818 research outputs found
Static Pairwise Annihilation in Complex Networks
We study static annihilation on complex networks, in which pairs of connected
particles annihilate at a constant rate during time. Through a mean-field
formalism, we compute the temporal evolution of the distribution of surviving
sites with an arbitrary number of connections. This general formalism, which is
exact for disordered networks, is applied to Kronecker, Erd\"os-R\'enyi (i.e.
Poisson) and scale-free networks. We compare our theoretical results with
extensive numerical simulations obtaining excellent agreement. Although the
mean-field approach applies in an exact way neither to ordered lattices nor to
small-world networks, it qualitatively describes the annihilation dynamics in
such structures. Our results indicate that the higher the connectivity of a
given network element, the faster it annihilates. This fact has dramatic
consequences in scale-free networks, for which, once the ``hubs'' have been
annihilated, the network disintegrates and only isolated sites are left.Comment: 7 Figures, 10 page
Polη, Polζ and Rev1 together are required for G to T transversion mutations induced by the (+)- and (−)-trans-anti-BPDE-N(2)-dG DNA adducts in yeast cells
Benzo[a]pyrene is an important environmental mutagen and carcinogen. Its metabolism in cells yields the mutagenic, key ultimate carcinogen 7R,8S,9S,10R-anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide, (+)-anti-BPDE, which reacts via its 10-position with N(2)-dG in DNA to form the adduct (+)-trans-anti-BPDE-N(2)-dG. To gain molecular insights into BPDE-induced mutagenesis, we examined in vivo translesion synthesis and mutagenesis in yeast cells of a site-specific 10S (+)-trans-anti-BPDE-N(2)-dG adduct and the stereoisomeric 10R (−)-trans-anti-BPDE-N(2)-dG adduct. In wild-type cells, bypass products consisted of 76% C, 14% A and 7% G insertions opposite (+)-trans-anti-BPDE-N(2)-dG; and 89% C, 4% A and 4% G insertions opposite (−)-trans-anti-BPDE-N(2)-dG. Translesion synthesis was reduced by ∼26–37% in rad30 mutant cells lacking Polη, but more deficient in rev1 and almost totally deficient in rev3 (lacking Polζ) mutants. C insertion opposite the lesion was reduced by ∼24–33% in rad30 mutant cells, further reduced in rev1 mutant, and mostly disappeared in the rev3 mutant strain. The insertion of A was largely abolished in cells lacking either Polη, Polζ or Rev1. The insertion of G was not detected in either rev1 or rev3 mutant cells. The rad30 rev3 double mutant exhibited a similar phenotype as the single rev3 mutant with respect to translesion synthesis and mutagenesis. These results show that while the Polζ pathway is generally required for translesion synthesis and mutagenesis of the (+)- and (−)-trans-anti-BPDE-N(2)-dG DNA adducts, Polη, Polζ and Rev1 together are required for G→T transversion mutations, a major type of mutagenesis induced by these lesions. Based on biochemical and genetic results, we present mechanistic models of translesion synthesis of these two DNA adducts, involving both the one-polymerase one-step and two-polymerase two-step models
Base Sequence Context Effects on Nucleotide Excision Repair
Nucleotide excision repair (NER) plays a critical role in maintaining the integrity of the genome when damaged by bulky DNA lesions, since inefficient repair can cause mutations and human diseases notably cancer. The structural properties of DNA lesions that determine their relative susceptibilities to NER are therefore of great interest. As a model system, we have investigated the major mutagenic lesion derived from the environmental carcinogen benzo[a]pyrene (B[a]P),
10S (+)-trans-anti-B[a]P-N2-dG in six different sequence contexts that differ in how the lesion is positioned in relation to nearby guanine amino groups. We have obtained molecular structural data by NMR and MD simulations, bending properties from gel electrophoresis studies, and NER data obtained from human HeLa cell extracts for our six investigated sequence contexts. This model system suggests that disturbed Watson-Crick base pairing is a better recognition signal than a flexible bend, and that these can act in concert to provide an enhanced signal. Steric hinderance between the minor groove-aligned lesion and nearby guanine amino groups determines the exact nature of the disturbances. Both nearest neighbor and more distant neighbor sequence contexts have an impact. Regardless of the exact distortions, we hypothesize that they provide a local thermodynamic destabilization signal for repair
One-electron Oxidation of a Pyrenyl Photosensitizer Covalently Attached to DNA and Competition Between its Further Oxidation and DNA Hole Injection
The photosensitized hole injection and guanine base damage phenomena have been investigated in the DNA sequence, 5′-d(CATG[subscript 1] [superscript Py]CG[subscript 2]TCCTAC) with a site-specifically positioned pyrene-like (Py) benzo[a]pyrene 7,8-diol 9,10-epoxide-derived N[superscript 2]-guanine adduct (G[subscript 1] [superscript Py]). Generation of the Py radical cation and subsequent hole injection into the DNA strand by a 355 nm nanosecond laser pulses (∼4 mJ cm[superscript −2]) results in the transformation of G[subscript 1] [superscript Py] to the imidazolone derivative Iz[subscript 1] [superscript Py] and a novel G[subscript 1] [superscript Py*] photoproduct that has a mass larger by 16 Da (M+16) than the mass (M) of G[subscript 1] [superscript Py]. In addition, hole transfer and the irreversible oxidation of G[subscript 2], followed by the formation of Iz[subscript 2] was observed (Yun et al. [2007], J. Am. Chem. Soc., 129, 9321). Oxygen-18 and deuterium isotope labeling methods, in combination with an extensive analysis of the MS/MS fragmentation patterns of the individual dG[superscript Py*] nucleoside adduct and other data show that dG[superscript Py*] has an unusual structure with a ruptured cyclohexenyl ring with a carbonyl group at the rupture site and intact guanine and pyrenyl residues. The formation of this product competes with hole injection and thus diminishes the efficiency of oxidation of guanines within the oligonucleotide strand by at least 15% in comparison with that in the dG[superscript Py] nucleoside adduct.National Institutes of Health (U.S.) (Grant R01 CA110261
Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase
We have investigated how a benzo[a]pyrene-derived N2-dG adduct, 10S(+)-trans-anti-[BP]-N2-dG ([BP]G*), is processed in a well-characterized Pol I family model replicative DNA polymerase, Bacillus fragment (BF). Experimental results are presented that reveal relatively facile nucleotide incorporation opposite the lesion, but very inefficient further extension. Computational studies follow the possible bypass of [BP]G* through the pre-insertion, insertion and post-insertion sites as BF alternates between open and closed conformations. With dG* in the normal B-DNA anti conformation, BP seriously disturbs the polymerase structure, positioning itself either deeply in the pre-insertion site or on the crowded evolving minor groove side of the modified template, consistent with a polymerase-blocking conformation. With dG* in the less prevalent syn conformation, BP causes less distortion: it is either out of the pre-insertion site or in the major groove open pocket of the polymerase. Thus, the syn conformation can account for the observed relatively easy incorporation of nucleotides, with mutagenic purines favored, opposite the [BP]G* adduct. However, with the lesion in the BF post-insertion site, more serious distortions caused by the adduct even in the syn conformation explain the very inefficient extension observed experimentally. In vivo, a switch to a potentially error-prone bypass polymerase likely dominates translesion bypass
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Mechanisms of interaction of radiation with matter
This project is concerned with studies of biological activity-structure relationships in which the mechanisms of interaction of ionizing radiation and benzopyrene (PB) compounds with DNA are being investigated and compared. Emphasis is focused on effects of DNA conformation on its mechanisms of interaction with ionizing radiation, on the influence of structure and stereochemistry of BP metabolites on mechanisms of DNA damage, and on influence of DNA conformation on interactions between BP metabolites and DNA molecules, and the structures of the complexes and adducts which are formed. One basic theme of this project is the use of photoexcited states of BP and nucleic acids as probes of these interactions. In part I of this report, recent progress on elucidating the structures of selected BP-oligonucleotide model adducts by high resolution NMR and gel electrophoresis techniques is summarized. It is shown that the stereochemical properties of benzo(a)pyrene diol epoxide-DNA adducts play a crucial role in determining their interactions with certain exonucleases. These results provide useful models for deriving a better understanding of differences biological activities of BP compounds and the relationships between mutagenicities and the structure properties of BP-DNA adducts. In Part II of this report, a new time-resolved method based on picosecond laser pulse techniques for elucidating the electronic levels involved in electron photoemission and electron transfer in BP and nucleic acid solids is described
PCNA Ubiquitination Is Important, But Not Essential for Translesion DNA Synthesis in Mammalian Cells
Translesion DNA synthesis (TLS) is a DNA damage tolerance mechanism in which specialized low-fidelity DNA polymerases bypass replication-blocking lesions, and it is usually associated with mutagenesis. In Saccharomyces cerevisiae a key event in TLS is the monoubiquitination of PCNA, which enables recruitment of the specialized polymerases to the damaged site through their ubiquitin-binding domain. In mammals, however, there is a debate on the requirement for ubiquitinated PCNA (PCNA-Ub) in TLS. We show that UV-induced Rpa foci, indicative of single-stranded DNA (ssDNA) regions caused by UV, accumulate faster and disappear more slowly in Pcna(K164R/K164R) cells, which are resistant to PCNA ubiquitination, compared to Pcna(+/+) cells, consistent with a TLS defect. Direct analysis of TLS in these cells, using gapped plasmids with site-specific lesions, showed that TLS is strongly reduced across UV lesions and the cisplatin-induced intrastrand GG crosslink. A similar effect was obtained in cells lacking Rad18, the E3 ubiquitin ligase which monoubiquitinates PCNA. Consistently, cells lacking Usp1, the enzyme that de-ubiquitinates PCNA exhibited increased TLS across a UV lesion and the cisplatin adduct. In contrast, cells lacking the Rad5-homologs Shprh and Hltf, which polyubiquitinate PCNA, exhibited normal TLS. Knocking down the expression of the TLS genes Rev3L, PolH, or Rev1 in Pcna(K164R/K164R) mouse embryo fibroblasts caused each an increased sensitivity to UV radiation, indicating the existence of TLS pathways that are independent of PCNA-Ub. Taken together these results indicate that PCNA-Ub is required for maximal TLS. However, TLS polymerases can be recruited to damaged DNA also in the absence of PCNA-Ub, and perform TLS, albeit at a significantly lower efficiency and altered mutagenic specificity
Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion
7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following oxidative damage of DNA by reactive oxygen species, is processed differently by replicative and bypass polymerases. Our kinetic primer extension studies demonstrate that the bypass polymerase Dpo4 preferentially inserts C opposite oxoG, and also preferentially extends from the oxoG•C base pair, thus achieving error-free bypass of this lesion. We have determined the crystal structures of preinsertion binary, insertion ternary, and postinsertion binary complexes of oxoG-modified template-primer DNA and Dpo4. These structures provide insights into the translocation mechanics of the bypass polymerase during a complete cycle of nucleotide incorporation. Specifically, during noncovalent dCTP insertion opposite oxoG (or G), the little-finger domain–DNA phosphate contacts translocate by one nucleotide step, while the thumb domain–DNA phosphate contacts remain fixed. By contrast, during the nucleotidyl transfer reaction that covalently incorporates C opposite oxoG, the thumb-domain–phosphate contacts are translocated by one nucleotide step, while the little-finger contacts with phosphate groups remain fixed. These stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases
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