gap at low applied bias. This is observed in air as well as in vacuum down to cryogenic temperatures. The voltage dependence of the differential conductance exhibits a peak structure, which is suggestive of the charge carrier transport being mediated by the molecular energy bands of DNA.     

Carcinogenesis of asbestos switched on by inducing cross-linkage between DNA complementary pair bases

Since the beginning of the 1980s, Dai Qianhuan predicted based upon his di-region theory that the carcinogenesis switched on by the so-called physical carcinogenic factors including radiation, asbestos and foreign matter implantation, is just initiated through the cross-linking between DNA complementary pair bases induced by them. In this note, it was evidenced with the DNA filter elution method that the oxygenase activated by asbestos induces the cross-linking between DNA inter-strands and DNA-protein with dosage correlation, in which over 80% of DNA inter-strand cross-link ratio account for the total cross-link ratio. Obviously, both of the cross-linkages are just induced by hydroxyl free radical, HO ·, because the ferrous ion increased the cross-link ratios up to several times through Fenton reaction and vitamin C inhibited the cross-link ratios with factors of 8–9 by destroying the hydroxyl radical. Non-carcinogen but with lower free radical formation energy, pyrene, by culturing with asbestos gave 3–4 times cross-link ratios than the original ratios induced by asbestos only. Estradiol, an endogenous carcinogen, as a bio-electrophilic species but with higher free radical formation energy by culturing with asbestos, gave only 1.2 time cross-link ratios than expected ones. Ferrous ion which can increase HO · concentration through Fenton reaction, increased the ratios to 2–2.5 times in the former case but only 1.2 time in the latter case. Vitamin C, a free radical scavenger, gave a powerful inhibition to the cross-linking with a factor of 8–11 in the former case but a weak inhibition with a factor of 1.2 only in the latter case. So, it is evidenced further that the cross-linkages induced by asbestos are originated from hydroxyl radical. Reasonable structures of the cross-linking products induced by asbestos or hydroxyl radical have been depicted based upon AMI MO theory. These structures have been verified further by a reasonable explanation of the mutational spectrum induced by hydroxyl radical.     

Capture of hydroxymethylene and its fast disappearance through tunnelling

Singlet carbenes exhibit a divalent carbon atom whose valence shell contains only six electrons, four involved in bonding to two other atoms and the remaining two forming a non-bonding electron pair. These features render singlet carbenes so reactive that they were long considered too short-lived for isolation and direct characterization. This view changed when it was found that attaching the divalent carbon atom to substituents that are bulky and/or able to donate electrons produces carbenes that can be isolated and stored. N-heterocyclic carbenes are such compounds now in wide use, for example as ligands in metathesis catalysis. In contrast, oxygen-donor-substituted carbenes are inherently less stable and have been less studied. The pre-eminent case is hydroxymethylene, H-C-OH; although it is the key intermediate in the high-energy chemistry of its tautomer formaldehyde, has been implicated since 1921 in the photocatalytic formation of carbohydrates, and is the parent of alkoxycarbenes that lie at the heart of transition-metal carbene chemistry, all attempts to observe this species or other alkoxycarbenes have failed. However, theoretical considerations indicate that hydroxymethylene should be isolatable. Here we report the synthesis of hydroxymethylene and its capture by matrix isolation. We unexpectedly find that H-C-OH rearranges to formaldehyde with a half-life of only 2 h at 11 K by pure hydrogen tunnelling through a large energy barrier in excess of 30 kcal mol(-1).     

Direct observation of individual RecA filaments assembling on single DNA molecules

Escherichia coli RecA is essential for the repair of DNA double-strand breaks by homologous recombination. Repair requires the formation of a RecA nucleoprotein filament. Previous studies have indicated a mechanism of filament assembly whereby slow nucleation of RecA protein on DNA is followed by rapid growth. However, many aspects of this process remain unclear, including the rates of nucleation and growth and the involvement of ATP hydrolysis, largely because visualization at the single-filament level is lacking. Here we report the direct observation of filament assembly on individual double-stranded DNA molecules using fluorescently modified RecA. The nucleoprotein filaments saturate the DNA and extend it approximately 1.6-fold. At early time points, discrete RecA clusters are seen, permitting analysis of single-filament growth from individual nuclei. Formation of nascent RecA filaments is independent of ATP hydrolysis but is dependent on the type of nucleotide cofactor and the RecA concentration, suggesting that nucleation involves binding of approximately 4-5 ATP-RecA monomers to DNA. Individual RecA filaments grow at rates of 3-10 nm s(-1). Growth is bidirectional and, in contrast to nucleation, independent of nucleotide cofactor, suggesting addition of approximately 2-7 monomers s(-1). These results are in accord with extensive genetic and biochemical studies, and indicate that assembly in vivo is controlled at the nucleation step. We anticipate that our approach and conclusions can be extended to the related eukaryotic counterpart, Rad51 (see ref.), and to regulation by assembly mediators.     

基于熵测度和SQP方法的跳频信号时频表示

提出了一种基于三阶Renyi熵测度的双向高斯核函数,分析了核参数与熵测度的变化规律,并利用逐步二次规划法对其进行优化.与信号相关径向高斯核函数时频分布相比,该方法不需要任何先验假定,能够有效反映交叉项在时频分布中的大小,获取优化的时频表示,从而提高了跳频信号的参数估计精度,同时可以适应低信噪比环境.仿真结果验证了基于熵测度优化时频表示法分析跳频信号的有效性和实用性.     

Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase

The genomes of aerobic organisms suffer chronic oxidation of guanine to the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases misread oxoG residues and insert adenine instead of cytosine opposite the oxidized base. Both bases in the resulting A*oxoG mispair are mutagenic lesions, and both must undergo base-specific replacement to restore the original C*G pair. Doing so represents a formidable challenge to the DNA repair machinery, because adenine makes up roughly 25% of the bases in most genomes. The evolutionarily conserved enzyme adenine DNA glycosylase (called MutY in bacteria and hMYH in humans) initiates repair of A*oxoG to C*G by removing the inappropriately paired adenine base from the DNA backbone. A central issue concerning MutY function is the mechanism by which A*oxoG mispairs are targeted among the vast excess of A*T pairs. Here we report the use of disulphide crosslinking to obtain high-resolution crystal structures of MutY-DNA lesion-recognition complexes. These structures reveal the basis for recognizing both lesions in the A*oxoG pair and for catalysing removal of the adenine base.     

Direct observation of ligand recognition by T cells

The activation of T cells through interaction of their T-cell receptors with antigenic peptide bound to major histocompatibility complex (MHC) on the surface of antigen presenting cells (APCs) is a crucial step in adaptive immunity. Here we use three-dimensional fluorescence microscopy to visualize individual peptide-I-E(k) class II MHC complexes labelled with the phycobiliprotein phycoerythrin in an effort to characterize T-cell sensitivity and the requirements for forming an immunological synapse in single cells. We show that T cells expressing the CD4 antigen respond with transient calcium signalling to even a single agonist peptide-MHC ligand, and that the organization of molecules in the contact zone of the T cell and APC takes on the characteristics of an immunological synapse when only about ten agonists are present. This sensitivity is highly dependent on CD4, because blocking this molecule with antibodies renders T cells unable to detect less than about 30 ligands.     

蛋白质电子跳跃转移与溶剂化电子结构

本文综述了生物体内电荷跳跃转移的一些新特征。重点阐述了蛋白质电荷转移过程中一种可能的中间体--溶剂化电子--的结构性质特征以及在蛋白质长程电荷转移中的重要作用。蛋白质中存在着诸多基团、分子片或电正性区域,比如:质子化的碱性支链基团、芳香环、极性肽链、螺旋及结构水簇等,它们可以俘获电子、然后释放,扮演着电子跳跃转移中继站的作用。这种基于溶剂化电子的电子跳跃转移模式构成了蛋白质内电子长程转移的新途径。     

Direct measurement of the transfer rate of chloroplast DNA into the nucleus

Gene transfer from the chloroplast to the nucleus has occurred over evolutionary time. Functional gene establishment in the nucleus is rare, but DNA transfer without functionality is presumably more frequent. Here, we measured directly the transfer rate of chloroplast DNA (cpDNA) into the nucleus of tobacco plants (Nicotiana tabacum). To visualize this process, a nucleus-specific neomycin phosphotransferase gene (neoSTLS2) was integrated into the chloroplast genome, and the transfer of cpDNA to the nucleus was detected by screening for kanamycin-resistant seedlings in progeny. A screen for kanamycin-resistant seedlings was conducted with about 250,000 progeny produced by fertilization of wild-type females with pollen from plants containing cp-neoSTLS2. Sixteen plants of independent origin were identified and their progenies showed stable inheritance of neoSTLS2, characteristic of nuclear genes. Thus, we provide a quantitative estimate of one transposition event in about 16,000 pollen grains for the frequency of transfer of cpDNA to the nucleus. In addition to its evident role in organellar evolution, transposition of cpDNA to the nucleus in tobacco occurs at a rate that must have significant consequences for existing nuclear genes.     

Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast

Conjugative plasmids of Escherichia coli can mobilize DNA transmission from this bacterium to the yeast Saccharomyces cerevisiae. The process shares some of the features of conjugation between bacteria and could be evolutionarily significant in promoting trans-kingdom genetic exchange.     

Direct observation of the alignment of ferromagnetic spins by antiferromagnetic spins

The arrangement of spins at interfaces in a layered magnetic material often has an important effect on the properties of the material. One example of this is the directional coupling between the spins in an antiferromagnet and those in an adjacent ferromagnet, an effect first discovered in 1956 and referred to as exchange bias. Because of its technological importance for the development of advanced devices such as magnetic read heads and magnetic memory cells, this phenomenon has received much attention. Despite extensive studies, however, exchange bias is still poorly understood, largely due to the lack of techniques capable of providing detailed information about the arrangement of magnetic moments near interfaces. Here we present polarization-dependent X-ray magnetic dichroism spectro-microscopy that reveals the micromagnetic structure on both sides of a ferromagnetic-antiferromagnetic interface. Images of thin ferromagnetic Co films grown on antiferromagnetic LaFeO3 show a direct link between the arrangement of spins in each material. Remanent hysteresis loops, recorded for individual ferromagnetic domains, show a local exchange bias. Our results imply that the alignment of the ferromagnetic spins is determined, domain by domain, by the spin directions in the underlying antiferromagnetic layer.