Effects of Intrachain Interactions on the Knot Size of a Polymer

Knots occur frequently in our daily life and also in long polymers. Studies of spontaneously occurring knots in a linear polymer have focused on their size and probabilities. In this work, we report counterintuitive phenomena about knot sizes and explain them by an analytic theory. Our simulations show that short-range intrachain attractions (repulsions) lead to shrinking (swelling) of knot sizes, trends which follow intuition. However, long-range attractions (repulsions) surprisingly lead to swelling (shrinking) of knot sizes. Such counterintuitive trends are because larger knots contain more interacting monomer pairs if the interaction range is larger than a critical value. The critical interaction range varies from a fraction of to multiple persistence lengths, and so the long-range interaction regime can be reached for DNA, peptide chains, or synthetic polymers under depletion attractions induced by colloids (e.g., proteins) or via Coulomb repulsions. Our results suggest that probabilities and sizes of knots can be controlled <i>independently</i> through adjusting the range and the strength of intrachain interactions

Comparisons of a Polymer in Confinement versus Applied Force

The similarities and differences between geometric and tensile constraints on polymers have not been fully investigated. Here we use theory (blob models) and simulations to present a comprehensive comparison between polymers in these two situations. For a polymer in good solvent, the effect of tensile force <i>f</i> on extension in the Pincus regime is similar to the effect of cylindrical confinement in the de Gennes regime after mapping the characteristic length <i>k</i>_<i>B</i><i>T</i>/<i>f</i> to the cylindrical diameter <i>D</i>, where <i>k</i>_<i>B</i><i>T</i> is the thermal energy. However, the comparison of the effects of tension and confinement on extension is lacking when <i>k</i>_<i>B</i><i>T</i>/<i>f</i> and <i>D</i> are less than the thermal blob size <i>b</i>, referred to as extended Pincus regime and extended de Gennes regime, respectively. In the extended Pincus regime, force can still segregate the ideal-coils with the size of ∼<i>k</i>_<i>B</i><i>T</i>/<i>f</i>, resulting in the scaling of extension <i>L</i>_∥ ∼ (<i>k</i>_<i>B</i><i>T</i>/<i>f</i>)⁻¹. In the extended de Gennes regime, excluded volume interaction is not sufficient to segregate the ideal-coils with the size of <i>D</i>, resulting in the scaling <i>L</i>_∥ ∼ <i>D</i>^–2/3 different from the scaling in the extended Pincus regime. In addition to the scaling of extension, the scaling of fluctuation in extension σ is also compared in the extended Pincus or extended de Gennes regime. It is found that σ is independent of <i>f</i> and <i>D</i>, which reflects the ideal-chain behavior. All of the above scaling relations are validated by Monte Carlo simulations. Simulation and scaling results are also used to determine the experimental conditions needed to access the extended de Gennes and de Gennes regimes in various single molecule experiments

Metastable Tight Knots in Semiflexible Chains

Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simulations. We observe metastable knots on DNA, as predicted by Grosberg and Rabin. Furthermore, we extend their theory to incorporate the finite width of chains and show an agreement between our simulations and the modified theory for real chains. Our results suggest localized knots spontaneously occur in long DNA and the contour length in the knot ranges from 600 to 1800 nm

Effect of Nanoslit Confinement on the Knotting Probability of Circular DNA

Monte Carlo simulations are used to study the knotting probability of circular DNA confined in a slit. We systematically vary the slit height, the width, and the contour length of the DNA molecule. We find that the trend in knotting probability with respect to slit height can be monotonic or nonmonotonic, depending on the width and contour length. The nonmonotonic trend is caused by two competing factors: the increase of the effective persistence length and the increase of segment density by slit confinement. These factors are antagonistic, in the sense that the increase in effective persistence length disfavors knot formation, whereas the increase in segment density favors the knotting probability. Our simulation results bring to light the importance of both chain length and width for slit-confined circular DNA and can be used to guide future experiments which aim to produce populations of knotted DNA through cyclization or catalyzed double-strand passage reactions in confinement

Effects of ethephon on DNA methylation and gene expressions associated with shortened internodes in maize

<p>In this study, the molecular mechanism underlying ethephon-induced shortened internodes in maize was investigated using Zhengdan958 maize variety. The ethephon treatment was performed by spraying 225 mL/ha Ethephon 40% SL onto the foliage at the eight-expanded-leaves stage. The differentially expressed genes in the young internodes under ethephon treatment were identified through methylation-sensitive amplified fragment length polymorphism (MSAP), start codon targeted polymorphism (SCoT) and cDNA-amplified fragment length polymorphism (AFLP) analyses. MSAP results showed the methylation sites were widely distributed in both the ethephon-treated (at 27.8%) and control plants (30.1%). This suggested that ethephon treatment modified the methylation patterns; with 3.0% of the sites being hyper-methylated and 7.3% demethylated compared with the control. Based on SCoT analysis, 148 transcript derived fragments (TDFs) were obtained in the ethephon-treated plants. Among them, 38 were up-regulated (25.7%) and 47 down-regulated (31.8%). cDNA-AFLP analysis using 70 primer pairs identified 1635 TDFs in the ethephon-treated and the control plants. Of these, 600 and 564 TDFs were up- and down-regulated by the ethephon treatment, respectively. BLASTX analysis on 50 (randomly selected) differentially expressed TDFs divided them into several categories based on their putative biological functions: signal transduction (6%), resistance-related (14%), energy and metabolism (22%), transcription (4%), cell apoptosis (2%), unknown functional proteins (42%) and unknown genes (10%). Our results revealed that ethephon treatment could induce DNA methylation variation principally by increasing the demethylation tendency. This is suggested to play roles in stress-defence genes expression regulation and the differentially expressed genes could be associated with shortened internodes in maize.</p

Discovery of Novel Nucleotide Prodrugs with Improved Potency Against HCV Variants Carrying NS5B S282T Mutation

Resistant HCV variants carrying NS5B S282T mutation confer reduced sensitivity to sofosbuvir, the sole marketed NS5B polymerase inhibitor. On the basis of the finding that 2′-α-F-2′-β-<i>C</i>-methylcytidine 5′-triphosphate (<b>8</b>) was more potent than sofosbuvir’s active metabolite on inhibition of both wild-type and S282T mutant polymerase, a dual-prodrug approach has been established. Twenty-nine phosphoramidates with <i>N</i>⁴-modified cytosine were designed, synthesized, and evaluated for anti-HCV activity. The results showed that compounds <b>4c</b>–<b>4e</b> and <b>4m</b> (EC₅₀ = 0.19–0.25 μM) exhibited comparable potency to that of sofosbuvir (EC₅₀ = 0.15 μM) on inhibition of wild-type replicons. Notably, <b>4c</b> (EC₅₀ = 0.366 μM) was 1.5-fold more potent than sofosbuvir (EC₅₀ = 0.589 μM) on inhibition of S282T mutant replicons. In vitro metabolic studies disclosed the possible metabolic pathways of <b>4c</b>. The toxicity study results indicated a good safety profile of <b>4c</b>. Together, <b>4c</b>–<b>4e</b> and <b>4m</b> hold promise for drug development for the treatment of HCV infection, especially the resistant variants with NS5B S282T mutation

Down-regulated HOXB7 decreased cell proliferation in vivo and its effect on cell cycle distribution.

<p>(A) Tumors generated by injection of EC109/KYSE150 with stable knockdown HOXB7 protein and control cells. (B) The weight and volume of tumors from the HOXB7-knockdown cells were relatively lower than those from the control cells. (C) Representative histograms analyzed by flow cytometry showed the cell cycle profiles of the ESCC cells. In the cells with stable knockdown HOXB7 protein, the cell number at S and G2 phases decreased compared with the control cells. (D) Proportion of cells in different phases of the cell cycle. Error bars represent mean±SD from 3 independent experiments. *, P<0.05.</p

Immunohistochemical detection of HOXB7 in ESCC specimens and Kaplan-Meier survival curve for ESCC patients.

<p>(A) Representative sample of paired normal tissues (a, b) and ESCC (c, d). In the normal esophageal epithelial, HOXB7 expression was mainly limited to the nucleus of the epithelial cells located in the basal and suprabasal layers, whereas in the ESCC, HOXB7-positive cells were broadly observed in the tumor (Case no. 53865). (B) Figure a and b, negative control, with primary antibody replaced by PBS (Case no. 40146). Figure c and d, low expression of HOXB7 in ESCC (Case no. 42873). Figure e and f, high expression of HOXB7 in ESCC (Case no. 36840). (C) Kaplan-Meier survival curve for 177 patients in the cohort I. The median survival time was 45 months for high expression patients, which was significantly shorter than the 137 months for low expression patients (P = 0.007). (D) Kaplan-Meier survival curve for 103 patients in the cohort II. The median survival time was 19 months for high expression patients, which was significantly shorter than the 34 months for low expression patients (P = 0.001).</p

Independent predictors of survival time in multivariate analysis.

<p>Independent predictors of survival time in multivariate analysis.</p

Association between HOXB7 expression and clinical characteristics of patients with ESCC in the cohort I (n = 177) and cohort II (n = 103).

<p>Association between HOXB7 expression and clinical characteristics of patients with ESCC in the cohort I (n = 177) and cohort II (n = 103).</p