Accessing chain length dependent termination rate coefficients of methyl methacrylate (MMA) via the reversible addition fragmentation chain transfer (RAFT) process

The RAFT-CLD-T methodology is demonstrated to be not only applicable to 1-substituted monomers such as styrene and acrylates, but also to 1,1-disubstituted monomers such as MMA. The chain length of the terminating macromolecules is controlled by CPDB in MMA bulk free radical polymerization at 80 degrees C. The evolution of the chain length dependent termination rate coefficient, k(t)(i,i), was constructed in a step-wise fashion, since the MMA/CPDB system displays hybrid behavior (between conventional and living free radical polymerization) resulting in initial high molecular weight polymers formed at low RAFT agent concentrations. The obtained CLD of k(t) in MMA polymerizations is compatible with the composite model for chain length dependent termination. For the initial chain-length regime, up to a degree of polymerization of 100, k(t) decreases with alpha (in the expression k(t)(i,i) = k(t)(0) . i(-alpha)) being close to 0.65 at 80 degrees C. At chain lengths exceeding 100, the decrease is less pronounced (affording an alpha of 0.15 at 80 degrees C). However, the data are best represented by a continuously decreasing nonlinear functionality implying a chain length dependent alpha.

Self-Organization of n-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule

We demonstrate a chain length dependent crossover in the structural properties of linear hydrocarbon (n-alkane) chains using detailed atomistic simulations in explicit water. We identify a number of exotic structures of the polymer chain through energy minimization of representative snapshots collected from molecular dynamics trajectory. While the collapsed state is ring-like (circular) for small chains (CnH2n+2; n <= 20) and spherical for very long ones (n = 100), we find the emergence of ordered helical structures at intermediate lengths (n similar to 40). We find different types of disordered helices and toroid-like structures at n = 60. We also report a sharp transition in the stability of the collapsed state as a function of the chain length through relevant free energy calculations. While the collapsed state is only marginally metastable for C20H42, a clear bistable free energy surface emerges only when the chain is about 30 monomers long. For n = 30, the polymer exhibits an intermittent oscillation between the collapsed and the coil structures, characteristic of two stable states separated by a small barrier.

Theoretical Estimation of Length Dependent In-Plane Stiffness of Single Walled Carbon Nanotubes Using the Nonlocal Elasticity Theory

In the present paper, Eringen's nonlocal elasticity theory is employed to evaluate the length dependent in-plane stiffness of single-walled carbon nanotubes (SWCNTs). The SWCNT is modeled as an Euler-Bernoulli beam and is analyzed for various boundary conditions to evaluate the length dependent in-plane stiffness. It has been found that the nonlocal scaling parameter has a significant effect on the length dependent in-plane stiffness of SWCNTs. It has been observed that as the nonlocal scale parameter increases the stiffness ratio of SWCNT decreases. In nonlocality, the cantilever SWCNT has high in-plane stiffness as compared to the simply-supported and the clamped cases.

Synthesis and chain-length dependent properties of monodisperse oligo(9,9-di-n-octylfluorene-2,7-vinylene)s

A series of monodisperse oligo(9,9-di-n-octylfluorene-2,7-vinylene)s (OFVs) with fluorene units up to 11 has been synthesized following a divergent approach. Chain length was found to affect not only photophysical properties but also thermal properties. Absorption and photoluminescence spectra are red-shifted with increasing chain length. The effective conjugated length has been extrapolated to be as long as 19 fluorene vinylene units, indicative of a well-conjugated system. With the number of fluorene units > 5, the oligomers exhibit nematic mesomorphism. Glass transition temperature (T-g) and clearing point temperature (T-c) increase with increasing molecular length and with those of OFV11 up to 71 and 230 degrees C, respectively. The oligomers can form uniform films by solution casting for fabrication of light-emitting diodes. With a device structure of ITO/ PEDOT:PSS/OFV11/Ca/Al, a current efficiency of 0.8 cd.A(-1) at a brightness of 1300 cd.m(-2) along with a maximum brightness of 2690 cd.m(-2) have been realized. This performance is notably superior to that of the corresponding polymer.

Well-defined higher-molecular-weight polyacrylonitrile via RAFT technique in the presence of disulfide compounds as a source of chain transfer agent

Well-defined polyacrylonitrile with a higher number-average molecular weight (R.) up to 200,000 and a lower polydispersity index (PDI, 1.7-2.0) was firstly obtained via reversible addition-fragmentation chain transfer (RAFT) process. This was achieved by selecting a stable, easy way to prepare disulfide compound intermediates including bis(thiobenzoyl) disulfide (BTBDS) and bis(thiophenylacetoyl) disulfide (BTPADS) to react with azobis(isobutyronitrile) to directly synthesize RAFT agents in situ.

A Novel Strategy to Branched Polyacrylonitrile Via One-Pot RAFT Copolymerization of Acrylonitrile and an Asymmetrical Divinyl Monomer

Branched polyacrylonitriles were prepared via the one-pot radical copolymerization of acrylonitirle and an asymmetric divinyl monomer (allyl methacrylate) that possesses both a higher reactive methacrylate and a lower reactive allyl. RAFT technique was used to keep a low-propagation chain concentration via a fast reversible chain transfer euilibration and thus the cross-linking was prevented until a high level of monomer conversions. This novel strategy was demonstrated to engenerate a branched architecture with abundant pendant functional vinyl and nitrile groups, and controlled molecular weight as a behavior of controlled/living radical polymerization characteristics. The effect of the various experimental parameters, including temperature, brancher to monomer molar ratio, and chain transfer agent to initiator molar ratio, on the control Of moleculer dimension (molecular weight and polydispersity indices) and the degree of branching were investigated in detail. Moreover, H-1 NMR and gel permeation chromatography confirm the branched architecture of the resultant polymer. The intrinsic viscosity of the copolymer is also lower than the linear counterpart.

2-cyanoprop-2-yl dithiobenzoate mediated reversible addition-fragmentation chain transfer polymerization of acrylonitrile targeting a polymer with a higher molecular weight

The reversible addition-fragmentation chain transfer (RAFT) polymerization of acrylonitrile (AN) mediated by 2-cyanoprop-2-yl dithiobenzoate was first applied to synthesize polyacrylonitrile (PAN) with a high molecular weight up to 32,800 and a polydispersity index as low as 1.29. The key to success was ascribed to the optimization of the experimental conditions to increase the fragmentation reaction efficiency of the intermediate radical. In accordance with the atom transfer radical polymerization of AN, ethylene carbonate was also a better solvent candidate for providing higher controlled/living RAFT polymerization behaviors than dimethylformamide and dimethyl sulfoxide. The various experimental parameters, including the temperature, the molar ratio of dithiobenzoate to the initiator, the molar ratio of the monomer to dithiobenzoate, the monomer concentration, and the addition of the comonomer, were varied to improve the control of the molecular weight and polydispersity index. The molecular weights of PANS were validated by gel permeation chromatography along with a universal calibration procedure and intrinsic viscosity measurements. H-1 NMR analysis confirmed the high chain-end functionality of the resultant polymers.

High accuracy curve fits for chirality, length and diameter dependent initial modulus of single walled carbon nanotubes

Many previous studies regarding the estimation of mechanical properties of single walled carbon nanotubes (SWCNTs) report that, the modulus of SWCNTs is chirality, length and diameter dependent. Here, this dependence is quantitatively described in terms of high accuracy curve fit equations. These equations allow us to estimate the modulus of long SWCNTs (lengths of about 100-120 nm) if the value at the prescribed low lengths (lengths of about 5-10 nm) is known. This is supposed to save huge computational time and expense. Also, based on the observed length dependent behavior of SWCNT initial modulus, we predict that, SWCNT mechanical properties such as Young's modulus, secant modulus, maximum tensile strength, failure strength, maximum tensile strain and failure strain might also exhibit the length dependent behavior along with chirality and length dependence. (C) 2010 Elsevier B.V. All rights reserved.

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

The prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. Flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. Surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. How, therefore, does the translation machinery interpret a “stop” codon? We provide evidence, based on ribosomal profiling and “stop” codon depletion shortly before coding sequence ends, that mRNA 3′ ends may contribute to distinguishing stop from sense in a context-dependent manner. We further propose that such context-dependent termination/readthrough suppression near transcript ends enables genetic code evolution.

Tradeoff of average service cost and average delay for the state dependent M/M/1 queue

The optimal tradeoff between average service cost rate and average delay, is addressed for a M/M/1 queueing model with queue-length dependent service rates, chosen from a finite set. We provide an asymptotic characterization of the minimum average delay, when the average service cost rate is a small positive quantity V more than the minimum average service cost rate required for stability. We show that depending on the value of the arrival rate, the assumed service cost rate function, and the possible values of the service rates, the minimum average delay either a) increases only to a finite value, b) increases without bound as log(1/V), or c) increases without bound as 1/V, when V down arrow 0. We apply the analysis to a flow-level resource allocation model for a wireless downlink. We also investigate the asymptotic tradeoff for a sequence of policies which are obtained from an approximate fluid model for the M/M/1 queue.

Yeast RNase III triggers polyadenylation-independent transcription termination

Transcription termination of messenger RNA (mRNA) is normally achieved by polyadenylation followed by Rat1p-dependent 5'-3' exoribonuleolytic degradation of the downstream transcript. Here we show that the yeast ortholog of the dsRNA-specific ribonuclease III (Rnt1p) may trigger Rat1p-dependent termination of RNA transcripts that fail to terminate near polyadenylation signals. Rnt1p cleavage sites were found downstream of several genes, and the deletion of RNT1 resulted in transcription readthrough. Inactivation of Rat1p impaired Rnt1p-dependent termination and resulted in the accumulation of 3' end cleavage products. These results support a model for transcription termination in which cotranscriptional cleavage by Rnt1p provides access for exoribonucleases in the absence of polyadenylation signals.

Eccentric torque-producing capacity is influenced by muscle length in older healthy adults

Considering the importance of muscle strength to functional capacity in the elderly, the study investigated the effects of age on isokinetic performance and torque production as a function of muscle length. Eleven younger (24.2±2.9years) and seventeen older men (62.7±2.5years) were subjected to concentric and eccentric isokinetic knee extension/flexion at 60°.s-1 and 120°.s-1 through a functional range of motion. The older group presented lower peak torque (Nm) than the young group for both isokinetic contraction types (age effect, p<0.001). Peak torque deficits in the older group were near 30% and 29% for concentric and eccentric contraction, respectively. Concentric peak torque was lower at 120.s-1 than at 60.s-1 for both groups (angular velocity effect, p<0.001). Eccentric knee extension torque was the only exercise tested that showed an interaction effect between age and muscle length (p<0.001), which suggested different torque responses to the muscle length between groups. Compared with the young group, the eccentric knee extension torque was 22% to 56% lower in the older group, with the deficits being lower in the shortened muscle length (22-27%) and higher (33-56%) in stretched muscle length. In older men, the production of eccentric knee strength seems to be muscle length-dependent. At more stretched positions, older subjects lose the capacity to generate eccentric knee extension torque. More studies are needed to assess the mechanisms involved in eccentric strength preservation with aging and its relationship with muscle length.

Aggregation of huntingtin in yeast varies with the length of the polyglutamine expansion and the expression of chaperone proteins

Huntington's disease (HD) is an inherited neurodegenerative disorder caused by polyglutamine (polyQ) expansions in the huntingtin (Ht) protein. A hallmark of HD is the proteolytic production of an N-terminal fragment of Ht, containing the polyQ repeat, that forms aggregates in the nucleus and cytoplasm of affected neurons. Proteins with longer polyQ repeats aggregate more rapidly and cause disease at an earlier age, but the mechanism of aggregation and its relationship to disease remain unclear. To provide a new, genetically tractable model system for the study of Ht, we engineered yeast cells to express an N-terminal fragment of Ht with different polyQ repeat lengths of 25, 47, 72, or 103 residues, fused to green fluorescent protein. The extent of aggregation varied with the length of the polyQ repeat: at the two extremes, most HtQ103 protein coalesced into a single large cytoplasmic aggregate, whereas HtQ25 exhibited no sign of aggregation. Mutations that inhibit the ubiquitin/proteasome pathway at three different steps had no effect on the aggregation of Ht fragments in yeast, suggesting that the ubiquitination of Ht previously noted in mammalian cells may not inherently be required for polyQ length-dependent aggregation. Changing the expression levels of a wide variety of chaperone proteins in yeast neither increased nor decreased Ht aggregation. However, Sis1, Hsp70, and Hsp104 overexpression modulated aggregation of HtQ72 and HtQ103 fragments. More dramatically, the deletion of Hsp104 virtually eliminated it. These observations establish yeast as a system for studying the causes and consequences of polyQ-dependent Ht aggregation.

Characterization of a Full-Length TTP Family Member Association with RNA Sequence Elements

Post-transcriptional regulation of cytoplasmic mRNAs is an efficient mechanism of regulating the amounts of active protein within a eukaryotic cell. RNA sequence elements located in the untranslated regions of mRNAs can influence transcript degradation or translation through associations with RNA-binding proteins. Tristetraprolin (TTP) is the best known member of a family of CCCH zinc finger proteins that targets adenosine-uridine rich element (ARE) binding sites in the 3’ untranslated regions (UTRs) of mRNAs, promoting transcript deadenylation through the recruitment of deadenylases. More specifically, TTP has been shown to bind AREs located in the 3’-UTRs of transcripts with known roles in the inflammatory response. The mRNA-binding region of the protein is the highly conserved CCCH tandem zinc finger (TZF) domain. The synthetic TTP TZF domain has been shown to bind with high affinity to the 13-mer sequence of UUUUAUUUAUUUU. However, the binding affinities of full-length TTP family members to the same sequence and its variants are unknown. Furthermore, the distance needed between two overlapping or neighboring UUAUUUAUU 9-mers for tandem binding events of a full-length TTP family member to a target transcript has not been explored. To address these questions, we recombinantly expressed and purified the full-length C. albicans TTP family member Zfs1. Using full-length Zfs1, tagged at the N-terminus with maltose binding protein (MBP), we determined the binding affinities of the protein to the optimal TTP binding sequence, UUAUUUAUU. Fluorescence anisotropy experiments determined that the binding affinities of MBP-Zfs1 to non-canonical AREs were influenced by ionic buffer strength, suggesting that transcript selectivity may be affected by intracellular conditions. Furthermore, electrophoretic mobility shift assays (EMSAs) revealed that separation of two core AUUUA sequences by two uridines is sufficient for tandem binding of MBP-Zfs1. Finally, we found evidence for tandem binding of MBP-Zfs1 to a 27-base RNA oligonucleotide containing only a single ARE-binding site, and showed that this was concentration and RNA length dependent; this phenomenon had not been seen previously. These data suggest that the association of the TTP TZF domain and the TZF domains of other species, to ARE-binding sites is highly conserved. Domains outside of the TZF domain may mediate transcript selectivity in changing cellular conditions, and promote protein-RNA interactions not associated with the ARE-binding TZF domain.

In summary, the evidence presented here suggests that Zfs1-mediated decay of mRNA targets may require additional interactions, in addition to ARE-TZF domain associations, to promote transcript destabilization and degradation. These studies further our understanding of post-transcriptional steps in gene regulation.

Binding of Gemini Bisbenzimidazole Drugs with Human Telomeric G-Quadruplex Dimers: Effect of the Spacer in the Design of Potent Telomerase Inhibitors

The study of anticancer agents that act via stabilization of telomeric G-quadruplex DNA (G4DNA) is important because such agents often inhibit telomerase activity. Several types of G4DNA binding ligands are known. In these studies, the target structures often involve a single G4 DNA unit formed by short DNA telomeric sequences. However, the 3'-terminal single-stranded human telomeric DNA can form higher-order structures by clustering consecutive quadruplex units (dimers or nmers). Herein, we present new synthetic gemini (twin) bisbenzimidazole ligands, in which the oligo-oxyethylene spacers join the two bisbenzimidazole units for the recognition of both monomeric and dimeric G4DNA, derived from d(T2AG3)4 and d(T2AG3) 8 human telomeric DNA, respectively. The spacer between the two bisbenzimidazoles in the geminis plays a critical role in the G4DNA stability. We report here (i) synthesis of new effective gemini anticancer agents that are selectively more toxic towards the cancer cells than the corresponding normal cells; (ii) formation and characterization of G4DNA dimers in solution as well as computational construction of the dimeric G4DNA structures. The gemini ligands direct the folding of the single-stranded DNA into an unusually stable parallel-stranded G4DNA when it was formed in presence of the ligands in KCl solution and the gemini ligands show spacer length dependent potent telomerase inhibition properties.