Direct observation of hole transfer through double-helical DNA over 100 A

Mechanism of photo-induced electron transfer and the subsequent hole transfer in DNA has been studied extensively, but so far we are not aware of any reliable report of the observation of the long-distance hole-transfer process. In this article, we demonstrate the results of direct observation for the long-distance hole transfer in double-helical DNA over 100 A with time-resolved transient absorption measurements. DNA conjugated with naphthalimide (NI) and phenothiazine (PTZ) (which worked as electron-acceptor and donor molecules, respectively) at both 5' ends was synthesized to observe the hole-transfer process. Site-selective charge injection into G by means of the adenine-hopping process was accomplished by excitation of NI with a 355-nm laser flash. Transient absorption around 400 nm, which was assigned to the NI radical anion, was observed immediately after the irradiation of a laser flash, indicating that the charge separation between NI and the nearest G occurred. Then, the transient absorption of the PTZ radical cation (PTZ(*+)) at 520 nm was emerged, which was attributed to the hole transfer through DNA to the PTZ site. By monitoring the time profiles of the transient absorption of PTZ(*+) for NI-A(6)-(GA)(n)-PTZ and NI-A(6)-(GT)(n)-PTZ (n = 2, 3, 4, 6, 8, 12) (base sequences correspond to those for DNA modified with NI), the long-distance hole-transfer process from G to PTZ, which occurred in the time scale of microsecond to millisecond, was observed directly. By assuming an average distance of 3.4 A between base-pairs, total distance reaches 100 A for n = 12 sequences. Our results clearly show the direct observation of the long-distance hole transfer over 100 A.     

Single-molecule observation of DNA charge transfer

DNA charge transfer highly depends on the electronic interaction between base pairs and reflects the difference in the base composition and sequence. For the purpose of investigating the charge transfer process of individual DNA molecules and the optical readout of DNA information at the single-molecule level, we performed single-molecule observation of the DNA charge transfer process by using single-molecule fluorescence spectroscopy. The DNA charge transfer process, leading to the oxidation of the fluorescent dye, was explored by monitoring the on-off signal of the dye after the charge injection by the excitation of a photosensitizer. The photobleaching efficiency of the dyes by the DNA charge transfer specifically depended on the base sequence and mismatch base pair, demonstrating the discrimination of the individual DNA information. Based on this approach, the optical readout of a single-base mismatch contained in a target DNA was performed at the single-molecule level.     

Cellular asymmetry and individuality in directional sensing

It is generally assumed that single cells in an isogenic population, when exposed to identical environments, exhibit the same behavior. However, it is becoming increasingly clear that, even in a genetically identical population, cellular behavior can vary significantly among cells. Here we explore this variability in the gradient-sensing response of Dictyostelium cells when exposed to repeated spatiotemporal pulses of chemoattractant. Our experiments show the response of a single cell to be highly reproducible from pulse to pulse. In contrast, a large variability in the response direction and magnitude is observed from cell to cell, even when different cells are exposed to the same pulse. First, these results indicate that the gradient-sensing network has inherent asymmetries that can significantly impact the ability of cells to faithfully sense the direction of extracellular signals (cellular asymmetry). Second, we find that the magnitude of this asymmetry varies greatly among cells. Some cells are able to accurately follow the direction of an extracellular stimulus, whereas, in other cells, the intracellular asymmetry dominates, resulting in a polarization axis that is independent of the direction of the extracellular cue (cellular individuality). We integrate these experimental findings into a model that treats the effective signal a cell detects as the product of the extracellular signal and the asymmetric intracellular signal. With this model we successfully predict the population response. This cellular individuality and asymmetry might fundamentally limit the fidelity of signal detection; in contrast, however, it might be beneficial by diversifying phenotypes in isogenic populations.     

p53 binds single-stranded DNA ends and catalyzes DNA renaturation and strand transfer.

The p53 tumor-suppressor protein has previously been shown to bind double-stranded and single-stranded DNA. We report that the p53 protein can bind single-stranded DNA ends and catalyze DNA renaturation and DNA strand transfer. Both a bacterially expressed wild-type p53 protein and a glutathione S-transferase-wild-type p53 fusion protein catalyzed renaturation of different short (25- to 76-nt) complementary single-stranded DNA fragments and promoted strand transfer between short (36-bp) duplex DNA and complementary single-stranded DNA. Mutant p53 fusion proteins carrying amino acid substitutions Glu-213, Ile-237, or Tyr-238, derived from mutant p53 genes of Burkitt lymphomas, failed to catalyze these reactions. Wild-type p53 had significantly higher binding affinity for short (36- to 76-nt) than for longer (> or = 462-nt) single-stranded DNA fragments in an electrophoretic mobility-shift assay. Moreover, electron microscopy showed that p53 preferentially binds single-stranded DNA ends. Binding of DNA ends to p53 oligomers may allow alignment of complementary strands. These findings suggest that p53 may play a direct role in the repair of DNA breaks, including the joining of complementary single-stranded DNA ends.     

Femtosecond direct observation of charge transfer between bases in DNA

Charge transfer in supramolecular assemblies of DNA is unique because of the notion that the pi-stacked bases within the duplex may mediate the transport, possibly leading to damage and/or repair. The phenomenon of transport through pi-stacked arrays over a long distance has an analogy to conduction in molecular electronics, but the mechanism still needs to be determined. To decipher the elementary steps and the mechanism, one has to directly measure the dynamics in real time and in suitably designed, structurally well characterized DNA assemblies. Here, we report our first observation of the femtosecond dynamics of charge transport processes occurring between bases within duplex DNA. By monitoring the population of an initially excited 2-aminopurine, an isomer of adenine, we can follow the charge transfer process and measure its rate. We then study the effect of different bases next to the donor (acceptor), the base sequence, and the distance dependence between the donor and acceptor. We find that the charge injection to a nearest neighbor base is crucial and the time scale is vastly different: 10 ps for guanine and up to 512 ps for inosine. Depending on the base sequence the transfer can be slowed down or inhibited, and the distance dependence is dramatic over the range of 14 A. These observations provide the time scale, and the range and efficiency of the transfer. The results suggest the invalidity of an efficient wire-type behavior and indicate that long-range transport is a slow process of a different mechanism.     

The terminal nucleotide of the Mu genome controls catalysis of DNA strand transfer

Members of the transposase/retroviral-integrase superfamily use a single active site to perform at least two reactions during transposition of a DNA transposon or a retroviral cDNA. They hydrolyze a DNA sequence at the end of the mobile DNA and then join this DNA end to a target DNA (a reaction called DNA strand transfer). Critical to understanding the mechanism of recombination is elucidating how these distinct reactions are orchestrated by the same active site. Here we find that DNA substrates terminating in a dideoxynucleotide allow Mu transposase to hydrolyze a target DNA, combining aspects of both natural reactions. Analyses of the sequence preferences for target hydrolysis and of the structure of the cleaved product indicate that this reaction is promoted by the active site in the conformation that normally promotes DNA strand transfer. Dissecting the DNA requirements for target hydrolysis reveals that the ribose of the last nucleotide of the Mu DNA activates transposase's catalytic potential, even when this residue is not a direct chemical participant. These findings provide insight into the molecular mechanism insuring that DNA strand transfer ordinarily occurs rather than inappropriate DNA cleavage. The required presence of the terminal nucleotide in the transposase active site creates a great advantage for the attached 3'OH to serve as nucleophile.     

Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome

We have investigated the question whether during chromosomal DNA replication in Escherichia coli the two DNA strands may be replicated with differential accuracy. This possibility of differential replication fidelity arises from the distinct modes of replication in the two strands, one strand (the leading strand) being synthesized continuously, the other (the lagging strand) discontinuously in the form of short Okazaki fragments. We have constructed a series of lacZ strains in which the lac operon is inserted into the bacterial chromosome in the two possible orientations with regard to the chromosomal replication origin oriC. Measurement of lac reversion frequencies for the two orientations, under conditions in which mutations reflect replication errors, revealed distinct differences in mutability between the two orientations. As gene inversion causes a switching of leading and lagging strands, these findings indicate that leading and lagging strand replication have differential fidelity. Analysis of the possible mispairs underlying each specific base pair substitution suggests that the lagging strand replication on the E. coli chromosome may be more accurate than leading strand replication.     

Cranial asymmetry in Eocene archaeocete whales and the evolution of directional hearing in water

Eocene archaeocete whales gave rise to all modern toothed and baleen whales (Odontoceti and Mysticeti) during or near the Eocene-Oligocene transition. Odontocetes have asymmetrical skulls, with asymmetry linked to high-frequency sound production and echolocation. Mysticetes are generally assumed to have symmetrical skulls and lack high-frequency hearing. Here we show that protocetid and basilosaurid archaeocete skulls are distinctly and directionally asymmetrical. Archaeocete asymmetry involves curvature and axial torsion of the cranium, but no telescoping. Cranial asymmetry evolved in Eocene archaeocetes as part of a complex of traits linked to directional hearing (such as pan-bone thinning of the lower jaws, mandibular fat pads, and isolation of the ear region), probably enabling them to hear the higher sonic frequencies of sound-producing fish on which they preyed. Ultrasonic echolocation evolved in Oligocene odontocetes, enabling them to find silent prey. Asymmetry and much of the sonic-frequency range of directional hearing were lost in Oligocene mysticetes during the shift to low-frequency hearing and bulk-straining predation.     

Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins

Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels.     

B protein of bacteriophage mu is an ATPase that preferentially stimulates intermolecular DNA strand transfer.

A DNA strand-transfer reaction is an early step in the transposition of phage Mu. It has been shown that an efficient reaction in vitro requires, in addition to buffer and salt, only the Mu A protein, Mu B protein, host protein HU, ATP, and Mg2+. We have determined that, of the three protein factors involved, only the Mu B protein has an ATPase activity. The Mu B ATPase is stimulated by Mu A protein and DNA but not by either of these factors alone. Double-stranded DNA is a much better cofactor than single-stranded DNA, but there is no apparent sequence specificity. In the absence of the Mu B protein and/or ATP, the intermolecular Mu DNA strand-transfer reaction is extremely inefficient, and the strand-transfer products are predominantly the result of an intramolecular reaction. This contrasts with the efficient intermolecular reaction that occurs if Mu B protein and ATP are provided. The Mu B protein, in the presence of Mu A protein and protein HU, therefore, seems to facilitate interactions between potential DNA target sites and pairs of Mu DNA ends.     

Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer

In 1999, Wan et al. [Proc. Natl. Acad. Sci. USA 96, 6014-6019] published a pioneering paper that established the entanglement between DNA base pair motions and the transfer time of the charge carrier. The DNA assemblies contained an ethidium covalently bound via a flexible alkyl chain to the 5' hydroxyl group of the DNA backbone. Although covalently attached, the loose way in which the ethidium was linked to DNA allowed for large degrees of conformational freedom and thus raised some concern with respect to conformational inhomogeneity. In this letter, we report studies on a different set of ethidium DNA conjugates. In contrast to the "Caltech systems," these conjugates contain ethidium tightly incorporated (as a base pair surrogate) into the DNA base stack, opposite to an abasic site analog. Despite the tight binding, we found that charge transfer from the photoexcited ethidium base pair surrogate across two or more base pairs is several orders of magnitude slower than in case of the DNA systems bearing the tethered ethidium. To further broaden the scope of this account, we compared (oxidative) electron hole transfer and (reductive) electron transfer using the same ethidium chromophore as a charge donor in combination with two different charge acceptors. We found that both electron and hole transfer are characterized by similar rates and distance dependencies. The results demonstrate the importance of nuclear motions and conformational flexibility and underline the presence of a base gating mechanism, which appears to be generic to electronic transfer processes through pi-stacked nucleic acids.     

Mitozantrone-induced toxicity and DNA strand breaks in leukaemic cells

By applying the fluorometric analysis of DNA unwinding (FADU) the in vitro effect of mitozantrone on DNA strand breaks was studied in seven different human leukaemic/lymphoma cell lines and in fresh leukaemic samples from seven patients with acute myeloid leukaemia refractory to conventional treatment. Pulse exposure to mitozantrone for 30 min invariably caused strand breaks. In the cell lines JM 1, KM3 and RPM I 8420 DNA strand breakage was progressive upon further incubation in drug free medium. These cell lines were killed by pulse exposure to mitozantrone. In the cell lines Molt 4, Daudi, Raji and HL-60, the DNA strand breaks induced by mitozantone were only moderate and these cell lines were also resistant to killing by mitozantrone in vitro. The leukaemic cells of one of the seven patients behaved also like the cell lines that were sensitive and a complete remission was achieved in this patient using mitozantrone as single agent therapy. The other patients with a pattern similar to the resistant cell lines proved to be clinically refractory. Thus mitozantrone induces rapidly progressive DNA strand breaks as early as 30 min in leukaemic cells that are sensitive. The measurement of DNA strand breaks by the fluorometric analysis of DNA unwinding is a rapid method which might predict response to drugs whose major effect is on the induction of strand breaks.     

Histones H1 and H5 interact preferentially with crossovers of double-helical DNA.

The interaction of the linker histones H1 and H5 from chicken erythrocyte chromatin with pBR322 was studied as a function of the number of superhelical turns in circular plasmid molecules. Supercoiled plasmid DNA was relaxed with topoisomerase I so that a population with a narrow distribution of topoisomers, containing from zero to five superhelical turns, was obtained. None of the topoisomers contained alternative non-B-DNA structures. Histone-DNA complexes formed at either 25 or 100 mM NaCl final concentration and at histone-DNA molar ratios ranging from 10 to 150 were analyzed by agarose gel electrophoresis. The patterns of disappearance of individual topoisomer bands from the gel were interpreted as an indication of preference of the linker histones for crossovers of double-helical DNA. This preference was observed at both salt concentrations, being more pronounced under conditions of low ionic strength. Isolated H5 globular domain also caused selective disappearance of topoisomers from the gel, but it did so only at very high peptide-DNA molar ratios. The observed preference of the linker histones for crossovers of double-helical DNA is viewed as a part of the mechanism involved in the sealing of the two turns of DNA around the histone octamer.     

Accumulation of DNA strand breaks and methotrexate cytotoxicity.

There was a progressive formation of strand breaks in mature DNA of Ehrlich ascites tumor cells that were treated with methotrexate. Cells were labeled with [14C]thymidine before incubation with methotrexate, and DNA strand breaks were measured by alkaline and by neutral filter elution methods. DNA single-strand breaks accumulated in a linear fashion as a function of time during the first 10 hr of incubation with 2 microM methotrexate. Thereafter, the accumulation of DNA strand breaks deviated from linearity because of progressive cell death. The extent of DNA strand breakage in cells that had been incubated with methotrexate for 24 hr was as high as in cells that had been irradiated with 300 rads. DNA strand breaks persisted in cells that were incubated, after exposure to methotrexate, in medium containing thymidine, hypoxanthine, and nonessential amino acids, indicating that these strand breaks were poorly repaired. Cell death commenced after 10 hr of incubation with methotrexate and continued during the following 3-4 days. These findings suggest that cell death was due to a lethal accumulation of DNA strand breaks. The formation of DNA strand breaks is probably due to inefficient DNA repair, resulting from the inhibition of syntheses of thymidylate and of purine nucleotides. The accumulation of DNA strand breaks was minimal in growth-arrested cells, which are resistant to methotrexate toxicity.     

DNA strand breaks and death of thymocytes induced byN-methyl-N-nitrosourea

Summary N-Methyl-N-nitrosourea (MNU) is a potent carcinogen in various sites of experimental animals and induces thymic lymphoma in rats, which has long been hard to induce by any carcinogen. To analyze the action of MNU on thymocytes, DNA strand breaking in thymocytes from the MNU-treated rat and that in MNU-treated cultured thymocytes were assayed. Fluorometric analysis of DNA unwinding (FADU assay), first reported by Birnboim and Jevcak to detect X-ray-induced DNA damage, was modified and applied to detect DNA damage in thymocytes treated with MNU in vitro or in vivo. In the present modified method, cell lysate was admixed with 0.15M sodium hydroxide, and DNA unwinding was processed at pH 12.0 for up to 2 h at 0° C in iced water. Double-stranded DNA remaining after alkaline reaction was detected by binding ethidium bromide and measuring its fluorescence. The severity of DNA damage, both in vivo and in vitro, depended on the MNU concentration. In addition, the sequential survival rate and cell-size distribution of thymocytes treated with MNU in vitro were investigated. A close relationship between the severity of DNA damage and cell death was demonstrated in MNU-treated thymocytes, and DNA damage by a non-cell-killing dose of MNU was detected with this FADU assay. MNU-induced cell death is not programmed as in apoptosis, which is caused in thymocytes physiologically, immunologically and by X-ray irradiation or corticoids.Abbreviations used MNU N-methyl-N-nitrosourea - FADU fluorometric analysis of DNA unwinding - PBS calcium- and magnesium-free phosphate-buffered saline     

Structural chromosome abnormalities,increased DNA strand breaks and DNA strand break repair deficiency in dermal fibroblasts from old female human donors

Dermal fibroblasts provide a paradigmatic model of cellular adaptation to long-term exogenous stress and ageing processes driven thereby. Here we addressed whether fibroblast ageing analysed ex vivo entails genome instability. Dermal fibroblasts from human female donors aged 20–67 years were studied in primary culture at low population doubling. Under these conditions, the incidence of replicative senescence and rates of age-correlated telomere shortening were insignificant. Genome-wide gene expression analysis revealed age-related impairment of mitosis, telomere and chromosome maintenance and induction of genes associated with DNA repair and non-homologous end-joining, most notably XRCC4 and ligase 4. We observed an age-correlated drop in proliferative capacity and age-correlated increases in heterochromatin marks, structural chromosome abnormalities (deletions, translocations and chromatid breaks), DNA strand breaks and histone H2AX-phosphorylation. In a third of the cells from old and middle-aged donors repair of X-ray induced DNA strand breaks was impaired despite up-regulation of DNA repair genes. The distinct phenotype of genome instability, increased heterochromatinisation and (in 30% of the cases futile) up-regulation of DNA repair genes was stably maintained over several cell passages indicating that it represents a feature of geroconversion that is distinct from cellular senescence, as it does not encompass a block of proliferation.     

Sequence-specific assembly of FtsK hexamers establishes directional translocation on DNA

FtsK is a homohexameric, RecA-like dsDNA translocase that plays a key role in bacterial chromosome segregation. The FtsK regulatory γ-subdomain determines directionality of translocation through its interaction with specific 8 base pair chromosomal sequences [(KOPS); FtsK Orienting/Polarizing Sequence(s)] that are cooriented with the direction of replication in the chromosome. We use millisecond-resolution ensemble translocation and ATPase assays to analyze the assembly, initiation, and translocation of FtsK. We show that KOPS are used to initiate new translocation events rather than reorient existing ones. By determining kinetic parameters, we show sigmoidal dependences of translocation and ATPase rates on ATP concentration that indicate sequential cooperative coupling of ATP hydrolysis to DNA motion. We also estimate the ATP coupling efficiency of translocation to be 1.63-2.11 bp of dsDNA translocated/ATP hydrolyzed. The data were used to derive a model for the assembly, initiation, and translocation of FtsK hexamers.     

ATP-independent DNA strand transfer catalyzed by protein(s) from meiotic cells of the yeast Saccharomyces cerevisiae.

An activity that catalyzes the transfer of a strand from a duplex linear molecule of DNA to a complementary circular single strand can be detected in crude extracts from mitotic and meiotic cells of the yeast Saccharomyces cerevisiae by adding yeast single-stranded DNA binding proteins. This DNA strand-transfer activity increases greater than 15-fold during meiosis in MATa/MAT alpha diploids prior to the detection of a 100- to 1000-fold increase in homologous chromosomal recombination. No increase is observed in MATa/MATa or MAT alpha/MAT alpha cells, which do not undergo meiosis when shifted to meiotic medium, suggesting the activity is related to meiotic recombination. The activity is named strand-transfer protein alpha (STP alpha) and has been extensively purified from the meiotic cells (6 hr after exposure to sporulation medium). The apparent molecular mass of STP alpha is 38 kDa under denaturing conditions. The DNA strand-transfer reaction catalyzed by STP alpha requires homologous single-stranded and double-stranded DNA and Mg2+ but no nucleotide cofactor. Yeast single-stranded DNA binding proteins stimulate the reaction at least 10-fold. Among the products analyzed by electron microscopy were typical strand-exchange structures.     

Inhibition of diethylnitrosamine-induced strand breaks in liver DNA by disulfiram

Summary Disulfiram (DSF) delayed the appearance of diethylnitrosamine (DEN)-induced strand breaks in liver DNA of rats. The fragmentation of liver DNA produced by DEN was studied 4 and 24 h after administration of the carcinogen on alkaline sucrose gradients. A single dose of 500 mg/kg DSF given 1 h prior to carcinogen treatment delayed for at least 4 h the DEN —induced strand breaks in liver DNA. A single DSF pretreatment, however, did not protect against carcinogen-induced strand breaks when observed 24 h after DEN injection. It is possible that continuous administration of DSF might inhibit the DEN-produced damage of the genetic material.

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Hemmung von Diäthylnitrosamin-induzierten Strangbrüchen in Leber DNS durch Disulfiram

Zusammenfassung Disulfiram (DSF) verzögert das Auftreten von Diäthylnitrosamin (DEN)-induzierten Strangbrüchen der DNS in Leberzellen von Ratten. Eine durch DEN erzeugte Fragmentierung der DNS wird 4 bzw. 24 Std nach der Carcinogengabe mit Hilfe eines alkalischen Sucrose-Gradienten untersucht. Eine Einzeldosis von 500 mg/kg DSF 1 Std vor dem Carcinogen verabreicht, verhindert Strangbrüche der Leber DNS für mindestens 4 Std. Die Vorbehandlung mit DSF schützt jedoch nicht vor Strangbrüchen nach einer längeren Periode von z. B. 24 Std. Möglicherweise verhindert eine fortgesetzte Behandlung mit DSF die DEN-induzierte Schädigung von genetischem Material.