Mismatch recognition by the human MutS homologs hMSH2-hMSH6 is regulated by adenosine nucleotide binding, supporting the hypothesis that it functions as a molecular switch. Here we show that ATP-induced release of hMSH2-hMSH6 from mismatched DNA is prevented if the ends are blocked or if the DNA is circular. We demonstrate that mismmatched DNA provokes ADP-->ATP exchange, resulting in a discernible conformational transition that converts hMSH2-hMSH6 into a sliding clamp capable of hydrolysis-independent diffusion along the DNA backbone. Our results support a model for bidirectional mismatch repair in which stochastic loading of multiple ATP-bound hMSH2-hMSH6 sliding clamps onto mismatch-containing DNA leads to activation of the repair machinery and/or other signaling effectors similar to G protein switches.

Type II DNA topoisomerases actively reduce the fractions of knotted and catenated circular DNA below thermodynamic equilibrium values. To explain this surprising finding, we designed a model in which topoisomerases introduce a sharp bend in DNA. Because the enzymes have a specific orientation relative to the bend, they act like Maxwell's demon, providing unidirectional strand passage. Quantitative analysis of the model by computer simulations proved that it can explain much of the experimental data. The required sharp DNA bend was demonstrated by a greatly increased cyclization of short DNA fragments from topoisomerase binding and by direct visualization with electron microscopy.T ype II topoisomerases are essential enzymes that pass one DNA through another and thereby remove DNA entanglements. They make a transient double-stranded break in a gate segment (G segment) that allows passage by another segment (T segment) of the same or another DNA molecule (reviewed in refs. 1 and 2). Thus, these enzymes have the potential to convert real DNA molecules into phantom chains that freely pass through themselves to generate an equilibrium distribution of knots, catenanes, and supercoils.The actual picture is more complex and more interesting. The observed steady-state fractions of knotted, catenated, and supercoiled DNAs produced by type II topoisomerases are up to two orders of magnitude lower than at equilibrium (3). Thermodynamically, there is no contradiction in this finding because the enzymes use the energy of ATP hydrolysis. Active topology simplification by topoisomerases has an important biological consequence. It helps explain how topoisomerases can remove all DNA entanglements under the crowded cellular conditions which favor the opposite outcome. The challenge, though, is to understand how type II topoisomerases actively simplify DNA topology. Topology is a global property of circular DNA molecules, and yet it is determined by the much smaller topoisomerases, which can act only locally.Two models have been suggested to explain active simplification of DNA topology. First, if type II topoisomerases corral the T segment within a small loop of DNA containing the G segment, active disentanglement would result (3). However, it was pointed out when this model was suggested (3) that to account for the large effects observed, the loop trapping would need substantial energy input from ATP hydrolysis for the transport of the DNA along the enzymes, and these enzymes are energetically efficient (4). Moreover, no direct experimental data supporting the model have been presented.Second, a kinetic proofreading model proposed that two successive bindings of T segments are required for strand passage (5). The first binding event converts the enzyme bound with a G segment to an activated state. An assumption of the model is that segment collision in the knotted state occurs about 1͞P k times more often than in the unknotted state, where P k is the equilibrium probability of knotting. Our computer simulations below show that th...

Fas, a tumor necrosis factor family receptor, is activated by the membrane protein Fas ligand (FasL) expressed on various immune cells. Fas signaling triggers apoptosis and induces inflammatory cytokine production. Among the Fas induced cytokines, the IL-1β family cytokines require proteolysis to gain biological activity. Inflammasomes, which respond to pathogens and danger signals, cleave IL-1β cytokines via caspase-1. The mechanisms, by which Fas regulates IL-1β activation, however, remain unresolved. Here, we demonstrate that macrophages exposed to TLR ligands upregulate Fas, which renders them responsive to receptor engagement by Fas ligand. Fas signaling activates caspase-8 in macrophages and dendritic cells leading to the maturation of IL-1β and IL-18 independently of inflammasomes or Rip3. Hence, Fas controls a novel non-canonical IL-1β activation pathway in myeloid cells, which could play an essential role in inflammatory processes, tumor surveillance and control of infectious diseases.

Small amphiphilic molecules, also known as hydrotropes, are too small to form micelles in aqueous solutions. However, aqueous solutions of nonionic hydrotropes show the presence of a dynamic, loose, non-covalent clustering in the water-rich region, This clustering can be viewed as "micelle-like structural fluctuations". Although these fluctuations are short ranged (approximately 1 nm) and short lived (10 ps-50 ps), they may lead to thermodynamic anomalies. In addition, many experiments on aqueous solutions of hydrotropes show the occasional presence of mesoscale (approximately 100 nm) inhomogeneities. We have combined results obtained from molecular dynamics simulations, small-angle neutron scattering, and dynamic light-scattering experiments carried out on tertiary butyl alcohol (hydrotrope)-water solutions and on tertiary butyl alcohol-water-cyclohexane (hydrophobe) solutions to elucidate the nature and structure of these inhomogeneities. We have shown that stable mesoscale inhomogeneities occur in aqueous solutions of nonionic hydrotropes only when the solution contains a third, more hydrophobic, component. Moreover, these inhomogeneities exist in ternary systems only in the concentration range where structural fluctuations and thermodynamic anomalies are observed in the binary water-hydrotrope solutions. Addition of a hydrophobe seems to stabilize the water-hydrotrope structural fluctuations, and leads to the formation of larger (mesoscopic) droplets. The structure of these mesoscopic droplets is such that they have a hydrophobe-rich core, surrounded by a hydrogen-bonded shell of water and hydrotrope molecules. These droplets can be extremely long-lived, being stable for over a year. We refer to the phenomenon of formation of mesoscopic droplets in aqueous solutions of nonionic hydrotropes containing hydrophobes, as mesoscale solubilization. This phenomenon may represent a ubiquitous feature of nonionic hydrotropes that exhibit clustering in water, and may have important practical applications in areas, such as drug delivery, where the replacement of traditional surfactants may be necessary.

We have resolved a long-standing issue in the discussion on the origin of the mesoscale inhomogeneities observed in aqueous solutions of tertiary butyl alcohol (TBA). We have shown that the formation of stable mesoscale particles (of about 100 nm in size) can be triggered by the addition of trace amounts of propylene oxide (an impurity expected to be present in all commercial samples of TBA) to a solution, which was previously filtered at a low temperature to remove these inhomogeneities. We hypothesize that these particles are aggregates of mixed clathrate-hydrates that are formed through the stabilization of fluctuations of the intrinsic structure in TBA aqueous solutions by the clathrate-forming ability of propylene oxide.

Motivated by controversies in the literature on the microscopic and mesoscopic structure of some aqueous solutions, we have performed static and dynamic light-scattering experiments in aqueous solutions of 3-methylpyridine (3MP) and tertiary butyl alcohol (TBA). In addition to the microscopic concentration fluctuations we have found the presence of reproducible mesoscopic inhomogeneities, which become especially pronounced below room temperature. We find that the observed inhomogeneities are near-spherical Brownian aggregates of a size from a hundred to a few hundred nm. We speculate that these aggregates are long-lived metastable clathrate-like precursors triggered by minute traces of impurities in these solutions.

Claspin is an essential protein for the ATR-dependent activation of the DNA replication checkpoint response in Xenopus and human cells. Here we describe the purification and characterization of human Claspin. The protein has a ring-like structure and binds with high affinity to branched DNA molecules. These findings suggest that Claspin may be a component of the replication ensemble and plays a role in the replication checkpoint by directly associating with replication forks and with the various branched DNA structures likely to form at stalled replication forks because of DNA damage.

BLM, WRN, and p53 are involved in the homologous DNA recombination pathway. The DNA structure-specific helicases, BLM and WRN, unwind Holliday junctions (HJ), an activity that could suppress inappropriate homologous recombination during DNA replication. Here, we show that purified, recombinant p53 binds to BLM and WRN helicases and attenuates their ability to unwind synthetic HJ in vitro. The p53 248W mutant reduces abilities of both to bind HJ and inhibit helicase activities, whereas the p53 273H mutant loses these abilities. Moreover, full-length p53 and a C-terminal polypeptide (residues 373-383) inhibit the BLM and WRN helicase activities, but phosphorylation at Ser 376 or Ser 378 completely abolishes this inhibition. Following blockage of DNA replication, Ser 15 phospho-p53, BLM, and RAD51 colocalize in nuclear foci at sites likely to contain DNA replication intermediates in cells. Our results are consistent with a novel mechanism for p53-mediated regulation of DNA recombinational repair that involves p53 post-translational modifications and functional protein-protein interactions with BLM and WRN DNA helicases. Bloom and Werner syndromes (BS and WS)1 are autosomal recessive disorders characterized by immune deficiency, cancer predisposition, and chromosomal instability (1). The products of the genes responsible for these disorders, BLM and WRN, are ATP-dependent DNA helicases that exhibit 3Ј to 5Ј polarity. Mutations in the BLM or WRN genes disrupt their helicase activity, which may be important for the phenotypic traits associated with these hereditary diseases (2).Homologous recombination (HR) is required for genetic exchange during meiosis, repair of complex lesions in DNA, and the segregation of chromosomes at cell division. Expression of the BLM or WRN helicases in Saccharomyces cerevisiae containing a mutation in sgs1, a BLM and WRN homolog, suppresses their increased rates of illegitimate recombination and HR (3). BLM and its yeast homologue, Sgs1, functionally interact with topoisomerase III (4), whereas the WRN interaction with DNA polymerase ␦ is apparently required for some aspect of DNA replication and/or repair (5, 6). Recent reports indicate that both of these helicases recognize and disrupt alternative DNA structures, including G-quadruplex DNA and Holliday junctions (HJ) (7-11). HJ arise as intermediates during HR and can occur spontaneously, or during DNA replication and the repair of DNA damage (12). BLM and WRN may promote ATP-dependent translocation of HJ to eliminate DNA recombination intermediates, thereby reducing inappropriate DNA recombination in vivo (10, 11). p53 suppresses genomic instability, particularly in response to DNA damage (13,14). p53 also has been implicated in HR. Evidence of p53 modulation of HR includes the following: (a) overexpression of wild-type p53 (WT p53) can down-regulate the rate of HR between SV40 molecules (15); (b) the rate of HR is increased in p53 mutant cell lines (16 -18); (c) p53 has 3Ј to 5Ј exonuclease and DNA strand transfer activities (19); and...