Activity of DNA vaccines encoding self or heterologous Her-2/neu in Her-2 or neu transgenic mice

To assess the efficacy of self versus heterologous ErbB-2 vaccines, the reactivity to human and rat ErbB-2 (Her-2 and neu, respectively) DNA vaccines were tested in normal, Her-2 or neu transgenic mice. When immunized with either Her-2 or neu DNA, normal BALB/c and C57BL/6 mice produced cross-reactive T cells, but only antigen specific antibodies. In Her-2 Tg mice, weak to no anti-Her-2 response was induced by either self Her-2 or heterologous neu DNA, demonstrating profound tolerance to Her-2 and the inability to induce anti-Her-2 immunity with either vaccine. In NeuT mice, vaccination with self neu but not heterologous Her-2 DNA induced anti-neu antibodies and delayed spontaneous tumorigenesis. Both neu and Her-2 DNA induced anti-neu T cell response, but depletion of CD8 T cells did not change the delay in tumorigenesis. Therefore, in NeuT mice, both self and heterologous DNA activated anti-neu T cells, although T cell response did not reach sufficient level to suppress spontaneous tumorigenesis. Rather, induction of anti-neu antibodies by self neu DNA is associated with the delay in spontaneous tumor growth. Overall, NeuT mice were more responsive to DNA vaccination than Her-2 Tg mice and this may be associated with the continuous production of neu by the 10 mammary glands undergoing tumor progression.     

Mechanics of DNA flexibility visualized by selective 2'-amine acylation at nucleotide bulges

We used selective acylation of 2'-amine-substituted nucleotides to visualize local backbone conformations that occur preferentially at bulged sites in DNA duplexes. 2'-Amine acylation reports local nucleotide flexibility because unconstrained 2'-amino nucleotides more readily reach a reactive conformation in which the amide-forming transition state is stabilized by interactions between the amine nucleophile and the adjacent 3'-phosphodiester group. Bulged 2'-amine-substituted cytidine nucleotides react approximately 20-fold more rapidly than nucleotides constrained by base-pairing at 35 degrees C. In contrast, base-paired 2'-amine-substituted nucleotides flanked by a 5' or 3' bulge react two- or six-fold more rapidly, respectively, than the perfectly paired duplex. The relative lack of 2'-amine reactivity for nucleotides adjacent to a DNA bulge emphasizes, first, that structural perturbations do not extend significantly into the flanking duplex structure. Second, the exquisite sensitivity towards very local perturbations in nucleic acid structure suggests that 2'-amine acylation can be used to chemically interrogate deletion mutations in DNA. Finally, these data support the mechanical interpretation that the reactive ribose conformation for 2'-amine acylation requires that the base lies out of the helix and in the major groove, a mechanistic insight useful for designing 2'-amine-based sensors.     

Wing 1 of protein HOP2 is as important as helix 3 in DNA binding by MD simulation

The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis-specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed. Despite losing some hydrogen bonds, the W1-mutant DNA complex was rescued by stronger hydrophobic interactions. For the wild type and W1-mutant, the protein was found to slide along the DNA grooves as the DNA rolls along its double-helix axis. This motion could be functionally important to facilitate the precise positioning of the single-stranded DNA with the homologous double-stranded DNA. The sliding motion was reduced in the W1-mutant. The H-mutant nearly lost all intermolecular interactions. Moreover, an additional mutation in wing 1 (Y65A/K67A/Q68A/K69A) also caused complete complex dissociation. Therefore, both wing 1 and helix 3 make important contribution to the DNA binding, which could be important to the strand invasion function of HOP2 homodimer and HOP2-MND1 heterodimer. Similar to cocking a medieval crossbow with the archer’s foot placed in the stirrup, wing 1 may push the minor groove to cause distortion while helix 3 grabs the major groove.     

Levels of 5-hydroxymethyl-2'-deoxyuridine in DNA from women participating in an intervention trial of low-fat and low-energy diets

Oxidative DNA damage in blood appears to be useful as a marker of systemic oxidative stress levels. Dietary factors such as fat and energy intakes have been indicated to affect oxidative stress levels, and this may be an important mechanism by which diet can modulate cancer risk. The primary objective of this study was to investigate the effects of dietary intervention in premenopausal women on the levels of one type of oxidative DNA damage: 5-hydroxymethyl-2'-deoxyuridine. The trial randomly assigned women to control, low-fat, low-energy or combination low-fat/low-energy diets for 12 weeks. Blood samples were obtained every 2 weeks, and DNA was analysed for the levels of 5-hydroxymethyl-2'-deoxyuridine. Levels of DNA damage declined with time in each diet arm, including the control arm. The decreases were greater in the two arms with low-energy intake, but not significantly so. The numbers of women who exhibited decreased 5-hydroxymethyl-2'-deoxyuridine levels at 12 weeks versus baseline levels, however, was significantly greater in women assigned to any intervention diet (79%) than in the control arm (50%). Low-fat and low-energy diets therefore had a small effect on changes in oxidative DNA damage levels. The women participating in this study were not selected on the basis of increased cancer risk; therefore, they may have had low baseline levels of damage that were not amenable to further reduction by dietary change.     

Phosphorylation of histone H2AX at M phase in human cells without DNA damage response

A variant of histone H2A, H2AX, is phosphorylated on Ser139 in response to DNA double-strand breaks (DSBs), and clusters of the phosphorylated form of H2AX (gamma-H2AX) in nuclei of DSB-induced cells show foci at breakage sites. Here, we show phosphorylation of H2AX in a cell cycle-dependent manner without any detectable DNA damage response. Western blot and immunocytochemical analyses with the anti-gamma-H2AX antibody revealed that H2AX is phosphorylated at M phase in HeLa cells. In ataxia-telangiectasia cells lacking ATM kinase activity, gamma-H2AX was scarcely detectable in the mitotic chromosomes, suggesting involvement of ATM in M-phase phosphorylation of H2AX. Single-cell gel electrophoresis assay and Western blot analysis with the anti-phospho-p53 (Ser15) antibody indicated that H2AX in human M-phase cells is phosphorylated independently of DSB and DNA damage signaling. Even in the absence of DNA damage, phosphorylation of H2AX in normal cell cycle progression may contribute to maintenance of genomic integrity.     

Variation of DNA photocleavage efficiency for [(TL)2Ru(dpp)]Cl2 complexes where TL=2,2'-bipyridine, 1,10-phenanthroline, or 4,7-diphenyl-1,10-phenanthroline

The complexes [(bpy)₂Ru(dpp)]Cl₂, [(phen)₂Ru(dpp)]Cl₂, and [(Ph₂phen)₂Ru(dpp)]Cl₂ (where dpp = 2,3-bis(2-pyridyl)pyrazine, bpy = 2,2′-bipyridine, phen = 1,10-phenanthroline, Ph₂phen = 4,7-diphenyl-1,10-phenanthroline) have been investigated and found to photocleave DNA via an oxygen-mediated pathway. These light absorbing complexes possess intense metal-to-ligand charge transfer (MLCT) transitions in the visible region of the spectrum. The [(TL)₂Ru(dpp)]²⁺ systems populate ³MLCT states after visible light excitation, giving rise to emissions in aqueous solution centered at 692, 690, and 698 nm for TL = bpy, phen, and Ph₂phen respectively. The ³MLCT states and emissions are quenched by O₂, producing a reactive oxygen species. These complexes photocleave DNA with varying efficiencies, [(Ph₂phen)₂Ru(dpp)]²⁺ > [(phen)₂Ru(dpp)]²⁺ > [(bpy)₂Ru(dpp)]²⁺. The presence of the polyazine bridging ligand will allow these chromophores to be incorporated into larger supramolecular assemblies.     

Death of p53-defective cells triggered by forced mitotic entry in the presence of DNA damage is not uniquely dependent on Caspase-2 or the PIDDosome

Much effort has been put in the discovery of ways to selectively kill p53-deficient tumor cells and targeting cell cycle checkpoint pathways has revealed promising candidates. Studies in zebrafish and human cell lines suggested that the DNA damage response kinase, checkpoint kinase 1 (Chk1), not only regulates onset of mitosis but also cell death in response to DNA damage in the absence of p53. This effect reportedly relies on ataxia telangiectasia mutated (ATM)-dependent and PIDDosome-mediated activation of Caspase-2. However, we show that genetic ablation of PIDDosome components in mice does not affect cell death in response to γ-irradiation. Furthermore, Chk1 inhibition largely failed to sensitize normal and malignant cells from p53^−/− mice toward DNA damaging agents, and p53 status did not affect the death-inducing activity of DNA damage after Chk1 inhibition in human cancer cells. These observations argue against cross-species conservation of a Chk1-controlled cell survival pathway demanding further investigation of the molecular machinery responsible for cell death elicited by forced mitotic entry in the presence of DNA damage in different cell types and model organisms.     

A complex composed of at least two HeLa nuclear proteins protects preferentially one DNA strand of the simple (gt)n(ga)m containing region of intron 2 in HLA-DRB-genes

Electrophoretic mobility shift assays reveal that HeLa neuclear proteins bind fast and with measurable affinity to target DNAs containing mixed simple repetitive (gt)_n(ga)_m stretches. Preincubation of the proteins at elevated temperature prevents the formation of the major DNA/protein complex in favour of several distinct assemblies. A similar pattern of retarded bands was observed employing higher salt concentrations in binding reaction. Thus conformational changes of different proteins appear to influence the complex rather than alternating DNA structures. Separation of the total nuclear extract into a water soluble and an insoluble protein fraction leads to a complete loss of target DNA bindinlg capability of the fractions. The binding capacity is restored by combining the two fractions suggesting that at least two protein components are necessary to form a complex with the target sequence. The proteins can be differentiated into head sensitive, water soluble and temporary stable, water insoluble, respectively. Furthermore, specifically binding polypeptides are not detectable by Southwestern analyses, probably because the essential components are separated during electrophoresis. DNase 1 footpoint analyses yield four different protein binding regions only on the (gt)_n(ga)_m harbouring strand. The footprints cover larger portions of the mixed simple repeat in addition to a portion 5′ of the (gt)_n part. Hence at lealst two nuclear protein components of unknown biological function have to be present simultaneously to protect preferentially the (gt)_n(ga)_m-containing strand intron 2 in HLA-DRB genes     

Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding

Escherichia coli UvrD is a superfamily 1 DNA helicase and single-stranded DNA (ssDNA) translocase that functions in DNA repair and plasmid replication and as an anti-recombinase by removing RecA protein from ssDNA. UvrD couples ATP binding and hydrolysis to unwind double-stranded DNA and translocate along ssDNA with 3′-to-5′ directionality. Although a UvrD monomer is able to translocate along ssDNA rapidly and processively, DNA helicase activity in vitro requires a minimum of a UvrD dimer. Previous crystal structures of UvrD bound to a ssDNA/duplex DNA junction show that its 2B sub-domain exists in a “closed” state and interacts with the duplex DNA. Here, we report a crystal structure of an apo form of UvrD in which the 2B sub-domain is in an “open” state that differs by an ∼ 160° rotation of the 2B sub-domain. To study the rotational conformational states of the 2B sub-domain in various ligation states, we constructed a series of double-cysteine UvrD mutants and labeled them with fluorophores such that rotation of the 2B sub-domain results in changes in fluorescence resonance energy transfer. These studies show that the open and closed forms can interconvert in solution, with low salt favoring the closed conformation and high salt favoring the open conformation in the absence of DNA. Binding of UvrD to DNA and ATP binding and hydrolysis also affect the rotational conformational state of the 2B sub-domain, suggesting that 2B sub-domain rotation is coupled to the function of this nucleic acid motor enzyme.     

Structure of duplex DNA containing the cisplatin 1,2-{Pt(NH3)2}-d(GpG) cross-link at 1.77 Å resolution

We report the 1.77-Å resolution X-ray crystal structure of a dodecamer DNA duplex with the sequence 5′-CCTCTGGTCTCC-3′ that has been modified to contain a single engineered 1,2-cis-{Pt(NH₃)₂}²⁺-d(GpG) cross-link, the major DNA adduct of cisplatin. These data represent a significant improvement in resolution over the previously published 2.6-Å structure. The ammine ligands in this structure are clearly resolved, leading to improved visualization of the cross-link geometry with respect to both the platinum center and to the nucleobases, which adopt a higher energy conformation. Also better resolved are the deoxyribose sugar puckers, which allow us to re-examine the global structure of platinum-modified DNA. Another new feature of this model is the location of four octahedral [Mg(H₂O)₆]²⁺ ions associated with bases in the DNA major groove and the identification of 124 ordered water molecules that participate in hydrogen-bonding interactions with either the nucleic acid or the diammineplatinum(II) moiety.     

Association of maternal and nutrient supply line factors with DNA methylation at the imprinted IGF2/H19 locus in multiple tissues of newborn twins

Epigenetic events are crucial for early development, but can be influenced by environmental factors, potentially programming the genome for later adverse health outcomes. The insulin-like growth factor 2 (IGF2)/H19 locus is crucial for prenatal growth and the epigenetic state at this locus is environmentally labile. Recent studies have implicated maternal factors, including folate intake and smoking, in the regulation of DNA methylation at this locus, although data are often conflicting in the direction and magnitude of effect. Most studies have focused on single tissues and on one or two differentially-methylated regions (DMRs) regulating IGF2/H19 expression. In this study, we investigated the relationship between multiple shared and non-shared gestational/maternal factors and DNA methylation at four IGF2/H19 DMRs in five newborn cell types from 67 pairs of monozygotic and 49 pairs of dizygotic twins. Data on maternal and non-shared supply line factors were collected during the second and third trimesters of pregnancy and DNA methylation was measured via mass spectrometry using Sequenom MassArray EpiTyper analysis. Our exploratory approach showed that the site of umbilical cord insertion into the placenta in monochorionic twins has the strongest positive association with methylation in all IGF2/H19 DMRs (p < 0.05). Further, evidence for tissue- and locus-specific effects were observed, emphasizing that responsiveness to environmental exposures in utero cannot be generalized across genes and tissues, potentially accounting for the lack of consistency in previous findings. Such complexity in responsiveness to environmental exposures in utero has implications for all epigenetic studies investigating the developmental origins of health and disease.     

The Observation of Ultrafast Excited-state Dynamical Evolution In B800- Partially or Completely Released LH2 of Rhodobacter sphaeroides 601 at Room Temperature

Abstract

Photodynamics of two kinds of peripheral antenna complexes (LU2 of Rhodobacter sphaeroides, native LH2 (RS601) and B800-released LH2 where B800-BChls were partially or completely removed with different pH treatments), were studied using femtosecond pump-probe technique at different laser wavelengths. The obtained results for these samples with different B800/B850 ratios demonstrated that under the excitation around B800 nm, the photoabsorption and photobleaching dynamics were caused by the direct excitation of upper excitonic levels of B850 and excited state of B800 pigments, respectively. Furthermore, the removal of B800 pigments had little effect on the energy transfer processes of B850 interband/intraband transfer.     

Steric and Electrostatic Effects at the C2 Atom Substituent Influence Replication and Miscoding of the DNA Deamination Product Deoxyxanthosine and Analogs by DNA Polymerases

Deoxyinosine (dI) and deoxyxanthosine (dX) are both formed in DNA at appreciable levels in vivo by deamination of deoxyadenosine (dA) and deoxyguanosine (dG), respectively, and can miscode. Structure-activity relationships for dA pairing have been examined extensively using analogs but relatively few studies have probed the roles of the individual hydrogen-bonding atoms of dG in DNA replication. The replicative bacteriophage T7 DNA polymerase/exonuclease and the translesion DNA polymerase Sulfolobus solfataricus pol IV were used as models to discern the mechanisms of miscoding by DNA polymerases. Removal of the 2-amino group from the template dG (i.e., dI) had little impact on the catalytic efficiency of either polymerase, as judged by either steady-state or pre-steady-state kinetic analysis, although the misincorporation frequency was increased by an order of magnitude. dX was highly miscoding with both polymerases, and incorporation of several bases was observed. The addition of an electronegative fluorine atom at the 2-position of dI lowered the oligonucleotide T_m and strongly inhibited incorporation of dCTP. The addition of bromine or oxygen (dX) at C2 lowered the T_m further, strongly inhibited both polymerases, and increased the frequency of misincorporation. Linear activity models show the effects of oxygen (dX) and the halogens at C2 on both DNA polymerases as mainly due to a combination of both steric and electrostatic factors, producing a clash with the paired cytosine O2 atom, as opposed to either bulk or perturbation of purine ring electron density alone.     

Enhanced DNA photocleavage properties of Ru(II) terpyridine complexes upon incorporation of methylphenyl substituted terpyridine and/or the polyazine bridging ligand dpp (2,3-bis(2-pyridyl)pyrazine)

The heteroleptic complexes, [(MePhtpy)RuCl(dpp)](PF₆) and [(tpy)RuCl(dpp)](PF₆), have been synthesized, characterized, and investigated with respect to their photophysical, redox, and DNA photocleavage properties (where MePhtpy = 4′-(4-methylphenyl)-2,2′:6′,2′′-terpyridine and dpp = 2,3-bis(2-pyridyl)pyrazine, tpy = 2,2′:6′,2′′-terpyridine). The X-ray crystal structure confirms the identity of the new [(MePhtpy)RuCl(dpp)](PF₆) complex. These heteroleptic complexes were found to photocleave DNA in the presence of oxygen, unlike the previously studied complex, [Ru(tpy)₂](PF₆)₂. The photophysical, redox, and DNA photocleavage properties of the heteroleptic complexes were compared with those of the homoleptic complexes, [Ru(MePhtpy)₂](PF₆)₂ and [Ru(tpy)₂](PF₆)₂. The heteroleptic complexes showed intense metal to ligand charge transfer (MLCT) transition at lower energy ([(MePhtpy)RuCl(dpp)](PF₆), 522 nm; [(tpy)RuCl(dpp)](PF₆), 516 nm) and longer excited state lifetimes as compared to the homoleptic complexes. The [Ru(MePhtpy)₂]²⁺ complex was found to photocleave DNA in contrast to [Ru(tpy)₂]²⁺. The introduction of a methylphenyl group on the tepyridine ligand not only enhances the ³MLCT excited state lifetime but also increases the lipophilicity and thereby the DNA binding ability of the molecule. An increase in lipophilicity upon addition of a methylphenyl group on the 2,2′:6′,2′′-terpyridine ligand was confirmed by determination of the partition coefficient ([(MePhtpy)RuCl(dpp)](PF₆), log P = +1.16; [(tpy)RuCl(dpp)](PF₆), log P = −1.27). The heteroleptic complexes photocleave DNA more efficiently than the homoleptic complexes, with the greatest activity being observed for the newly prepared [(MePhtpy)RuCl(dpp)](PF₆) complex.