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.     

Mg2+/Ca2+与DNA碱基和水相互作用的量子化学研究

采用高水平量子化学方法,MP2/6-311G(d,p),对气相中的Mg2+/Ca2+与DNA碱基和水的相互作用进行了研究,优化base-M-(H2O)n(M=Mg2+/Ca2+,n=1~2)的几何结构,计算其结合能和电荷分布等性质.结果表明,Mg2+与配体碱基及水的距离要比Ca2+与其配体距离更近,Mg2+与其配体的平均距离要比Ca2+小0.03nm左右.Mg2+与其配体的结合能要比Ca2+的大60~70kcal/mol左右,随着水数目的增加,离子与配体的结合能力逐渐减弱,Mg2+/Ca2+到水和碱基的平均距离越来越大,但变化幅度较小.金属离子的电荷主要转移到水中.     

Li+/Be2+与DNA碱基和水相互作用的量子化学研究

采用量子化学方法 B3LYP/6-311+G(d,p)对气相中的Li+/Be2+与4种DNA碱基和水的相互作用进行研究,优化Li+/Be2+与碱基及水形成的复合物的几何结构,计算其结合能和电荷分布等.结果表明,Be2+与配体碱基及水的距离要比与Li+的距离小0.3左右;Be2+与其配体的结合能要远比与Li+的配合能大.随着水数目的增加,Li+/Be2+到配位原子的平均距离越来越大,但变化幅度较小.在复合物中,金属离子的正电荷主要转移到水中.     

Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing

Almost all DNA polymerases show a strong preference for incorporating the nucleotide that forms the correct Watson-Crick base pair with the template base. In addition, the catalytic efficiencies with which any given polymerase forms the four possible correct base pairs are roughly the same. Human DNA polymerase-iota (hPoliota), a member of the Y family of DNA polymerases, is an exception to these rules. hPoliota incorporates the correct nucleotide opposite a template adenine with a several hundred to several thousand fold greater efficiency than it incorporates the correct nucleotide opposite a template thymine, whereas its efficiency for correct nucleotide incorporation opposite a template guanine or cytosine is intermediate between these two extremes. Here we present the crystal structure of hPoliota bound to a template primer and an incoming nucleotide. The structure reveals a polymerase that is 'specialized' for Hoogsteen base-pairing, whereby the templating base is driven to the syn conformation. Hoogsteen base-pairing offers a basis for the varied efficiencies and fidelities of hPoliota opposite different template bases, and it provides an elegant mechanism for promoting replication through minor-groove purine adducts that interfere with replication.     

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.     

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。     

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.     

Crossover between classical and quantum shot noise in chaotic cavities

The discreteness of charge in units of e led Schottky in 1918 to predict that the electrical current in a vacuum tube fluctuates even if all spurious noise sources are eliminated carefully. This phenomenon is now widely known as shot noise. In recent years, shot noise in mesoscopic conductors, where charge motion is quantum-coherent over distances comparable to the system size, has been studied extensively. In those experiments, charge does not propagate as an isolated entity through free space, as for vacuum tubes, but is part of a degenerate and quantum-coherent Fermi sea of charges. It has been predicted that shot noise in mesoscopic conductors can disappear altogether when the system is tuned to a regime where electron motion becomes classically chaotic. Here we experimentally verify this prediction by using chaotic cavities where the time that electrons dwell inside can be tuned. Shot noise is present for large dwell times, where the electron motion through the cavity is 'smeared' by quantum scattering, and it disappears for short dwell times, when the motion becomes classically deterministic.     

NMR study of parallel-stranded tetraplex formation by the hexadeoxynucleotide d(TG4T).

Multistranded DNA structures based upon guanine association have been proposed to be important in the structure of chromosome telomeres and in immunoglobulin class switching. Nucleic acids containing runs of guanine bases form a number of structures in vitro, including fold-back structures (Fig. 1a) and parallel-stranded quadruplex structures in DNA and RNA. The features of fold-back structures have now been determined at high-resolution. The different structures are probably based on a tetrad of hydrogen-bonded guanine bases (Fig. 1b), with buffer conditions and sequence effects mediating isomerization between the different forms. Here we use NMR spectroscopy to investigate the solution structure of the complex formed by the hexadeoxynucleotide d(TG4T) in the presence of sodium ions. We have observed the formation of a parallel-stranded quadruplex containing hydrogen-bonded tetrads of guanine. The parallel-stranded form differs significantly from the fold-back form, with individual nucleotide conformations being closer to those of B-form DNA.     

Unusual helical packing in crystals of DNA bearing a mutation hot spot

The target sequence of the restriction enzyme NarI (GGCGCC) is a hot spot for the -2 frameshift mutagenesis (GGCGCC----GGCC) induced by the chemical carcinogens such as N-2-acetyl-aminofluorene. Of the guanine residues, all of which show equal reactivity towards the carcinogen, only binding to the 3'-most proximal guanine within the NarI site is able to trigger the frameshift event. We selected the non-palindromic dodecamer d(ACCGGCGCCACA), whose sequence corresponds to the most mutagenic NarI site in pBR322 DNA; for X-ray structure analysis. Its molecular structure determined at 2.8 A resolution reveals significant deviations from the structure of canonical B-form DNA, with partial opening of three G-C base pairs, high propeller twist values and sequence-dependent three-centred hydrogen bonds. This crystal structure shows a novel kind of packing in which helices are locked together by groove-backbone interactions. The partial opening of G-C base pairs is induced by interactions of phosphate anionic oxygen atoms with the amino group of cytosine bases. This provides a model for close approach of DNA molecules during biological processes, such as recombination.     

Electrical conduction through DNA molecules

The question of whether DNA is able to transport electrons has attracted much interest, particularly as this ability may play a role as a repair mechanism after radiation damage to the DNA helix. Experiments addressing DNA conductivity have involved a large number of DNA strands doped with intercalated donor and acceptor molecules, and the conductivity has been assessed from electron transfer rates as a function of the distance between the donor and acceptor sites. But the experimental results remain contradictory, as do theoretical predictions. Here we report direct measurements of electrical current as a function of the potential applied across a few DNA molecules associated into single ropes at least 600 nm long, which indicate efficient conduction through the ropes. We find that the resistivity values derived from these measurements are comparable to those of conducting polymers, and indicate that DNA transports electrical current as efficiently as a good semiconductor. This property, and the fact that DNA molecules of specific composition ranging in length from just a few nucleotides to chains several tens of micrometres long can be routinely prepared, makes DNA ideally suited for the construction of mesoscopic electronic devices.     

Detection in vivo of protein-DNA interactions within the lac operon of Escherichia coli

Studies of the sequence-specific binding of proteins to DNA have so far relied on in vitro experiments using cloned restriction fragments containing the relevant DNA sequences. We have applied the genomic sequencing technique of Church and Gilbert to show that the interactions observed in vitro occur in vivo. We use this approach to study the binding of regulatory proteins to the lac operon in vivo and detect changes in the reactivity (inhibition or enhancement) of guanines to methylation by dimethyl sulphate caused by the proximity of proteins to the N-7 atom of these guanines. We can detect the simultaneous binding of the catobolite gene activator protein (CAP) and the Lac repressor to their specific recognition sequences, and following induction of the lac operon we observe effects that are related to RNA polymerase binding or RNA elongation. We have successfully used oligonucleotide probes as short as 17 bases to display genomic sequence.     

三-(五氟苯基)咔咯锰配合物与DNA碱基的相互作用理论研究

采用DFT/B3LYP方法对三-(五氟苯基)咔咯锰配合物(TPFC)Mn(Ⅲ)与DNA的4种碱基以及碱基对的轴向配位性质进行了理论研究.计算结果表明:以相同碱基的不同原子作为配位原子时,与(TPFC)Mn(Ⅲ)的配位能力不同,其中氧原子的配位能力强;(TPFC)Mn(Ⅲ)主要以插入的方式与A=T和C≡G碱基对结合;无论...     

Structure of an adenine-cytosine base pair in DNA and its implications for mismatch repair

Mutational pathways rely on introducing changes in the DNA double helix. This may be achieved by the incorporation of a noncomplementary base on replication or during genetic recombination, leading to substitution mutation. In vivo studies have shown that most combinations of base-pair mismatches can be accommodated in the DNA double helix, albeit with varying efficiencies. Fidelity of replication requires the recognition and excision of mismatched bases by proofreading enzymes and post-replicative mismatch repair systems. Rates of excision vary with the type of mismatch and there is some evidence that these are influenced by the nature of the neighbouring sequences. However, there is little experimental information about the molecular structure of mismatches and their effect on the DNA double helix. We have recently determined the crystal structures of several DNA fragments with guanine X thymine and adenine X guanine mismatches in a full turn of a B-DNA helix and now report the nature of the base pairing between adenine and cytosine in an isomorphous fragment. The base pair found in the present study is novel and we believe has not previously been demonstrated. Our results suggest that the enzymatic recognition of mismatches is likely to occur at the level of the base pairs and that the efficiency of repair can be correlated with structural features.     

粒子弱荷的研究

为了研究有质量的中微子，在理论上引入了粒子（基本费米子、中间玻色子和强子）弱荷的新概念首次报道了弱荷守恒定律，并提出了检验弱荷是否存在的实验方案，根据弱荷的手征性，合理地解释了宇称不守恒的原因，根据弱荷的对称性扩展了标准模型，指出所有的中微子都是有质量的Dirac粒子，但是右手中微子和左手反中微子的弱荷为零，它们不参与弱相互作用，因而称为暗粒子。     

平行苯环和夹心小基团体系间电荷转移的研究

利用密度泛函理论(DFT)对两苯环和夹心小基团NO、H2O和NH+4的体系进行了电荷转移研究.通过改变两苯环间距获得不同体系的能量和平衡几何构型.在模型A和模型C中当两苯环间距分别为0.60和0.58nm时有最大稳定化能,电荷转移显著.模型B中两苯环间距为0.53nm时有最大稳定化能,但电荷转移不显著.电子转移矩阵元Vrp在B3LYP 6-31G 水平用Koopmans理论计算.在模型A中随着两苯环间距增大,Vrp随之增大.Vrp在模型C的变化趋势与模型A的正好相反.在模型B中随着两苯环间距增大,Vrp先增大后减小.     

聚能射流长靶距下的侵彻仿真模型

提出了一个用于长靶距下聚能装药的断裂射流侵彻能力预测数值仿真模型.因聚能射流有很大的速度梯度,当它飞行数倍于标准炸高的距离后,射流被拉断为碎段,其穿甲能力大为降低.基于非线性瞬态动力学程序AUTODYN,研究了聚能装药射流的形成和大靶距下的断裂射流对不同靶体的侵彻和贯穿模拟.通过与实验结果比较,给出了一个用于预测长靶距下聚能装药射流侵彻能力的计算模型.与实验数据比较,所给模型可给出准确的预测结果.     

A specific partner for abasic damage in DNA.

In most models of DNA replication, Watson-Crick hydrogen bonding drives the incorporation of nucleotides into the new strand of DNA and maintains the complementarity of bases with the template strand. Studies with nonpolar analogues of thymine and adenine, however, have shown that replication is still efficient in the absence of hydrogen bonds. The replication of base pairs might also be influenced by steric exclusion, whereby inserted nucleotides need to be the correct size and shape to fit the active site against a template base. A simple steric-exclusion model may not require Watson-Crick hydrogen bonding to explain the fidelity of replication, nor should canonical purine and pyrimidine shapes be necessary for enzymatic synthesis of a base pair if each can fit into the DNA double helix without steric strain. Here we test this idea by using a pyrene nucleoside triphosphate (dPTP) in which the fluorescent 'base' is nearly as large as an entire Watson-Crick base pair. We show that the non-hydrogen-bonding dPTP is efficiently and specifically inserted by DNA polymerases opposite sites that lack DNA bases. The efficiency of this process approaches that of a natural base pair and the specificity is 10(2)-10(4)-fold. We use these properties to sequence abasic lesions in DNA, which are a common form of DNA damage in vivo. In addition to their application in identifying such genetic lesions, our results show that neither hydrogen bonds nor purine and pyrimidine structures are required to form a base pair with high efficiency and selectivity. These findings confirm that steric complementarity is an important factor in the fidelity of DNA synthesis.