Recent Developments in the Chemistry and Biology of G-Quadruplexes with Reference to the DNA Groove Binders

DNA is the chemotherapeutic target for treating diseases of genetic origin. Besides well-known double-helical structures (A, B, Z, parallel stranded-DNA etc.), DNA is capable of forming several multi-stranded structures (triplex, tetraplex, i-motif etc.) which have unique biological significance. The G-rich 3'-ends of chromosomes, called telomeres, are synthesized by telomerase, a ribonucleoprotein, and over-expression of telomerase is associated with cancer. The activity of telomerase is suppressed if the G-rich region is folded into the four stranded structures, called G-quadruplexes (G4-DNAs) using small synthetic ligands. Thus design and synthesis of new G4-DNA ligands is an attractive strategy to combat cancer. G4-DNA forming sequences are also prevalent in other genomic regions of biological significance including promoter regions of several oncogenes. Effective gene regulation may be achieved by inducing a G4-DNA structure within the G-rich promoter sequences. To date, several G4-DNA stabilizing ligands are known. DNA groove binders interact with the duplex B-DNA through the grooves (major and minor groove) in a sequence-specific manner. Some of the groove binders are known to stabilize the G4-DNA. However, this is a relatively under explored field of research. In this review, we focus on the recent advances in the understanding of the G4-DNA structures, particularly made from the human telomeric DNA stretches. We summarize the results of various investigations of the interaction of various organic ligands with the G4-DNA while highlighting the importance of groove binder-G4-DNA interactions.

Theoretical estimation of electromigration in metallic carbon nanotubes considering self-heating effect

In this paper, we estimate the solution of the electromigration diffusion equation (EMDE) in isotopically pure and impure metallic single-walled carbon nanotubes (CNTs) (SWCNTs) by considering self-heating. The EMDE for SWCNT has been solved not only by invoking the dependence of the electromigration flux on the usual applied static electric field across its two ends but also by considering a temperature-dependent thermal conductivity (κ) which results in a variable temperature distribution (T) along its length due to self-heating. By changing its length and isotopic impurity, we demonstrate that there occurs a significant deviation in the SWCNT electromigration performance. However, if κ is assumed to be temperature independent, the solution may lead to serious errors in performance estimation. We further exhibit a tradeoff between length and impurity effect on the performance toward electromigration. It is suggested that, to reduce the vacancy concentration in longer interconnects of few micrometers, one should opt for an isotopically impure SWCNT at the cost of lower κ, whereas for comparatively short interconnects, pure SWCNT should be used. This tradeoff presented here can be treated as a way for obtaining a fairly well estimation of the vacancy concentration and mean time to failure in the bundles of CNT-based interconnects. © 2012 IEEE.

Experimental Investigation on the Effect of Advanced Bus-Clamping Pulsewidth Modulation on Motor Acoustic Noise

Voltage source inverters (VSIs) supply nonsinusoidal voltages to induction motor drives, leading to line current distortion and torque pulsation. Conventional space vector pulsewidth modulation (PWM) techniques are widely used in VSIs on the account of good waveform quality and high dc bus utilization. In a conventional space vector PWM technique, the switching sequence begins with one zero state and ends with the other zero state in a subcycle. Some novel switching sequences have been proposed, which employ only one zero state but apply one of the two active states twice in a subcycle. One pair of such special switching sequences has recently been shown to reduce the pulsating torque considerably. In this paper, the conventional and special switching sequences are compared experimentally in terms of acoustic noise. In the low-and medium-speed ranges, the special switching sequence is seen to reduce the amplitude of the tonal component of noise at the switching frequency considerably and is also found to result in spread spectrum.

3-MANIFOLD GROUPS, KÄHLER GROUPS AND COMPLEX SURFACES

Let G be a Kahler group admitting a short exact sequence 1 -> N -> G -> Q -> 1 where N is finitely generated. (i) Then Q cannot be non-nilpotent solvable. (ii) Suppose in addition that Q satisfies one of the following: (a) Q admits a discrete faithful non-elementary action on H-n for some n >= 2. (b) Q admits a discrete faithful non-elementary minimal action on a simplicial tree with more than two ends. (c) Q admits a (strong-stable) cut R such that the intersection of all conjugates of R is trivial. Then G is virtually a surface group. It follows that if Q is infinite, not virtually cyclic, and is the fundamental group of some closed 3-manifold, then Q contains as a finite index subgroup either a finite index subgroup of the three-dimensional Heisenberg group or the fundamental group of the Cartesian product of a closed oriented surface of positive genus and the circle. As a corollary, we obtain a new proof of a theorem of Dimca and Suciu in Which 3-manifold groups are Kahler groups? J. Eur. Math. Soc. 11 (2009) 521-528] by taking N to be the trivial group. If instead, G is the fundamental group of a compact complex surface, and N is finitely presented, then we show that Q must contain the fundamental group of a Seifert-fibered 3-manifold as a finite index subgroup, and G contains as a finite index subgroup the fundamental group of an elliptic fibration. We also give an example showing that the relation of quasi-isometry does not preserve Kahler groups. This gives a negative answer to a question of Gromov which asks whether Kahler groups can be characterized by their asymptotic geometry.

Unraveling siRNA unzipping kinetics with graphene

Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (tau) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4742189]

Development of moving magnet type linear motor for dual piston compressor for pulse tube cryocooler

This paper describes the design, fabrication and testing of a moving magnet type linear motor of dual piston configuration for a pulse tube cryocooler for ground applications. Eight radially magnetized segmented magnets were used to form one set of a magnet ring. Four magnet rings of such type were constructed, in which one pair of rings has north-pole on its outer diameter and south-pole on inner diameter, while the other pair is it's complementary. The magnets were mounted with opposite poles together on the magnet holder with an axial moving shaft having a piston mounted on both ends of the shaft. The shaft movement was restricted to the axial direction by using C-clamp type flexures, mounted on both sides of the shaft. The force requirement for driving the compressor was calculated based on which the electrical circuit of motor is designed by proper selection of wire gauge and Ampere-turns. The flexure spring force estimation was done through simulation using ANSYS 11.0 and was verified experimentally; while the magnet spring force was determined experimentally. The motor with mounted piston was tested using a variable voltage and variable frequency power supply capable of driving 140 watts of load.

A Multilevel Inverter Scheme With Dodecagonal Voltage Space Vectors Based on Flying Capacitor Topology for Induction Motor Drives

This paper presents a multilevel inverter topology suitable for the generation of dodecagonal space vectors instead of hexagonal space vectors as in the case of conventional schemes. This feature eliminates all the 6n +/- 1 (n = odd) harmonics from the phase voltages and currents in the entire modulation range with an increase in the linear modulation range. The topology is realized by flying capacitor-based three-level inverters feeding from two ends of an open-end winding induction motor with asymmetric dc links. The flying capacitor voltages are tightly controlled throughout the modulation range using redundant switching states for any load power factor. A simple and fast carrier-based space-vector pulsewidth modulation (PWM) scheme is also proposed for the topology which utilizes only the sampled amplitudes of the reference wave for the PWM timing computation.

Self catalytic growth of SnO2 branched nanowires by thermal evaporation

For the first time, Tin oxide (SnO2) multiple branched nanowires (NWs) have been synthesized by thermal evaporation of tin (Sn) in presence of oxygen without use of metal catalysts at low substrate temperature of 500 degrees C. Synthesized product consists of multiple branched nanowires and were single crystalline in nature. Each of the nanowire capped with catalyst particle at their ends. Energy dispersive X-ray analysis on the nanowires and capped nanoparticle confirms that Sn act as catalyst for SnO2 nanowires growth. A self catalytic vapor-liquid-solid (VLS) growth mechanism was proposed to describe the SnO2 nanowires growth. (C) 2012 Elsevier B.V. All rights reserved.

Processing of DNA double-stranded breaks and intermediates of recombination and repair by saccharomyces cerevisiae Mre11 and its stimulation by Rad50, Xrs2, and Sae2 proteins

Saccharomyces cerevisiae RAD50, MRE11, and XRS2 genes are essential for telomere length maintenance, cell cycle checkpoint signaling, meiotic recombination, and DNA double-stranded break (DSB) repair via nonhomologous end joining and homologous recombination. The DSB repair pathways that draw upon Mre11-Rad50-Xrs2 subunits are complex, so their mechanistic features remain poorly understood. Moreover, the molecular basis of DSB end resection in yeast mre11-nuclease deficient mutants and Mre11 nuclease-independent activation of ATM in mammals remains unknown and adds a new dimension to many unanswered questions about the mechanism of DSB repair. Here, we demonstrate that S. cerevisiae Mre11 (ScMre11) exhibits higher binding affinity for single-over double-stranded DNA and intermediates of recombination and repair and catalyzes robust unwinding of substrates possessing a 3' single-stranded DNA overhang but not of 5' overhangs or blunt-ended DNA fragments. Additional evidence disclosed that ScMre11 nuclease activity is dispensable for its DNA binding and unwinding activity, thus uncovering the molecular basis underlying DSB end processing in mre11 nuclease deficient mutants. Significantly, Rad50, Xrs2, and Sae2 potentiate the DNA unwinding activity of Mre11, thus underscoring functional interaction among the components of DSB end repair machinery. Our results also show that ScMre11 by itself binds to DSB ends, then promotes end bridging of duplex DNA, and directly interacts with Sae2. We discuss the implications of these results in the context of an alternative mechanism for DSB end processing and the generation of single-stranded DNA for DNA repair and homologous recombination.

Human la protein interaction with GCAC near the initiator AUG enhances hepatitis C virus RNA replication by promoting linkage between 5 ` and 3 ` untranslated regions

Human La protein has been implicated in facilitating the internal initiation of translation as well as replication of hepatitis C virus (HCV) RNA. Previously, we demonstrated that La interacts with the HCV internal ribosome entry site (IRES) around the GCAC motif near the initiator AUG within stem-loop IV by its RNA recognition motif (RRM) (residues 112 to 184) and influences HCV translation. In this study, we have deciphered the role of this interaction in HCV replication in a hepatocellular carcinoma cell culture system. We incorporated mutation of the GCAC motif in an HCV monocistronic subgenomic replicon and a pJFH1 construct which altered the binding of La and checked HCV RNA replication by reverse transcriptase PCR (RT-PCR). The mutation drastically affected HCV replication. Furthermore, to address whether the decrease in replication is a consequence of translation inhibition or not, we incorporated the same mutation into a bicistronic replicon and observed a substantial decrease in HCV RNA levels. Interestingly, La overexpression rescued this inhibition of replication. More importantly, we observed that the mutation reduced the association between La and NS5B. The effect of the GCAC mutation on the translation-to-replication switch, which is regulated by the interplay between NS3 and La, was further investigated. Additionally, our analyses of point mutations in the GCAC motif revealed distinct roles of each nucleotide in HCV replication and translation. Finally, we showed that a specific interaction of the GCAC motif with human La protein is crucial for linking 5' and 3' ends of the HCV genome. Taken together, our results demonstrate the mechanism of regulation of HCV replication by interaction of the cis-acting element GCAC within the HCV IRES with human La protein.

Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA

The RecA filament formed on double-stranded (ds) DNA is proposed to be a functional state analogous to that generated during the process of DNA strand exchange. RecA polymerization and de-polymerization on dsDNA is governed by multiple physiological factors. However, a comprehensive understanding of how these factors regulate the processes of polymerization and de-polymerization of RecA filament on dsDNA is still evolving. Here, we investigate the effects of temperature, pH, tensile force, and DNA ends (in particular ssDNA overhang) on the polymerization and de-polymerization dynamics of the E. coli RecA filament at a single-molecule level. Our results identified the optimal conditions that permitted spontaneous RecA nucleation and polymerization, as well as conditions that could maintain the stability of a preformed RecA filament. Further examination at a nano-meter spatial resolution, by stretching short DNA constructs, revealed a striking dynamic RecA polymerization and de-polymerization induced saw-tooth pattern in DNA extension fluctuation. In addition, we show that RecA does not polymerize on S-DNA, a recently identified novel base-paired elongated DNA structure that was previously proposed to be a possible binding substrate for RecA. Overall, our studies have helped to resolve several previous single-molecule studies that reported contradictory and inconsistent results on RecA nucleation, polymerization and stability. Furthermore, our findings also provide insights into the regulatory mechanisms of RecA filament formation and stability in vivo.

Wide Voltage Input Receiver with Hysteresis Characteristic to Reduce Input Signal Noise Effect

In this paper, an input receiver with a hysteresis characteristic that can work at voltage levels between 0.9 V and 5 V is proposed. The input receiver can be used as a wide voltage range Schmitt trigger also. At the same time, reliable circuit operation is ensured. According to the research findings, this is the first time a wide voltage range Schmitt trigger is being reported. The proposed circuit is compared with previously reported input receivers, and it is shown that the circuit has better noise immunity. The proposed input receiver ends the need for a separate Schmitt trigger and input buffer. The frequency of operation is also higher than that of the previously reported receiver. The circuit is simulated using HSPICE at 035-mu m standard thin oxide technology. Monte Carlo analysis is conducted at different process conditions, showing that the proposed circuit works well for different process conditions at different voltage levels of operation. A noise impulse of (V-CC/2) magnitude is added to the input voltage to show that the receiver receives the correct logic level even in the presence of noise. Here, V-CC is the fixed voltage supply of 3.3 V.

Floquet generation of Majorana end modes and topological invariants

We show how Majorana end modes can be generated in a one-dimensional system by varying some of the parameters in the Hamiltonian periodically in time. The specific model we consider is a chain containing spinless electrons with a nearest-neighbor hopping amplitude, a p-wave superconducting term, and a chemical potential; this is equivalent to a spin-1/2 chain with anisotropic XY couplings between nearest neighbors and a magnetic field applied in the (z) over cap direction. We show that varying the chemical potential (or magnetic field) periodically in time can produce Majorana modes at the ends of a long chain. We discuss two kinds of periodic driving, periodic delta-function kicks, and a simple harmonic variation with time. We discuss some distinctive features of the end modes such as the inverse participation ratio of their wave functions and their Floquet eigenvalues which are always equal to +/- 1 for time-reversal-symmetric systems. For the case of periodic delta-function kicks, we use the effective Hamiltonian of a system with periodic boundary conditions to define two topological invariants. The first invariant is a well-known winding number, while the second invariant has not appeared in the literature before. The second invariant is more powerful in that it always correctly predicts the numbers of end modes with Floquet eigenvalues equal to + 1 and -1, while the first invariant does not. We find that the number of end modes can become very large as the driving frequency decreases. We show that periodic delta-function kicks in the hopping and superconducting terms can also produce end modes. Finally, we study the effect of electron-phonon interactions (which are relevant at finite temperatures) and a random noise in the chemical potential on the Majorana modes.

Nanoindentation for probing the mechanical behavior of molecular crystals-a review of the technique and how to use it

Nanoindentation is a technique which can be used to measure the mechanical properties of materials with high precision, even when they are only available in small quantities. As a result of this, nanoindentation has gained the attention of the crystal engineering community, who are not only interested in measuring the properties of single crystals of organic, inorganic and hybrid structures, but also wish to correlate the measured responses with the underlying structural features and intermolecular interactions. Keeping this emerging interest in view, a brief overview of the technique, with particular emphasis on the procedures for conducting experiments and analyzing the resulting data, is presented in this Tutorial style Highlight. The precautions that need to be taken and the properties that one can measure using nanoindentation are highlighted. This paper ends with a brief summary of the recent additional features that have been added to this technique and an outlook for nanoindentation within the context of crystal engineering.

Remarkable role of positional isomers in the design of sensors for the ratiometric detection of copper and mercury ions in water

Cation sensing properties of the three positional isomers of rhodamine based sensors (1-3) are studied in water. The sensors differ only in the position of pyridine's nitrogen. The chemosensor 1, with pyridine nitrogen at ortho-position, showed a selective colorimetric detection of Cu(II) ions in water, at physiological pH 7.4 and also in medium containing BSA (bovine serum albumin) and blood serum. Notably the compound 2 and 3, with pyridine end located at meta-and para-positions did not show any color change with Cu(II) ions, although both the compounds showed turn-on change both in color and fluorescence with Hg(II) ions specifically. All the probes showed ratiometric changes with the specific metal ions. The changing position of nitrogen also changed the complexation pattern of the sensors with the metal ions. Probe 1 showed 2 : 1 complexation with Cu(II), whereas 2 and 3 showed 1 : 1 complexation with Hg(II) ions. The mechanism investigation showed that the change in color upon addition of metal ions is due to the ring-opening of the spirolactam ring of the probes. Cu(II) interacted with ligand 1 through a three-point interaction mode comprising carbonyl oxygen, amido nitrogen and pyridine nitrogen end. But in case of 2 and 3, Hg2+ only interacted through pyridine nitrogen ends. Quantitative estimation of Cu2+ and Hg2+ in complex biological media such as bovine albumin protein (BSA) and human blood serum were performed using these sensors. Rapid on-site detection as well as discrimination of these toxic ions was demonstrated using easily prepared portable test-strips.