Diversity of DNA methyltransferases that recognize asymmetric target sequences

DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.

Enhanced Ion Anisotropy by Nonconventional Coordination Geometry: Single-Chain Magnet Behavior for a [{(FeL)-L-II}(2){Nb-IV(CN)(8)}] Helical Chain Compound Designed with Heptacoordinate Fe-II

Nonconventional heptacoordination in combination with efficient magnetic exchange coupling is shown to yield a 1-D heteronuclear {(FeNbIV)-Nb-II} compound with remarkable magnetic features when compared to other Fe(II)-based single chain magnets (SCM). Cyano-bridged heterometallic {3d-4d} and {3d-5d} chains are formed upon assembling Fe(II) bearing a pentadentate macrocycle as the blocking ligand with octacyano metallates, [M(CN)(8)](4-) (M = Nb-IV, Mo-IV, W-IV.) X-ray diffraction (single-crystal and powder) measurements reveal that the [{(H2O)Fe(L-1)}{M(CN)(8)}{Fe(L-1)}](infinity) architectures consist of isomorphous 1-D polymeric structures based on the alternation of {Fe(L-1)}(2+) and {M(CN)(8)}(4-) units (L-1 stands for the pentadentate macrocycle). Analysis of the magnetic susceptibility behavior revealed cyano-bridged {Fe-Nb} exchange interaction to be antiferromagnetic with J = -20 cm(-1) deduced from fitting an Ising model taking into account the noncollinear spin arrangement. For this ferrimagnetic chain a slow relaxation of its magnetization is observed at low temperature revealing a SCM behavior with Delta/k(B) = 74 K and tau(0) = 4.6 x 10(-11) s. The M versus H behavior exhibits a hysteresis loop with a coercive field of 4 kOe at 1 K and reveals at 380 mK magnetic avalanche processes, i.e., abrupt reversals in magnetization as H is varied. The origin of these characteristics is attributed to the combination of efficient {Fe-Nb} exchange interaction and significant anisotropy of the {Fe(L-1)) unit. High field EPR and magnetization experiments have revealed for the parent compound [Fe(L-1)(H2O)(2)]Cl-2 a negative zero field splitting parameter of D approximate to -17 cm(-1). The crystal structure, magnetic behavior, and Mossbauer data for [Fe(L-1)(H2O)(2)]Cl-2 are also reported.

Enhanced Ion Anisotropy by Nonconventional Coordination Geometry: Single-Chain Magnet Behavior for a [{(FeL)-L-II}(2){Nb-IV(CN)(8)}] Helical Chain Compound Designed with Heptacoordinate Fe-II

Nonconventional heptacoordination in combination with efficient magnetic exchange coupling is shown to yield a 1-D heteronuclear {(FeNbIV)-Nb-II} compound with remarkable magnetic features when compared to other Fe(II)-based single chain magnets (SCM). Cyano-bridged heterometallic {3d-4d} and {3d-5d} chains are formed upon assembling Fe(II) bearing a pentadentate macrocycle as the blocking ligand with octacyano metallates, [M(CN)(8)](4-) (M = Nb-IV, Mo-IV, W-IV.) X-ray diffraction (single-crystal and powder) measurements reveal that the [{(H2O)Fe(L-1)}{M(CN)(8)}{Fe(L-1)}](infinity) architectures consist of isomorphous 1-D polymeric structures based on the alternation of {Fe(L-1)}(2+) and {M(CN)(8)}(4-) units (L-1 stands for the pentadentate macrocycle). Analysis of the magnetic susceptibility behavior revealed cyano-bridged {Fe-Nb} exchange interaction to be antiferromagnetic with J = -20 cm(-1) deduced from fitting an Ising model taking into account the noncollinear spin arrangement. For this ferrimagnetic chain a slow relaxation of its magnetization is observed at low temperature revealing a SCM behavior with Delta/k(B) = 74 K and tau(0) = 4.6 x 10(-11) s. The M versus H behavior exhibits a hysteresis loop with a coercive field of 4 kOe at 1 K and reveals at 380 mK magnetic avalanche processes, i.e., abrupt reversals in magnetization as H is varied. The origin of these characteristics is attributed to the combination of efficient {Fe-Nb} exchange interaction and significant anisotropy of the {Fe(L-1)) unit. High field EPR and magnetization experiments have revealed for the parent compound [Fe(L-1)(H2O)(2)]Cl-2 a negative zero field splitting parameter of D approximate to -17 cm(-1). The crystal structure, magnetic behavior, and Mossbauer data for [Fe(L-1)(H2O)(2)]Cl-2 are also reported.

Folding a Polymer via Two-Point Interaction with an External Folding Agent: Use of H-Bonding and Charge-Transfer Interactions

A polymer containing electron-rich aromatic donors (1,5-dialkoxynaphthalene (DAN)) was coerced into a folded state by an external folding agent that contained an electron-deficient aromatic acceptor (pyromellitic diimide (PM)) unit. The donor-containing polymer was designed to carry a tertiary amine moiety in the linking segment, which served as an H-bonding site for reinforcing the interaction with the acceptor containing folding agent that also bore a carboxylic acid group. The H-bonding interaction of the carboxylic acid and the tertiary amine brings the PDI unit between two adjacent DAN units along the polymer backbone to induce charge-transfer (C-T) interactions, and this in turn causes the polymer chain to form a pleated structure. Evidence for the formation of such a pleated structure was obtained from NMR titration studies and also by monitoring the C-T band in their UV-visible spectra. By varying the length of the segment that links the PDI acceptor to the carboxylic acid group, we showed that the most effective folding agent was the one that had a single carbon spacer, as evident from the highest value of the association constant. Control experiments with propionic acid clearly demonstrated the importance of the additional C-T interactions for venerating the folded structures. Further, solution viscosity measurements in the presence of varying amounts of the folding agent revealed a gradual stiffening of the chain in the case of the PDI carrying carboxylic acid, whereas no such affect was seen in the case of simple propionic acid. These observations were supported by D FT calculations of the interactions of a dimeric model of the polymer with the various folding agents; here too the stability of the complex was seen to be highest in the case of the single carbon spacer.

Generation of Cationic Two-Coordinate Group-13 Ligand Systems by Spontaneous Halide Ejection: Remarkably Nucleophile-Resistant (Dimethylamino)borylene Complexes

Spontaneous ejection of chloride from a three-coordinate boron Lewis acid can be effected by employing very electron rich metal substituents and leads to the formation of a sterically unprotected terminal (dimethylamino)borylene complex that has a short metal-boron bond and remarkable resistance to attack by nucleophilic and protic reagents.

Mycobacterium tuberculosis UvrD1 and UvrA Proteins Suppress DNA Strand Exchange Promoted by Cognate and Noncognate RecA Proteins

DNA helicases are present in all kingdoms of life and play crucial roles in processes of DNA metabolism such as replication, repair, recombination, and transcription. To date, however, the role of DNA helicases during homologous recombination in mycobacteria remains unknown. In this study, we show that Mycobacterium tuberculosis UvrD1 more efficiently inhibited the strand exchange promoted by its cognate RecA, compared to noncognate Mycobacterium smegmatis or Escherichia coli RecA proteins. The M. tuberculosis UvrD1(Q276R) mutant lacking the helicase and ATPase activities was able to block strand exchange promoted by mycobacterial RecA proteins but not of E. coil RecA. We observed that M. tuberculosis UvrA by itself has no discernible effect on strand exchange promoted by E. coli RecA but impedes the reaction catalyzed by the mycobacterial RecA proteins. Our data also show that M. tuberculosis UvrA and UvrD1 can act together to inhibit strand exchange promoted by mycobacterial RecA proteins. Taken together, these findings raise the possibility that UvrD1 and UvrA might act together in vivo to counter the deleterious effects of RecA nucleoprotein filaments and/or facilitate the dissolution of recombination intermediates. Finally, we provide direct experimental evidence for a physical interaction between M. tuberculosis UvrD1 and RecA on one hand and RecA and UvrA on the other hand. These observations are consistent with a molecular mechanism, whereby M. tuberculosis UvrA and UvrD1, acting together, block DNA strand exchange promoted by cognate and noncognate RecA proteins.

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Single-File Diffusion of Confined Water Inside SWNTs: An NMR Study

We report a nuclear magnetic resonance (NMR) study of confined water inside similar to 1.4 nm diameter single-walled carbon nanotubes (SWNTs). We show that the confined water does not freeze even up to 223 K. A pulse field gradient (PFG) NMR method is used to determine the mean squared displacement (MSD) of the water molecules inside the nanotubes at temperatures below 273 K, where the bulk water outside the nanotubes freezes and hence does not contribute to the proton NMR signal. We show that the mean squared displacement varies as the square root of time, predicted for single-file diffusion in a one-dimensional channel. We propose a qualitative understanding of our results based on available molecular dynamics simulations.

Single-File Diffusion of Water Inside Narrow Carbon Nanorings

We use atomistic molecular dynamics (MD) simulations to study the diffusion of water molecules confined inside narrow (6,6) carbon nanorings. The water molecules form two oppositely polarized chains. It is shown that the effective interaction between these two chains is repulsive in nature. The computed mean-squared displacement (MSD) clearly shows a scaling with time similar to t(1/2), which is consistent with single-file diffusion (SFD). The time up to which the water molecules undergo SFD is shown to be the lifetime of the water molecules inside these chains. Simulations of "uncharged" water molecules inside the nanoring show the formation of several water chains and yield SFD. These observations conclusively prove that the diffusion is Fickian when there is a single chain of water and SFD is observed only when two or more chains are present.

Solution-Combustion Synthesized Nanocrystalline Li4Ti5O12 As High-Rate Performance Li-Ion Battery Anode

Nanocrystalline Li4Ti5O12 (LTO) crystallizing in cubic spinel-phase has been synthesized by single-step-solution-combustion method in less than one minute. LTO particles thus synthesized are flaky and highly porous in nature with a surface area of 12 m(2)/g. Transmission electron micrographs indicate the primary particles to be agglomerated crystallites of varying size between 20 and 50 nm with a 3-dimensional interconnected porous network. During their galvanostatic charge-discharge at varying rates, LTO electrodes yield a capacity value close to the theoretical value of 175 mA h/g at C/2 rate. The electrodes also exhibit promising capacity retention with little capacity loss over 100 cycles at varying discharge rates together with attractive discharge-rate capabilities yielding capacity values of 140 mA h/g and 70 mA h/g at 10 and 100 C discharge rates, respectively. The ameliorated electrode-performance is ascribed to nano and highly porous morphology of the electrodes that provide short diffusion-paths for Li in conjunction with electrolyte percolation through the electrode pores ensuring a high flux of Li.

Essential role of PI3-kinase pathway in p53-mediated transcription: Implications in cancer chemotherapy

The PI3-kinase pathway is the target of inactivation in achieving better cancer chemotherapy. Here, we report that p53-mediated transcription is inhibited by pharmacological inhibitors and a dominant-negative mutant of PI3-kinase, and this inhibition was relieved by a constitutively active mutant of PI3-kinase. Akt/PKB and mTOR, the downstream effectors of PI3-kinase, were also found to be essential. LY294002 (PI3-kinase inhibitor) pre-treatment altered the post-translational modifications and the sub-cellular localization of p53. Although LY294002 increased the chemosensitivity of cells to low concentrations of adriamycin (adriamycin-low), it protected the cells from cytotoxicity induced by high concentrations of adriamycin (adriamycin-high) in a p53-dependent manner. Further, we found that LY294002 completely abolished the activation of p53 target genes (particularly pro-apoptotic) under adriamycin-high conditions, whereas it only marginally repressed the p53 target genes under adriamycin-low conditions; in fact, it further activated the transcription of NOXA, HRK, APAF1 and CASP5 genes. Thus, the differential effect of PI3-kinase on p53 functions seems to be responsible for the differential regulation of DNA damage-induced cytotoxicity and cell death by PI3-kinase. Our finding becomes relevant in the light of ongoing combination chemotherapy trials with the PI3-kinase pathway inhibitors and underscores the importance of p53 status in the careful formulation of combination chemotherapies. Oncogene (2010) 29, 3605-3618; doi: 10.1038/onc.2010.123; published online 26 April 2010

New Solid State Forms of the Anti-HIV Drug Efavirenz. Conformational Flexibility and High Z ` Issues

Structural information on the solid forms of efavirenz, a non-nucleoside reverse transcriptase inhibitor, is limited, although various polymorphic forms of this drug have been patented. We report here structural studies of four new crystal forms a pure form, a cyclohexane solvate, and cocrystals with 1,4-cyclohexanedione and 4,4'-bipyridine. Temperature dependent single-crystal to single-crystal phase transitions are observed for the pure form and for the cyclohexane solvate with an increase in the number of symmetry independent molecules, Z', upon a lowering of temperature. Other issues related to these solid forms, such as thermal stability, conformational flexibility, and high Z' occurrences, are addressed by using a combined experimental and computational approach.

Surface freshwater from Bay of Bengal runoff and Indonesian Throughflow in the Tropical Indian Ocean

According to recent estimates, the annual total continental runoff into the Bay of Bengal (BoB) is about 2950 km 3, which is more than half that into the entire tropical Indian Ocean (IO). Here we use climatological observations to trace the seasonal pathways of near surface freshwater from BoB runoff and Indonesian Throughflow (ITF) by removing the net contribution from precipitation minus evaporation. North of 20 degrees S, the amount of freshwater from BoB runoff and ITF changes with season in a manner consistent with surface currents from drifters. BoB runoff reaches remote regions of the Arabian Sea; it also crosses the equator in the east to join the ITF. This freshwater subsequently flows west across the southern tropical IO in the South Equatorial Current.

Synthesis and magnetic properties of an amine-templated Fe2+ (S=2) sulfate with a distorted Kagome structure

An organically templated iron(II) sulfate of the composition [H3N(CH2)2NH2(CH2)2(NH3]4[FeII 9F18(SO4)6]â9H2O with a distorted Kagome structure has been synthesized under solvothermal conditions in the presence of diethylenetriamine. The distortion of the hexagonal bronze structure comes from the presence of two different types of connectivity between the FeF4O2 octahedra and the sulfate tetrahedra. This compound exhibits magnetic properties different from those of an Fe(II) compound with a perfect Kagome structure and is a canted antiferromagnet at low temperatures.