Françoise Remacle

DNA computing circuits using libraries of DNAzyme subunits

Biological systems that are capable of performing computational operations could be of use in bioengineering and nanomedicine, and DNA and other biomolecules have already been used as active components in biocomputational circuits. There have also been demonstrations of DNA/RNA-enzyme-based automatons, logic control of gene expression, and RNA systems for processing of intracellular information. However, for biocomputational circuits to be useful for applications it will be necessary to develop a library of computing elements, to demonstrate the modular coupling of these elements, and to demonstrate that this approach is scalable. Here, we report the construction of a DNA-based computational platform that uses a library of catalytic nucleic acids (DNAzymes), and their substrates, for the input-guided dynamic assembly of a universal set of logic gates and a half-adder/half-subtractor system. We demonstrate multilayered gate cascades, fan-out gates and parallel logic gate operations. In response to input markers, the system can regulate the controlled expression of anti-sense molecules, or aptamers, that act as inhibitors for enzymes.

Measurement and laser control of attosecond charge migration in ionized iodoacetylene.

Electronic movement flashing into view Numerous chemical processes begin with ionization: the ejection of an electron from a molecule. What happens in the immediate aftermath of that event? Kraus et al. explored this question in iodoacetylene by detecting and analyzing the spectrum of emitted high harmonics (see the Perspective by Ueda). They traced the migration of the residual positively charged hole along the molecular axis on a time scale faster than a quadrillionth of a second. They thereby characterized the capacity of a laser field to steer the holes motion in appropriately oriented molecules. Science, this issue p. 790; see also p. 740 High harmonics reveal fine details of electronic rearrangement in a molecule in the first instants after ionization. [Also see Perspective by Ueda] The ultrafast motion of electrons and holes after light-matter interaction is fundamental to a broad range of chemical and biophysical processes. We advanced high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately after ionization of iodoacetylene while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi–field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes.

All-DNA finite-state automata with finite memory

Biomolecular logic devices can be applied for sensing and nano-medicine. We built three DNA tweezers that are activated by the inputs H+/OH-; ; nucleic acid linker/complementary antilinker to yield a 16-states finite-state automaton. The outputs of the automata are the configuration of the respective tweezers (opened or closed) determined by observing fluorescence from a fluorophore/quencher pair at the end of the arms of the tweezers. The system exhibits a memory because each current state and output depend not only on the source configuration but also on past states and inputs.

Electrochemically driven sequential machines: an implementation of copper rotaxanes.

We propose to use the redox states and ligand reorganization characteristics of a copper rotaxane mechanical machine to realize a finite-state machine, that is, a logic machine that possesses an integral memory unit. These compounds provide two definite advantages for the implementation of finite-state set–reset machines: 1) A large ligand reorganization when the redox state of the Cu ion changes, which leads to a clear and reliably observable molecular hysteresis and 2) a rate of reorganization comparable to the voltage sweep rate in cyclic voltammetry. We provide concrete experimental results and a simulation as proof of the principle of the operation of an all-electrochemical-cyclable finite-state machine. Catenanes and rotaxanes constitute an important class of artificial motors based on transition-metal complexes. In view of their proposed applications as logic machines, the rate of mechanical motion is an important factor and depends on the nature of the movement. 13] We have recently reported fast motors based on single-copper dynamic rotaxanes, which can pirouette between two positions around the axle on a millisecond timescale. The rotaxane is made of an axle that consists of a bidentate (2,2’-bipyridine) chelate ligand with two bulky stopper groups and a ring or wheel containing a bidentate 1,10phenantroline and a tridendate (terpyridine) binding site to which the copper ion can bind (see Figure 1). The electro-

Structure and energetics of two- and three-dimensional neutral, cationic, and anionic gold clusters Au5⩽n⩽9Z (Z=0,±1)

Low-energy structures are found on the potential energy surfaces of the neutral, cationic, and anionic gold clusters Au5⩽n⩽8Z(Z=0,±1) and on the neutral potential energy surface of Au9. These structures provide insights on the two to three dimensional (2D⇒3D) transition in small neutral and charged gold clusters. It is demonstrated that the size threshold for the 2D-3D coexistence is lower for cationic than neutral gold clusters: the 2D-3D coexistence develops for Au5+ and Au7+ on the cationic potential energy surfaces while only for Au9 on the neutral. Two metastable long-lived dianions of gold clusters are also reported.

pH-Programmable DNA Logic Arrays Powered by Modular DNAzyme Libraries

Nature performs complex information processing circuits, such the programmed transformations of versatile stem cells into targeted functional cells. Man-made molecular circuits are, however, unable to mimic such sophisticated biomachineries. To reach these goals, it is essential to construct programmable modular components that can be triggered by environmental stimuli to perform different logic circuits. We report on the unprecedented design of artificial pH-programmable DNA logic arrays, constructed by modular libraries of Mg(2+)- and UO(2)(2+)-dependent DNAzyme subunits and their substrates. By the appropriate modular design of the DNA computation units, pH-programmable logic arrays of various complexities are realized, and the arrays can be erased, reused, and/or reprogrammed. Such systems may be implemented in the near future for nanomedical applications by pH-controlled regulation of cellular functions or may be used to control biotransformations stimulated by bacteria.

Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates

The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits. We present a construction of the logically reversible Toffoli and Fredkin gates by implementing a library of predesigned Mg2+-dependent DNAzymes and their respective substrates. Although the logical reversibility, for which each set of inputs uniquely correlates to a set of outputs, is demonstrated, the systems manifest thermodynamic irreversibility originating from two quite distinct and nonrelated phenomena. (i) The physical readout of the gates is by fluorescence that depletes the population of the final state of the machine. This irreversible, heat-releasing process is needed for the generation of the output. (ii) The DNAzyme-powered logic gates are made to operate at a finite rate by invoking downhill energy-releasing processes. Even though the three bits of Toffoli’s and Fredkin’s logically reversible gates manifest thermodynamic irreversibility, we suggest that these gates could have important practical implication in future nanomedicine.

Pump and probe ultrafast electron dynamics in LiH: a computational study

A time-dependent multiconfiguration method with a large electronic basis set is used to compute the response of all the electrons of LiH to a few-cycle intense pump field followed by a probe pulse. The ultrashort pump pulse excites a coherent superposition of stationary electronic states and, by changing the pump parameters such as intensity, duration, polarization and phase of carrier frequency, one can steer the motion of the electrons. Particular attention is given to the control provided by the polarization and by the phase. For example, a change in polarization is used to select an electronic wave packet that is rotating in a plane perpendicular to the bond or rotation in a plane containing the bond. The electronic wave packet can be probed by a delayed second pulse. This delayed probe pulse is also included in the Hamiltonian with the result that the frequency dispersed probe spectrum can be computed and displayed as a two-dimensional plot.

miRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients

Significance The study of mRNA and microRNA (miRNA) expression profiles of cells and tissue has become a major tool for therapeutic development. The results of such experiments are expected to change the methods used in the diagnosis and prognosis of disease. We introduce surprisal analysis, an information-theoretic approach grounded in thermodynamics, to compactly transform the information acquired from microarray studies into applicable knowledge about the cancer phenotypic state. The analysis of mRNA and miRNA expression data from ovarian serous carcinoma, prostate adenocarcinoma, breast invasive carcinoma, and lung adenocarcinoma cancer patients and organ-specific control patients identifies cancer-specific signatures. We experimentally examine these signatures and their respective networks as possible therapeutic targets for cancer in single-cell experiments. Toward identifying a cancer-specific gene signature we applied surprisal analysis to the RNAs expression behavior for a large cohort of breast, lung, ovarian, and prostate carcinoma patients. We characterize the cancer phenotypic state as a shared response of a set of mRNA or microRNAs (miRNAs) in cancer patients versus noncancer controls. The resulting signature is robust with respect to individual patient variability and distinguishes with high fidelity between cancer and noncancer patients. The mRNAs and miRNAs that are implicated in the signature are correlated and are known to contribute to the regulation of cancer-signaling pathways. The miRNA and mRNA networks are common to the noncancer and cancer patients, but the disease modulates the strength of the connectivities. Furthermore, we experimentally assessed the cancer-specific signatures as possible therapeutic targets. Specifically we restructured a single dominant connectivity in the cancer-specific gene network in vitro. We find a deflection from the cancer phenotype, significantly reducing cancer cell proliferation and altering cancer cellular physiology. Our approach is grounded in thermodynamics augmented by information theory. The thermodynamic reasoning is demonstrated to ensure that the derived signature is bias-free and shows that the most significant redistribution of free energy occurs in programming a system between the noncancer and cancer states. This paper introduces a platform that can elucidate miRNA and mRNA behavior on a systems level and provides a comprehensive systematic view of both the energetics of the expression levels of RNAs and of their changes during tumorigenicity.

Protein Signaling Networks from Single Cell Fluctuations and Information Theory Profiling

Protein signaling networks among cells play critical roles in a host of pathophysiological processes, from inflammation to tumorigenesis. We report on an approach that integrates microfluidic cell handling, in situ protein secretion profiling, and information theory to determine an extracellular protein-signaling network and the role of perturbations. We assayed 12 proteins secreted from human macrophages that were subjected to lipopolysaccharide challenge, which emulates the macrophage-based innate immune responses against Gram-negative bacteria. We characterize the fluctuations in protein secretion of single cells, and of small cell colonies (n = 2, 3,···), as a function of colony size. Measuring the fluctuations permits a validation of the conditions required for the application of a quantitative version of the Le Chateliers principle, as derived using information theory. This principle provides a quantitative prediction of the role of perturbations and allows a characterization of a protein-protein interaction network.