Donor Wavefunctions in Si Gauged by STM Images

Saraiva AL, Salfi J, Bocquel J, Voisin B, Rogge S, Capaz RB, Calderón MJ, Koiller B

Physical Review B 93:045303 (2016)


The triumph of effective mass theory in describing the energy spectrum of dopants does not guar- antee that the model wavefunctions will withstand an experimental test. Such wavefunctions have recently been probed by scanning tunneling spectroscopy, revealing localized patterns of resonantly enhanced tunneling currents. We show that the shape of the conducting splotches resemble a cut through Kohn-Luttinger (KL) hydrogenic envelopes, which modulate the interfering Bloch states of conduction electrons. All the non-monotonic features of the current profile are consistent with the charge density fluctuations observed between successive {001} atomic planes, including a counter- intuitive reduction of the symmetry – a heritage of the lowered point group symmetry at these planes. A model-independent analysis of the diffraction figure constrains the value of the electron wavevector to k0 = (0.82 ± 0.03)(2π/aSi). Unlike prior measurements, averaged over a sizeable den- sity of electrons, this estimate is obtained directly from isolated electrons. We further investigate the model-specific anisotropy of the wave function envelope, related to the effective mass anisotropy. This anisotropy appears in the KL variational wave function envelope as the ratio between Bohr radii b/a. We demonstrate that the central cell corrected estimates for this ratio are encouragingly accurate, leading to the conclusion that the KL theory is a valid model not only for energies but for wavefunctions as well.



Recent Advances in the Synthesis and Functions of Reconfigurable Interlocked DNA Nanostructures

Lu C-H, Cecconello A, & Willner I

J. Am. Chem. Soc., in press (2016)


Interlocked circular DNA nanostructures, e.g. catenanes or rotaxanes, provide functional materials within the area of DNA nanotechnology. Specifically, the triggered reversible reconfiguration of the catenane or rotaxane structures provide means to yield new DNA switches, and to use them as dynamic scaffolds for controlling chemical functions and for the positioning of functional cargoes. The synthesis of two-ring catenanes, their switchable reconfiguration by pH, metal ions, and fuel/anti-fuel stimuli are presented, and the functions of these systems as a pendulum or rotor devices, or as switchable catalysts are described. Also, the synthesis of three-, five-, and seven-ring catenanes is presented and their switchable reconfiguration using fuel/anti-fuel strands, is addressed. The implementation of the dynamically reconfigured catenane structures for the programmed organization of Au nanoparticle assemblies that allows the plasmonic control of the fluorescence properties of Au nanoparticle/fluorophore loads associated with the scaffold, and for the operation of logic gates are discussed. Interlocked DNA rotaxanes and their different synthetic approaches are presented, and their switchable reconfiguration by means of fuel/anti-fuel strands or photonic stimuli are described. Specifically, the use of the rotaxane as a scaffold to organize Au nanoparticle assemblies and for the control of the fluorescence properties with Au nanoparticle/fluorophore hybrids loaded on the rotaxane scaffold are introduced. The future perspectives and challenges in the field of interlocked DNA nanostructures and the possible applications are discussed.



Stimuli-Responsive VEGF- and ATP-Aptamer-Based Microcapsules: Applications for Biomarker-Induced Controlled Release of an Anti-Cancer Drug, and Selective Targeted Cytotoxicity Toward Cancer Cells

Liao W-C, Y.S. Sohn, Riutin M, Cecconello A, Parak WJ, Nechushtai R, & Willner I

Advanced Functional Materials, in press (2016)


The synthesis of microcapsules consisting of DNA shells crosslinked by anti-VEGF or anti-ATP aptamers and loaded with tetramethylrhodamine-modified dextran, TMR-D, and Texas Red-modified dextran, TR-D, respectively, as fluorescence labels acting as models for drug loads, is described. The aptamer-functionalized microcapsules act as stimuli-responsive carriers for the triggered release of the fluorescent labels in the presence of the over-expressed cancer cell biomarkers VEGF or ATP, respectively. The VEGF- and ATP-responsive microcapsules are, also, loaded with the anti-cancer drug doxorubicin, in the form of DOX-functionalized dextran, DOX-D. The release of DOX-D from the respective microcapsules, proceeds in the presence of VEGF or ATP as triggers. Preliminary cell experiments reveal that the ATP-responsive DOX-D-loaded microcapsules undergo effective endocytosis into MDA-MB-231 cancer cells. The ATP-responsive DOX-D-loaded microcapsules incorporated into the MDA-MB-231 cancer cells reveal impressive cytotoxicity as compared to normal epithelial MCF-10A breast cells (50 % vs. 0 % cell death after 24 hours, respectively). The cytotoxicity of the ATP-responsive DOX-D-loaded microcapsules toward the cancer cells is attributed to the effective unlocking of the microcapsules by over-expressed ATP, and to the subsequent release of DOX from the dextran backbone under acidic conditions present in cancer cells (pH = 6.2).



DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles

Wu N & Willner I

Nano Letters, in press (2016)

see commentary :


Dimers of origami tiles are bridged by the Pb2+-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1–T2 and T3–T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb2+-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb2+-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1–T5–T4. In the presence of Pb2+-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb2+ or histidine as trigger cleaves the trimer to yield T5–T4 and T1 or the dimer T1–T5 and T4, respectively. In the presence of Pb2+-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging.



Quantum Simulation of the Hubbard Model with Dopant Atoms in Silicon

Salfi J,1 Mol JA, Rahman R, Klimeck G , Simmons MY, Hollenberg LCL, Rogge S

submitted online at arxiv:1507.06125


In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, single-site measurements in cold-atom quantum simulations of bosons revealed previously hidden local correlations. However, interacting Fermi-Hubbard systems connected to canonical open many-body physics problems are more difficult to simulate using cold atoms. To date, only ensemble measurements have been achieved, while the required single-site measurements and cooling remain formidable challenges. Here we demonstrate quantum simulation of a two-site Fermi-Hubbard system using subsurface Coulomb-coupled dopant atoms in silicon. Quasiparticle tunneling maps of individually identifiable coupled-spin states were obtained by scanning tunneling spectroscopy, at low effective temperatures, and resolving individual dopants. From the maps we quantified the two-body probability amplitudes and the entanglement of the overlapping (indistinguishable) fermions, enabling quantum simulation of a thought-experiment on a stretched covalent bond. Entanglement, determined by spin and orbital components, was found to in- crease with increasing dopant displacement, as interactions overcome tunneling, localizing spin. Looking ahead, we extracted the effective Hubbard interaction strength, which follows a hydrogenic, separation-tunable trend appropriate to simulate emergent Fermi-Hubbard phenomena in larger sets of dopants. These results pave the way for quantum simulation of larger scale correlated Fermi-Hubbard systems, exploiting atomic-scale fabrication to engineer interactions atom-by-atom.



Spatial Metrology of Dopants in Silicon with Exact Lattice Site Precision

Usman M, Bocquel J, Salfi J, Voisin B, Tankasala A, Rahman R, Simmons MY, Rogge S, Hollenberg LCL

submitted, online at arXiv1601.02326v1


The aggressive scaling of silicon-based nanoelectronics has reached the regime where device function is affected not only by the presence of individual dopants, but more critically their position in the structure. The quantitative determination of the positions of subsurface dopant atoms is an important issue in a range of applications from channel doping in ultra-scaled transistors to quantum information processing, and hence poses a significant challenge. Here, we establish a metrology combining low-temperature scanning tunnelling microscopy (STM) imaging and a comprehensive quantum treatment of the dopant-STM system to pin-point the exact lattice-site location of sub-surface dopants in silicon. The technique is underpinned by the observation that STM images of sub-surface dopants typically contain many atomic-sized features in ordered patterns, which are highly sensitive to the details of the STM tip orbital and the absolute lattice-site position of the dopant atom itself. We demonstrate the technique on two types of dopant samples in silicon – the first where phosphorus dopants are placed with high precision, and a second containing randomly placed arsenic dopants. Based on the quantitative agreement between STM measurements and multi-million-atom calculations, the precise lattice site of these dopants is determined, demonstrating that the metrology works to depths of about 36 lattice planes. The ability to uniquely determine the exact positions of subsurface dopants down to depths of 5 nm will provide critical knowledge in the design and optimisation of nanoscale devices for both classical and quantum computing applications.



Spatially resolved resonant tunneling on single atoms in silicon

Voisin B, Salfi J, Bocquel J, Rahman R, Rogge S

Journal of Physics Condensed Matter 27: 154203 (2015)
online at arxiv:1501.05042


The ability to control single dopants in solid-state devices has opened the way towards reliable quantum computation schemes. In this perspective it is essential to understand the impact of interfaces and electric fields, inherent to address coherent electronic manipulation, on the dopants atomic scale properties. This requires both fine energetic and spatial resolution of the energy spectrum and wave-function, respectively. Here we present an experiment fulfilling both conditions: we perform transport on single donors in silicon close to a vacuum interface using a scanning tunneling microscope (STM) in the single electron tunneling regime. The spatial degrees of freedom of the STM tip provide a versatility allowing a unique understanding of electrostatics. We obtain the absolute energy scale from the thermal broadening of the resonant peaks, allowing us to deduce the charging energies of the donors. Finally we use a rate equations model to derive the current in presence of an excited state, highlighting the benefits of the highly tunable vacuum tunnel rates which should be exploited in further experiments. This work provides a general framework to investigate dopant-based systems at the atomic scale.



Interface-induced heavy-hole/light-hole splitting of acceptors in silicon

Mol JA, Salfi J, Rahman R, Hsueh H, Miwa JA, Klimeck G, Simmons MY, Rogge S

Applied Physics Letters 106: 203110 (2015)
online at arxiv:1501.05669


The energy spectrum of spin-orbit coupled states of individual sub-surface boron acceptor dopants in silicon have been investigated using scanning tunneling spectroscopy at cryogenic temperatures. The spatially resolved tunnel spectra show two resonances, which we ascribe to the heavy- and light-hole Kramers doublets. This type of broken degeneracy has recently been argued to be advantageous for the lifetime of acceptor-based qubits [R. Ruskov and C. Tahan, Phys. Rev. B 88, 064308 (2013)]. The depth dependent energy splitting between the heavy- and light-hole Kramers doublets is consistent with tight binding calculations, and is in excess of 1 meV for all acceptors within the experimentally accessible depth range (<2 nm from the surface). These results will aid the development of tunable acceptor-based qubits in silicon with long coherence times and the possibility for electrical manipulation.



Time-frequency methods for coherent spectroscopy

Andrea Volpato and Elisabetta Collini

Optics Express 23, 240965, (2015)


Time-frequency decomposition techniques, borrowed from the signal-processing field, have been adapted and applied to the analysis of 2D oscillating signals. While the Fourier-analysis techniques available so far are able to interpret the information content of the oscillating signal only in terms of its frequency components, the time-frequency transforms (TFT) proposed in this work can instead provide simultaneously frequency and time resolution, unveiling the dynamics of the relevant beating components, and supplying a valuable help in their interpretation. In order to fully exploit the potentiality of this method, several TFTs have been tested in the analysis of sample 2D data. Possible artifacts and sources of misinterpretation have been identified and discussed.



Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: From basic principles to practical applications

Orbach R, Willner B, & Willner I

Chemical Communications 51:4144-4160 (2015)


This feature article addresses the implementation of catalytic nucleic acids as functional units for the construction of logic gates and computing circuits, and discusses the future applications of these systems. The assembly of computational modules composed of DNAzymes has led to the operation of a universal set of logic gates, to field programmable logic gates and computing circuits, to the development of multiplexers/demultiplexers, and to full-adder systems. Also, DNAzyme cascades operating as logic gates and computing circuits were demonstrated. DNAzyme logic systems find important practical applications. These include the use of DNAzyme-based systems for sensing and multiplexed analyses, for the development of controlled release and drug delivery systems, for regulating intracellular biosynthetic pathways, and for the programmed synthesis and operation of cascades.



Metalloporphyrin/G-quadruplexes: From basic properties to practical applications

Golub E, Lu CH, & Willner I

Journal of Porphyrins and Phthalocyanines 19:65-91 (2015)


Guanine-rich single-stranded nucleic acids self-assemble into G-quadruplex nanostructures (predominately in the presence of K+-ions). Metalloporphyrins bind to the G-quadruplex nanostructures to form supramolecular assemblies exhibiting unique catalytic, electrocatalytic and photophysical properties. This paper addresses the advances in the characterization and the implementation of the metalloporphyrin/G-quadruplexes complexes for various applications. Out of the different complexes, the most extensively studied complexes are the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme and the Zn(II)-protoporphyrin IX-functionalized G-quadruplex. Specifically, the hemin/G-quadruplex was found to act as a catalyst for driving different chemical transformations that mimic the native horseradish peroxidase enzyme, and, also, to function as an electrocatalyst for the reduction of H2O2. Also, the hemin/G-quadruplex stimulates interesting photophysical and photocatalytic processes such as the electron-transfer quenching of semiconductor quantum dots or the chemiluminescence resonance energy transfer to semiconductor quantum dots. Alternatively, Zn(II)-protoporphyrin IX associated with G-quadruplexes exhibit intensified fluorescence properties. Beyond the straightforward application of the metalloporphyrin/G-quadruplexes as catalysts that stimulate different chemical transformations, the specific catalytic, electrocatalytic and photocatalytic functions of hemin/G-quadruplexes are heavily implemented to develop sophisticated colorimetric, electrochemical, and optical sensing platforms. Also, the unique fluorescence properties of Zn(II)-protoporphyrin IX-functionalized G-quadruplexes are applied to develop fluorescence sensing platforms. The article exemplifies different sensing assays for analyzing DNA, ligand-aptamer complexes and telomerase activity using the metalloporphyrins/G-quadruplexes as transducing labels. Also, the use of the hemin/G-quadruplex as a probe to follow the operations of DNA machines is discussed.



Programmed Synthesis by Stimuli-Responsive DNAzyme-Modified Mesoporous SiO2 Nanoparticles

Balogh D, Garcia MAA, Albada HB, & Willner I

Angewandte Chemie - International Edition 54:11652-11656 (2015)


DNAzyme-capped mesoporous SiO2 nanoparticles (MP SiO2 NPs) are applied as stimuli-responsive containers for programmed synthesis. Three types of MP SiO2 NPs are prepared by loading the NPs with Cy3-DBCO (DBCO=dibenzocyclooctyl), Cy5-N3, and Cy7-N3, and capping the NP containers with the Mg2+, Zn2+, and histidine-dependent DNAzyme sequences, respectively. In the presence of Mg2+ and Zn2+ ions as triggers, the respective DNAzyme-capped NPs are unlocked, leading to the “click” reaction product Cy3-Cy5. In turn, in the presence of Mg2+ ions and histidine as triggers the second set of DNAzyme-capped NPs is unlocked leading to the Cy3-Cy7 conjugated product. The unloading of the respective NPs and the time-dependent formation of the products are followed by fluorescence spectroscopy (FRET). A detailed kinetic model for the formation of the different products is formulated and it correlates nicely with the experimental results.



Switchable Reconfiguration of a Seven-Ring Interlocked DNA Catenane Nanostructure

Lu C-H, Cecconello A, Qi X-J, Wu N, Jester S-S, Famulok M, Matthies M, Schmidt T-L, & Willner I

Nano Letters 15:7133-7137 (2015)

see commentary :


The synthesis, purification, and structure characterization of a seven-ring interlocked DNA catenane is described. The design of the seven-ring catenane allows the dynamic reconfiguration of any of the four rings (R1, R3, R4, and R6) on the catenane scaffold, or the simultaneous switching of any combination of two, three, or all four rings to yield 16 different isomeric states of the catenane. The dynamic reconfiguration across the states is achieved by implementing the strand-displacement process in the presence of appropriate fuel/antifuel strands and is probed by fluorescence spectroscopy. Each of the 16 isomers of the catenane can be transformed into any of the other isomers, thus allowing for 240 dynamic transitions within the system.



Information processing in parallel through directionally resolved molecular polarization components in coherent multidimensional spectroscopy

Tian-Min Yan, Barbara Fresch, Raphael D. Levine, Françoise Remacle F

The Journal of Chemical Physics 143:064106 (2015)


We propose that information processing can be implemented by measuring the directional components of the macroscopic polarization of an ensemble of molecules subject to a sequence of laser pulses. We describe the logic operation theoretically and demonstrate it by simulations. The measurement of integrated stimulated emission in different phase matching spatial directions provides a logic decomposition of a function that is the discrete analog of an integral transform. The logic operation is reversible and all the possible outputs are computed in parallel for all sets of possible multivalued inputs. The number of logic variables of the function is the number of laser pulses used in sequence. The logic function that is computed depends on the chosen chromophoric molecular complex and on its interactions with the solvent and on the two time intervals between the three pulses and the pulse strengths and polarizations. The outputs are the homodyne detected values of the polarization components that are measured in the allowed phase matching macroscopic directions, , where is the propagation direction of the ith pulse and { } is a set of integers that encode the multivalued inputs. Parallelism is inherently implemented because all the partial polarizations that define the outputs are processed simultaneously. The outputs, that are read directly on the macroscopic level, can be multivalued because the high dynamical range of partial polarization measurements by non linear coherent spectroscopy allows for fine binning of the signals. The outputs are uniquely related to the inputs so that the logic is reversible.



Parallel and Multivalued Logic by the Two-Dimensional Photon-Echo Response of a Rhodamine−DNA Complex

Barbara Fresch,Marco Cipolloni, Tian-Min Yan, Elisabetta Collini,R. D. Levine, and F. Remacle

J. Phys. Chem. Lett. 2015, 6, 1714−1718


Implementing parallel and multivalued logic operations at the molecular scale has the potential to improve the miniaturization and effi ciency of a new generation of nanoscale computing devices. Two-dimensional photon-echo spectroscopy is capable of resolving dynamical pathways on electronic and vibrational molecular states. We experimentally demonstrate the implementation of molecular decision trees, logic operations where all possible values of inputs are processed in parallel and the outputs are read simultaneously, by probing the laser-induced dynamics of populations and coherences in a rhodamine dye mounted on a short DNA duplex. The inputs are provided by the bilinear interactions between the molecule and the laser pulses, and the output values are read from the two dimensional molecular response at specific frequencies. Our results highlights how ultrafast dynamics between multiple molecular states induced by light− matter interactions can be used as an advantage for performing complex logic operations in parallel, operations that are faster than electrical switching.



Switchable Catalytic DNA Catenanes Nanoletters, 2015, 15 (3), pp 2099–210.

Lianzhe Hu, Chun-Hua Lu, and Itamar Willner, 2015
see commentary :


Two-ring interlocked DNA catenanes are synthesized and characterized. The supramolecular catenanes show switchable cyclic catalytic properties. In one system, the catenane structure is switched between a hemin/G-quadruplex catalytic structure and a catalytically inactive state. In the second catenane structure the catenane is switched between a catalytically active Mg2+-dependent DNAzyme-containing catenane and an inactive catenane state. In the third system, the interlocked catenane structure is switched between two distinct catalytic structures that include the Mg2+- and the Zn2+-dependent DNAzymes.



Ternary DNA Computing Using 3X3 Multiplication Matrices Chemical Science, 2015, 6, 1288-1292.

Orbach R, Lilienthal S, Klein M, Levine R, Remacle F, & Willner I (2014)!divAbstract


Non-Boolean computations implementing operations on multivalued variable, beyond base 2 allow enhanced computational complexity. We introduce DNA as a functional material for ternary computing, and particularly demonstrate the use of three-valued oligonucleotide inputs to construct a 3Å~3 multiplication table. The system consists of two three-valued inputs -1; 0; +1 and a fluorophore/quencher functional hairpin acting as computational and reporter module. The interaction of the computational hairpin module with the different values of the inputs yields a 3Å~3 multiplication matrix consisting of nine nanostructures that are read out by three distinct fluorescence intensities. By combining three different hairpin computational modules, modified each with a different fluorophore/quencher pair, and using different sets of inputs, the parallel operation of three multiplication tables is demonstrated.



A full-adder based on reconfigurable DNA-hairpin inputs and DNAzyme computing modules,
Edge article Chemical Science 5:3381-3387.

Orbach R, Wang F, Lioubashevski O, Levine RD, Remacle F, & Willner I (2014)!divAbstract


In nature, post-transcriptional alternative splicing processes expand the proteome biodiversity, providing means to synthesize various protein isoforms. We describe the input-guided assembly of a DNAzyme-based full-adder computing system, which mimics functions of the natural processes by increasing the diversity of logic elements by the reconfiguration of the inputs. The full-adder comprises the simultaneous operation of three inputs that yield two different output signals, acting as sum and carry bits. The DNAzyme-based full-adder system consists of a library of Mg2+-dependent DNAzyme subunits and their substrates that are modified by two different fluorophore/quencher pairs that encode the sum and carry outputs. The input-guided assembly of DNAzyme subunits, formed by three inputs composed of nucleic acid hairpin structures, leads to computing modules that yield the sum and carry outputs of the full-adder. In the presence of a single input the DNAzyme computing module yields the sum fluorescence output. In the presence of two of the inputs, the reconfiguration of the input structures proceeds, leading to an input-guided computing module that yields the carry fluorescence output. By introducing all the three inputs the sequential inter-input hybridization leads to the reconfiguration of the inputs into polymer wires. These include binding sites for two types of DNAzyme and their substrates leading to the carry and sum fluorescence outputs. The advantages of the simultaneous three-input operation of the full-adder and the possibilities to implement DNAzyme-based computing modules for cascading full-adders are discussed.



Spatially resolving valley quantum interference of a donor in silicon Nat Mater 13:605-610.

Salfi J, Mol JA, Rahman R, Klimeck G, Simmons MY, Hollenberg LCL, & Rogge S (2014)


Electron and nuclear spins of donor ensembles in isotopically pure silicon experience a vacuum-like environment, giving them extraordinary coherence. However, in contrast to a real vacuum, electrons in silicon occupy quantum superpositions of valleys in momentum space. Addressable single-qubit and two-qubit operations in silicon require that qubits are placed near interfaces, modifying the valley degrees of freedom associated with these quantum superpositions and strongly influencing qubit relaxation and exchange processes. Yet to date, spectroscopic measurements have only probed wavefunctions indirectly, preventing direct experimental access to valley population, donor position and environment. Here we directly probe the probability density of single quantum states of individual subsurface donors, in real space and reciprocal space, using scanning tunnelling spectroscopy.We directly observe quantum mechanical valley interference patterns associated with linear superpositions of valleys in the donor ground state. The valley population is found to be within 5% of a bulk donor when 2.85 _ 0.45nm from the interface, indicating that valley-perturbation-induced enhancement of spin relaxation will be negligible for depths greater than 3 nm. The observed valley interference will render two-qubit exchange gates sensitive to atomic-scale variations in positions of subsurface donors. Moreover, these results will also be of interest for emerging schemes proposing to encode information directly in valley polarization.



From Cascaded Catalytic Nucleic Acids to Enzyme–DNA Nanostructures: Controlling Reactivity, Sensing, Logic Operations, and Assembly of Complex Structures Chemical Reviews 114:2881-2941.

Wang F, Lu C-H, & Willner I (2014)



A two-ring interlocked DNA catenane rotor undergoing switchable transitions across three states Chemical Communications 50:4717-4720.

Qi X-J, Lu C-H, Cecconello A, Yang H-H, & Willner I (2014)!divAbstract


A two-ring (α/β) interlocked DNA catenane rotor system is described. Using appropriate fuel and anti-fuel strands, the triggered switchable rotation across three states S1, S2 and S3 associated with the circular track of ring α is demonstrated.



Switchable Reconfiguration of an Interlocked DNA Olympiadane Nanostructure Angewandte Chemie International Edition 53:7499-7503

Lu C-H, Qi X-J, Cecconello A, Jester S-S, Famulok M, & Willner I (2014)


Interlocked DNA rings (catenanes) are interesting reconfigurable nanostructures. The synthesis of catenanes with more than two rings is, however, hampered, owing to low yields of these systems. We report a new method for the synthesis of catenanes with a controlled number of rings in satisfactory yields. Our approach is exemplified by the synthesis of a five-ring DNA catenane that exists in four different configurations. By the use of nucleic acids as “fuels” and “antifuels”, the cyclic reconfiguration of the system across four states is demonstrated. One of the states, olympiadane, corresponds to the symbol of the Olympic Games. The five-ring catenane was implemented as a mechanical scaffold for the reconfiguration of Au NPs. The advantages of DNA catenanes over supramolecular catenanes include the possibility of generating highly populated defined states and the feasibility of tethering nanoobjects to the catenanes, which act as a mechanical scaffold to reconfigure the nanoobjects.



Molecular decision trees realized by ultrafast electronic spectroscopy

Barbara Fresch, Dawit Hiluf, Elisabetta Collini, R. D. Levine, and F. Remacle


See also the commentary by G. Scholes,
Light-powered molecular logic
goes nonlinear

The commentary by Stuart Dambrot
The lightness of being: Smaller computer logic components through photon-molecule interaction


One possible way to reduce the physical dimensions of a computing node is to instruct a molecule to evaluate a complicated logic function. This is even more so if several such functions are processed in parallel. The interaction between light and matter is a suitable route because it is bilinear, depending on both the properties of the laser and of themolecule; the outcome depends on the initial state of the molecule and there can be more than one distinct path leading to the readout signal. Two-dimensional photon spectroscopy is shown to have four paths originating from each interaction, thereby enabling, as shown in SI Text, quaternary logic. In the main text, we discuss the simpler case of binary logic.

DNAzyme-Based 2:1 and 4:1 Multiplexers and 1:2 Demultiplexer

Ron Orbach (a), Francoise Remacle (b), R.D. Levine (a) and Itamar Willner (a)

(a) Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel;
(b) Chemistry Department, B6c, University of Liège, 4000 Liège, Belgium

Scaffolding proteins play a central role in many regulatory cellular networks where signaling proteins trigger different, and even, orthogonal biological pathways. Such biological regulatory networks can be duplicated by multiplexer/demultiplexer logic operations. We present the use of libraries of the Mg2+-dependent DNAzyme subunits as computational moduli for the construction of a 2:1 and 4:1 multiplexers and a 1:2 demultiplexer. In the presence of the appropriate inputs, and the presence or absence of selector units, the guided assembly of the DNAzyme subunits to form active Mg2+-dependent DNAzyme proceeds. The formation of the active DNAzyme nanostructures is controlled by the energetics associated with the resulting duplexes between the inputs/selectors and the DNAzyme subunits. The library subunits are designed in such a way that in the presence of the appropriate inputs/selectors the inputs are knocked-down or triggered-on to yield the respective multiplexer/demultiplexer operations. Fluorescence is used as readout for the outputs of the logic operations. The DNAzyme-based multiplexer/demultiplexer systems present biomolecular assemblies for data compression and decompression.



Edge article
Chem. Sci., 2013, Accepted Article
DOI: 10.1039/C3SC52752B

Commentary by Iain Larmour


DNAzyme Based Toffoli and Fredkin Logic Gates: Logic Reversibility and Thermodynamic Irreversibility

Ron Orbach (a), Françoise Remacle (b), R. D. Levine (a) and Itamar Willner (a)

(a) Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel;
Chemistry Department, B6c, University of Liège, 4000 Liège, Belgium

The Toffoli and Fredkin gates were suggested to exhibit logic reversibility and thereby to 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 pre-designed Mg2+-dependent DNAzymes and their respective substrates. While 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 non-related 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 output. (ii) The DNAzyme powered logic gates are made to operate at a finite rate by invoking downhill energy-releasing processes. Albeit the three bits, Toffoli and Fredkin, logically reversible gates manifest thermodynamic irreversibility we suggest that these gates could have important practical implication in future nanomedicine.


Proc. Natl. Acad. Sci., USA, 109, 21228-21233 (2012)



Nucleic Acid-Driven DNA Machineries Synthesizing Mg2+-Dependent DNAzymes: An Interplay Between DNA Sensing and Logic Gate Operations

Ron Orbach, Lena Mostinski, Fuan Wang and Itamar Willner

Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel

Polymerase/nicking enzymes and nucleic acid scaffolds are implemented as DNA machines for the development of amplified DNA detection schemes, and for the design of logic gates. The analyte nucleic acid target acts, also, as input for the logic gates. In the presence of two DNA targets, acting as inputs, and appropriate DNA scaffolds, the polymerase-induced replication of the scaffolds followed by the nicking of the replication products are activated, leading to the autonomous synthesis of the Mg2+-dependent DNAzyme or the Mg2+-dependent DNAzyme subunits. These biocatalysts cleave a fluorophore/quencher-functionalized nucleic acid substrate, thus providing fluorescence signals for the sensing events or outputs for the logic gates. The systems are used to develop OR, AND, and Controlled-AND gates, and the DNA analyte targets represent two nucleic acid sequences of the Smallpox viral genome.



Chem. Eur. J., 18, 14689-14694 (2012)



A Three-Station DNA Catenane Rotary Motor with Controlled Directionality

Chun-Hua Lu (a), Alessandro Cecconello (a), Johann Elbaz (a), Alberto Credi (b) and Itamar Willner (a)

(a) Institute of Chemistry and The Minerva Center for Complex Biohybrid Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
(b) Photochemical Nanosciences Laboratory, Dipartimento di Chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy


The assembly of DNA machines represents a central effort in DNA nanotechnology. We report on the first DNA rotor system composed of a two-ring catenane. The DNA rotor ring rotates in dictated directions along a wheel, and it occupies three distinct sites. Hg2+/cysteine or pH (H+/OH–) act as fuels or antifuels in positioning the rotor ring. Analysis of the kinetics reveals directional clockwise or anticlockwise population of the target-sites (>85%), and the rotor’s direction is controlled by the shortest path on the wheel.


Nano Lett., 13, 2303-2308 (2013)