Dynamic allosteric control of noncovalent DNA catalysis reactions

Allosteric modulation of catalysis kinetics is prevalent in proteins and has been rationally designed for ribozymes. Here, we present an allosteric DNA molecule that, in its active configuration, catalyzes a noncovalent DNA reaction. The catalytic activity is designed to be modulated by the relative concentrations of two DNA regulator molecules, one an inhibitor and the other an activator. Dynamic control of the catalysis rate is experimentally demonstrated via three cycles of up and down regulation by a factor of over 10. Unlike previous works, both the allosteric receptor and catalytic core are designed, rather than evolved. This allows flexibility in the sequence design and modularity in synthetic network construction

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices

Multifractal analyses of daily rainfall time series in Pearl River basin of China

The multifractal properties of daily rainfall time series at the stations in Pearl River basin of China over periods of up to 45 years are examined using the universal multifractal approach based on the multiplicative cascade model and the multifractal detrended fluctuation analysis (MF-DFA). The results from these two kinds of multifractal analyses show that the daily rainfall time series in this basin have multifractal behavior in two different time scale ranges. It is found that the empirical multifractal moment function $K(q)$ of the daily rainfall time series can be fitted very well by the universal mulitifractal model (UMM). The estimated values of the conservation parameter $H$ from UMM for these daily rainfall data are close to zero indicating that they correspond to conserved fields. After removing the seasonal trend in the rainfall data, the estimated values of the exponent $h(2)$ from MF-DFA indicate that the daily rainfall time series in Pearl River basin exhibit no long-term correlations. It is also found that $K(2)$ and elevation series are negatively correlated. It shows a relationship between topography and rainfall variability.Comment: 16 pages, 7 figures, 1 table, accepted by Physica

Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics

Hybridization of DNA strands can be used to build molecular devices, and control of the kinetics of DNA hybridization is a crucial element in the design and construction of functional and autonomous devices. Toehold-mediated strand displacement has proved to be a powerful mechanism that allows programmable control of DNA hybridization. So far, attempts to control hybridization kinetics have mainly focused on the length and binding strength of toehold sequences. Here we show that insertion of a spacer between the toehold and displacement domains provides additional control: modulation of the nature and length of the spacer can be used to control strand-displacement rates over at least 3 orders of magnitude. We apply this mechanism to operate displacement reactions in potentially useful kinetic regimes: the kinetic proofreading and concentration-robust regimes

Determination of particulate and unburned hydrocarbon emissions from diesel engines fueled with biodiesel

Methyl esters of soybean oil, known as biodiesel, are receiving increasing attention as an alternative fuel for diesel engines. Biodiesel is a nontoxic, biodegradable, and renewable fuel with the potential to reduce engine exhaust emissions. However, previous results have shown that biodiesel produces a higher fraction of soluble organic material (SOF) in the exhaust particulate matter than petroleum-based diesel fuel although its total particulate emissions were lowered. Also, because biodiesel has a high boiling point and low volatility compared with diesel fuel, its unburned hydrocarbon vapor could be lost by deposition in the hydrocarbon sampling line. This loss could be the source of reported reductions in hydrocarbon emissions from biodiesel-fueled engines. No information about whether the typical measurement temperature for unburned hydrocarbons is suitable for biodiesel hydrocarbon measurement is available. In this project, the formation of SOF in diesel exhaust particulates and the deposition of hydrocarbons in heated sampling lines were studied experimentally and theoretically;The experimental results showed that biodiesel produced a higher SOF fraction in its total particulates than diesel fuel under virtually all engine operating conditions. The SOF fraction decreased with increasing filter temperature at constant dilution ratio and with increasing dilution ratio at constant filter temperature. Biodiesel injection tests, where a small quantity of neat biodiesel was injected into the exhaust gas showed that most of the unburned biodiesel showed up in the soluble organic fraction of the collected particulates. The response of the heated flame ionization detector did not match the concentration change of unburned biodiesel in the exhaust gas. Based on the predicted results from condensation and multicomponent adsorption models, adsorption of vapor phase hydrocarbons on the carbon particle surface is the primary source of the SOF in the total particulate matter. The condensation process, by itself, cannot explain the formation of SOF during the dilution process. Adsorption of hydrocarbons is also shown to take place during transport of the hydrocarbon sample, even at high temperature. At the standard hydrocarbon measurement temperature, adsorption onto the sampling line walls could affect the concentration of unburned hydrocarbons and biodiesel in the exhaust gas sample. However, when the hydrocarbon sampling line temperature was heated to 250°C, adsorption did not show significant effect on reducing the hydrocarbon concentration in the exhaust sample