Dna2 Helicase/Nuclease Causes Replicative Fork Stalling and Double-strand Breaks in the Ribosomal DNA of Saccharomyces cerevisiae

We have proposed that faulty processing of arrested replication forks leads to increases in recombination and chromosome instability in Saccharomyces cerevisiae and contributes to the shortened lifespan of dna2 mutants. Now we use the ribosomal DNA locus, which is a good model for all stages of DNA replication, to test this hypothesis. We show directly that DNA replication pausing at the ribosomal DNA replication fork barrier (RFB) is accompanied by the occurrence of double-strand breaks near the RFB. Both pausing and breakage are elevated in the early aging, hypomorphic dna2-2 helicase mutant. Deletion of FOB1, encoding the fork barrier protein, suppresses the elevated pausing and DSB formation, and represses initiation at rDNA ARSs. The dna2-2 mutation is synthetically lethal with {Delta}rrm3, encoding another DNA helicase involved in rDNA replication. It does not appear to be the case that the rDNA is the only determinant of genome stability during the yeast lifespan however since strains carrying deletion of all chromosomal rDNA but with all rDNA supplied on a plasmid, have decreased rather than increased lifespan. We conclude that the replication-associated defects that we can measure in the rDNA are symbolic of similar events occurring either stochastically throughout the genome or at other regions where replication forks move slowly or stall, such as telomeres, centromeres, or replication slow zones

Nanotube-Metal Junctions: 2- and 3- Terminal Electrical Transport

We address the quality of electrical contact between carbon nanotubes and metallic electrodes by performing first-principles calculations for the electron transmission through ideal 2- and 3-terminal junctions, thus revealing the physical limit of tube-metal conduction. The structural model constructed involves surrounding the tube by the metal atoms of the electrode as in most experiments; we consider metallic (5,5) and n-doped semiconducting (10,0) tubes surrounded by Au or Pd. In the case of metallic tubes, the contact conductance is shown to approach the ideal 4e^2/h in the limit of large contact area. For three-terminals, the division of flux among the different transmission channels depends strongly on the metal material. A Pd electrode has nearly perfect tube-electrode transmission and therefore turns off the straight transport along the tube. Our results are in good agreement with some recent experimental reports and clarify a fundamental discrepancy between theory and experiment.Comment: 5 pages, 5 figures, published version: some modified figures and clarifications in the tex

Interactions and Broken Time-Reversal Symmetry in Chaotic Quantum Dots

When treating interactions in quantum dots within a RPA-like approach, time-reversal symmetry plays an important role as higher-order terms -- the Cooper series -- need to be included when this symmetry is present. Here we consider model quantum dots in a magnetic field weak enough to leave the dynamics of the dot chaotic, but strong enough to break time-reversal symmetry. The ground state spin and addition energy for dots containing 120 to 200 electrons are found using local spin density functional theory, and we compare the corresponding distributions with those derived from an RPA-like treatment of the interactions. The agreement between the two approaches is very good, significantly better than for analogous calculations in the presence of time-reversal symmetry. This demonstrates that the discrepancies between the two approaches in the time-reversal symmetric case indeed originate from the Cooper channel, indicating that these higher-order terms might not be properly taken into account in the spin density functional calculations.Comment: 4 pages, 3 figure

Spin and Conductance-Peak-Spacing Distributions in Large Quantum Dots: A Density Functional Theory Study

We use spin-density-functional theory to study the spacing between conductance peaks and the ground-state spin of 2D model quantum dots with up to 200 electrons. Distributions for different ranges of electron number are obtained in both symmetric and asymmetric potentials. The even/odd effect is pronounced for small symmetric dots but vanishes for large asymmetric ones, suggesting substantially stronger interaction effects than expected. The fraction of high-spin ground states is remarkably large.Comment: 4 pages, 3 figure

Scrambling and Gate Effects in Realistic Quantum Dots

We evaluate the magnitude of two important mesoscopic effects using a realistic model of typical quantum dots. ``Scrambling'' and ``gate effect'' are defined as the change in the single-particle spectrum due to added electrons or gate-induced shape deformation, respectively. These two effects are investigated systematically in both the self-consistent Kohn-Sham (KS) theory and a Fermi liquid-like Strutinsky approach. We find that the genuine scrambling effect is small because the potential here is smooth. In the KS theory, a key point is the implicit inclusion of residual interactions in the spectrum; these dominate and make scrambling appear larger. Finally, the gate effect is comparable in the two cases and, while small, is able to cause gate-induced spin transitions.Comment: 5 pages, 3 figure

Significance of the dissociation of Dna2 by flap endonuclease 1 to Okazaki fragment processing in Saccharomyces cerevisiae

Okazaki fragments are initiated by short RNA/DNA primers, which are displaced into flap intermediates for processing. Flap endonuclease 1 (FEN1) and Dna2 are responsible for flap cleavage. Replication protein A (RPA)-bound flaps inhibit cleavage by FEN1 but stimulate Dna2, requiring that Dna2 cleaves prior to FEN1. Upon cleavage, Dna2 leaves a short flap, which is then cut by FEN1 forming a nick for ligation. Both enzymes require a flap with a free 5'-end for tracking to the cleavage sites. Previously, we demonstrated that FEN1 disengages the tracking mechanism of Dna2 to remove it from the flap. To determine why the disengagement mechanism evolved, we measured FEN1 dissociation of Dna2 on short RNA and DNA flaps, which occur during flap processing. Dna2 tracked onto these flaps but could not cleave, presenting a block to FEN1 entry. However, FEN1 disengaged these nonproductively bound Dna2 molecules, proceeding on to conduct proper cleavage. These results clarify the importance of disengagement. Additional results showed that flap substrate recognition and tracking by FEN1, as occur during fragment processing, are required for effective displacement of the flap-bound Dna2. Dna2 was recently shown to dissociate flap-bound RPA, independent of cleavage. Using a nuclease-defective Dna2 mutant, we reconstituted the sequential dissociation reactions in the proposed RPA/Dna2/FEN1 pathway showing that, even without cutting, Dna2 enables FEN1 to cleave RPA-coated flaps. In summary, RPA, Dna2, and FEN1 have evolved highly coordinated binding properties enabling one protein to succeed the next for proper and efficient Okazaki flap processing

Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates

Dna2 is a nuclease/helicase with proposed roles in DNA replication, double-strand break repair and telomere maintenance. For each role Dna2 is proposed to process DNA substrates with a 5'-flap. To date, however, Dna2 has not revealed a preference for binding or cleavage of flaps over single-stranded DNA. Using DNA binding competition assays we found that Dna2 has substrate structure specificity. The nuclease displayed a strong preference for binding substrates with a 5'-flap or some variations of flap structure. Further analysis revealed that Dna2 recognized and bound both the single-stranded flap and portions of the duplex region immediately downstream of the flap. A model is proposed in which Dna2 first binds to a flap base, and then the flap threads through the protein with periodic cleavage, to a terminal flap length of ~5 nt. This resembles the mechanism of flap endonuclease 1, consistent with cooperation of these two proteins in flap processing

Interplay of Mre11 Nuclease with Dna2 plus Sgs1 in Rad51-Dependent Recombinational Repair

The Mre11/Rad50/Xrs2 complex initiates IR repair by binding to the end of a double-strand break, resulting in 5′ to 3′ exonuclease degradation creating a single-stranded 3′ overhang competent for strand invasion into the unbroken chromosome. The nuclease(s) involved are not well understood. Mre11 encodes a nuclease, but it has 3′ to 5′, rather than 5′ to 3′ activity. Furthermore, mutations that inactivate only the nuclease activity of Mre11 but not its other repair functions, mre11-D56N and mre11-H125N, are resistant to IR. This suggests that another nuclease can catalyze 5′ to 3′ degradation. One candidate nuclease that has not been tested to date because it is encoded by an essential gene is the Dna2 helicase/nuclease. We recently reported the ability to suppress the lethality of a dna2Δ with a pif1Δ. The dna2Δ pif1Δ mutant is IR-resistant. We have determined that dna2Δ pif1Δ mre11-D56N and dna2Δ pif1Δ mre11-H125N strains are equally as sensitive to IR as mre11Δ strains, suggesting that in the absence of Dna2, Mre11 nuclease carries out repair. The dna2Δ pif1Δ mre11-D56N triple mutant is complemented by plasmids expressing Mre11, Dna2 or dna2K1080E, a mutant with defective helicase and functional nuclease, demonstrating that the nuclease of Dna2 compensates for the absence of Mre11 nuclease in IR repair, presumably in 5′ to 3′ degradation at DSB ends. We further show that sgs1Δ mre11-H125N, but not sgs1Δ, is very sensitive to IR, implicating the Sgs1 helicase in the Dna2-mediated pathway

A quasi-local mass for 2-spheres with negative Gauss curvature

We extend our previous definition of quasi-local mass to 2-spheres whose Gauss curvature is negative and prove its positivity.Comment: 10 pages, Science in China, Series A: Math, to appea