18,548 research outputs found
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 of
the daily rainfall time series can be fitted very well by the universal
mulitifractal model (UMM). The estimated values of the conservation parameter
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 from MF-DFA indicate
that the daily rainfall time series in Pearl River basin exhibit no long-term
correlations. It is also found that 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
Formal security proofs with minimal fuss: Implicit computational complexity at work
International audienceWe show how implicit computational complexity can be used in order to increase confidence in game-based security proofs in cryptography. For this purpose we extend CSLR, a probabilistic lambda-calculus with a type system that guarantees the existence of a probabilistic polynomial-time bound on computations. This allows us to define cryptographic constructions, feasible adversaries, security notions, computational assumptions, game transformations, and game-based security proofs in a unified framework. We also show that the standard practice of cryptographers, ignoring that polynomial-time Turing machines cannot generate all uniform distributions, is actually sound. We illustrate our calculus on cryptographic constructions for public-key encryption and pseudorandom bit generation
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