Development of a DNA sensor using a molecular logic gate

This communication reports the increase in fluorescence resonance energy transfer (FRET) efficiency between two laser dyes in the presence of deoxyribonucleic acid (DNA). Two types of molecular logic gates have been designed where DNA acts as input signal and fluorescence intensity of different bands are taken as output signal. Use of these logic gates as a DNA sensor has been demonstrated.     

A Visual Dual-Aptamer Logic Gate for Sensitive Discrimination of Prion Diseases-Associated Isoform with Reusable Magnetic Microparticles and Fluorescence Quantum Dots

Molecular logic gates, which have attracted increasing research interest and are crucial for the development of molecular-scale computers, simplify the results of measurements and detections, leaving the diagnosis of disease either “yes” or “no”. Prion diseases are a group of fatal neurodegenerative disorders that happen in human and animals. The main problem with a diagnosis of prion diseases is how to sensitively and selectively discriminate and detection of the minute amount of PrP^Res in biological samples. Our previous work had demonstrated that dual-aptamer strategy could achieve highly sensitive and selective discrimination and detection of prion protein (cellular prion protein, PrP^C, and the diseases associated isoform, PrP^Res) in serum and brain. Inspired by the advantages of molecular logic gate, we further conceived a new concept for dual-aptamer logic gate that responds to two chemical input signals (PrP^C or PrP^Res and Gdn-HCl) and generates a change in fluorescence intensity as the output signal. It was found that PrP^Res performs the “OR” logic operation while PrP^C performs “XOR” logic operation when they get through the gate consisted of aptamer modified reusable magnetic microparticles (MMPs-Apt1) and quantum dots (QDs-Apt2). The dual-aptamer logic gate simplifies the discrimination results of PrP^Res, leaving the detection of PrP^Res either “yes” or “no”. The development of OR logic gate based on dual-aptamer strategy and two chemical input signals (PrP^Res and Gdn-HCl) is an important step toward the design of prion diseases diagnosis and therapy systems.     

A reversible DNA-silver nanoclusters-based molecular fluorescence switch and its use for logic gate operation

Molecule-like silver nanoclusters (AgNCs) with few to tens of atoms are highly sensitive to the sequence and structure of DNA stabilizers. In this paper, a novel pH-triggered reversible molecular fluorescence switch is developed by taking advantage of the DNA-dependent fluorescence pH response of AgNCs. The DNA-AgNCs fluorescence switch simultaneously addresses concerns of simple construction strategy, efficient design and organic-solvent-free operation. Moreover, the excellent photostability and biocompatibility of AgNCs provide great potential for application of the DNA-AgNCs fluorescence switch in the development of functional molecular devices. Specifically, we apply the DNA-AgNCs fluorescence switch combined with the DNA sequence-dependent pH response pattern of AgNCs for construction of molecular logic gates.     

Demonstration of a universal surface DNA computer

A fundamental concept in computer science is that of the universal Turing machine, which is an abstract definition of a general purpose computer. A general purpose (universal) computer is defined as one which can compute anything that is computable. It has been shown that any computer which is able to simulate Boolean logic circuits of any complexity is such a general purpose computer. The field of DNA computing was founded in 1994 by Adleman's solution of a 7-bit instance of the Hamiltonian path problem. This work, as well as most of the subsequent experimental and theoretical investigations in the area, focused primarily upon the solution of NP-complete problems, which are a subset of the larger universal class of problems. In the present work a surface DNA computer capable of simulating Boolean logic circuits is demonstrated. This was done by constructing NOR and OR gates and combining them into a simple logic circuit. The NOR gate is one of the universal gates in Boolean logic, meaning that any other logic gate can be built from it alone. The circuit was solved using DNA-based operations, demonstrating the universal nature of this surface DNA computing model.     

Deoxyribozyme-based three-input logic gates and construction of a molecular full adder

We have developed an array of seven deoxyribozyme-based molecular logic gates that behaves as a full adder in a single solution, with three oligonucleotides as inputs and two independent fluorogenic cleavage reactions as carry and sum outputs. The sum output consisted of four new deoxyribozyme-based logic gates: an ANDAND gate and three ANDNOTANDNOT gates. These gates required the design of a generic three-input deoxyribozyme-based logic gate that can use any three-way combination of activating or inactivating inputs. This generic gate design utilizes an additional inverting element that hybridizes to convert YES logic into NOT logic and vice versa. The system represents the first solution-phase, single test tube, enzymatic full adder and shows the complexity of control over molecular scale events that can be achieved with deoxyribozyme-based logic gates. Similar systems could be applied to control autonomous therapeutic and diagnostic devices.     

Multiplexed sensing of mercury(II) and silver(I) ions: a new class of DNA electrochemiluminescent-molecular logic gates

Most of the DNA logic gates employ fluorescent or colorometric signals as their outputs, which were limited by the cumbersome handling procedures, lack of portability and lower sensitivity. To the best of our knowledge, the logic gates with electrochemiluminescent (ECL) signal as their outputs have not been reported. In response, we report here the construction of DNA molecular logic gates that produce ECL signals as their outputs, having the advantages of versatility, low background and simplified optical setup. The logic gates are based on the T-rich or C-rich oligonucleotides for the selective analysis of Hg(2+) and Ag(+) ions using energy or electron transfer-quenching path. Efficient and stable quenching of ECL of Ru bis(2,2'-bipyridine) (2,2'-bipyridine-4,4'-dicarboxylic acid) N-hydroxysuccinimide ester by oxidizing ferrocene at the Au electrode enabled us to use Hg(2+) and Ag(+) ions as inputs that activate logic gates, and to execute ECL of Ru(II) as readout signals for logic gate operations.     

Ferroelectric Hybrid Plasmonic Waveguide for All-Optical Logic Gate Applications

A ferroelectric hybrid plasmonic waveguide, made of a polycrystal lithium niobate waveguide separated from a gold film by a silicon dioxide isolation layer, is fabricated by use of laser molecular beam epitaxy growth, electron beam evaporation, and focused ion beam etching. Strong subwavelength mode confinement and excellent long-range propagation are achieved simultaneously for the hybrid plasmonic mode. An all-optical logic OR gate is also realized based on the ferroelectric hybrid plasmonic waveguide. This may provide a way for the study of all-optical logic gates and integrated photonic circuits.     

Fluorescence for biological logic gates

Biological logic gates are smart probes able to respond to biological conditions in behaviors similar to computer logic gates, and they pose a promising challenge for modern medicine. Researchers are creating many kinds of smart nanostructures that can respond to various biological parameters such as pH, ion presence, and enzyme activity. Each of these conditions alone might be interesting in a biological sense, but their interactions are what define specific disease conditions. Researchers over the past few decades have developed a plethora of stimuli‐responsive nanodevices, from activatable fluorescent probes to DNA origami nanomachines, many explicitly defining logic operations. Whereas many smart configurations have been explored, in this review we focus on logic operations actuated through fluorescent signals. We discuss the applicability of fluorescence as a means of logic gate implementation, and consider the use of both fluorescence intensity as well as fluorescence lifetime.     

DNA implementation of addition in which the input strands are separate from the operator strands

A DNA representation of Boolean logic for which the input strands are separate from the operator strands is described and used to construct a two-bit DNA adder. The successful operation of the adder for several test inputs demonstrates that digital molecular computation with a complexity of order 30 gates is feasible.     

A Novel Bio-Sensor Based on DNA Strand Displacement

DNA strand displacement technology performs well in sensing and programming DNA segments. In this work, we construct DNA molecular systems based on DNA strand displacement performing computation of logic gates. Specifically, a class of so-called “DNA neurons” are achieved, in which a “smart” way inspired by biological neurons encoding information is developed to encode and deliver information using DNA molecules. The “DNA neuron” is bistable, that is, it can sense DNA molecules as input signals, and release “negative” or “positive” signals DNA molecules. We design intelligent DNA molecular systems that are constructed by cascading some particularly organized “DNA neurons”, which could perform logic computation, including AND, OR, XOR logic gates, automatically. Both simulation results using visual DSD (DNA strand displacement) software and experimental results are obtained, which shows that the proposed systems can detect DNA signals with high sensitivity and accretion; moreover, the systems can process input signals automatically with complex nonlinear logic. The method proposed in this work may provide a new way to construct a sensitive molecular signal detection system with neurons spiking behavior in vitro, and can be used to develop intelligent molecular processing systems in vivo.     

Construction of logic gates with the fluorene-based small molecule/DNA probes

Fluorene-based small molecules (FSMs) have optical properties and can interact with DNA. In this paper, the integrated "INH" and "AND" gates operating in parallel are developed with the fluorene-based small molecule (FSM)/DNA probe. They are activated by taking advantage of the two-step fluorescence resonance energy transfer (FRET) process and the sequence-recognition mechanism of DNA. Then, a "NOT" gate is obtained with a molecular beacon-like probe (FSM-MB) by using the FSM as the fluorophore. Moreover, the "NOT" gate based on the FSM-MB probe can be used as a biosensor and has potential applications in label-free detection of target molecules.     

Metal ion-induced assembly of dipeptide-attached perylenediimide for fluorometric “turn on” detection of biologically important small molecule

A dipeptide-appended perylenediimide (PDI-CFF) fluorescent molecule was designed, synthesized, and characterized. Though the molecule does not dissolve in any individual solvent, it dissolves well in an organic/water mixed solvent system such as tetrahydrofuran/water. This new fluorescent molecule was self-assembled in a tetrahydrofuran/water mixture to form both nanofibrous network structures and a nano ring structure. It has shown nanofibril morphology by the interactions with ferric ions (PDI-CFF/Fe³⁺ system) with diminishing fluorescent property. Interestingly, L-ascorbic acid (LAA) interacts with the PDI-CFF/Fe³⁺ system, showing turn-on fluorescence. Another interesting feature is that the minimum detection limits for Fe³⁺ ions and LAA are at the submicromolar levels of 6.2 × 10⁻⁸ and 3 × 10⁻⁸ M, respectively. Moreover, the fluorescent (10 μM) signals can be monitored by the naked eye under handheld UV lamp irradiation at 365 nm, and this is very convenient for the real application. In this study, the molecule offers the opportunity for processing these sequential fluorescence responses in order to fabricate a implication logic gate that includes NOT, AND, and OR simple logic gates using chemical stimuli (ferric ions and LAA) as inputs and fluorescence emission at 536 nm as output. The detailed mechanism of interactions of Fe³⁺ with PDI-CFF and LAA with the PDI-CFF/Fe³⁺ system is vividly studied by using Fourier transform infrared (FT-IR) analysis and fluorescence. Moreover, this new molecule was reusable for several times without significant loss of its activity. The construction of logic gates using biologically important molecules/ions holds future promise for the design and development of new bio-logic gates.     

Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences.

We report the design, synthesis, and characterization of a molecular beacon (MB) consisting of two fluorescent dyes (Alexa 488 and RedX) for DNA and RNA analysis. In the absence of the target DNA or RNA the MB is in its stem-closed form and shows efficient energy transfer from the donor (Alexa) to the acceptor (RedX), generating mostly fluorescence from RedX. In the presence of the complementary target DNA the MB opened efficiently, hybridizes with the target DNA, and energy transfer is blocked in the stem-open form. This attachment to the target generates a fluorescence signature, which is clearly distinguishable from the fluorescence signature of the stem-closed form, allowing for ratiometric analysis of the fluorescence signal. In addition to steady-state fluorescence analysis, time resolved fluorescence (ps time range) and fluorescence depolarization studies were performed. We show that fluorescence lifetime and fluorescence depolarization measurements are useful analytical tools to optimize the MB design.     

分子信标DNA计算模型的研究进展与展望

由于分子信标具有结构简单,灵敏度高及反应迅速等优点,因此,利用分子信标进行数学问题的求解将成为可能.通过对分子信标的计算模型进行详细的介绍,并对分子信标的计算模型的研究思路进行了展望,据此思路,可以建立多种组合优化问题及逻辑门的分子信标计算模型.     

The path of the DNA along the dimer interface of topoisomerase II

The eukaryotic DNA topoisomerase II is a dyadic enzyme that, upon ATP binding, transports one duplex DNA (T-segment) through a transient double-stranded break in another (G-segment). The path of the T-segment involves the sequential crossing of three gates along the dimer interface: the entrance or N-gate, the DNA gate, and the exit or C-gate. Coordination among these gates is critical for dimer stability and the prevention of chromosome damage. This study examines DNA transactions by yeast topoisomerase II derivatives defective in gate function. The results indicate that, although the N-gate is not required for G-segment cleavage, the DNA gate per se is not able to widen unless ATP binds to the N-gate. Next, a captured T-segment cannot be held in the interdomainal region between the N-gate and the DNA gate. Finally, the G-segment can be religated while a T-segment is held in the central cavity of the enzyme between the DNA gate and the C-gate. These quaternary couplings for gate opening and closing suggest that topoisomerase II ensures a transient DNA gating state, during which dimer interface contacts are maximized and backtracking of the transported DNA is minimized.     

A biomolecular implementation of logically reversible computation with minimal energy dissipation

Energy dissipation associated with logic operations imposes a fundamental physical limit on computation and is generated by the entropic cost of information erasure, which is a consequence of irreversible logic elements. We show how to encode information in DNA and use DNA amplification to implement a logically reversible gate that comprises a complete set of operators capable of universal computation. We also propose a method using this design to connect, or 'wire', these gates together in a biochemical fashion to create a logic network, allowing complex parallel computations to be executed. The architecture of the system permits highly parallel operations and has properties that resemble well known genetic regulatory systems.     

Ultrasensitive DNA detection by cycle isothermal amplification based on nicking endonuclease and its application to logic gates

In recent years, an intense interest has grown in the DNA logic gates having high potential for computation at literally the “nano-size” level. A limitation of traditional DNA logic gates is that each target strand hybridizes with only a single copy of the probe. This 1:1 hybridization radio limits the gain of the approach and thus its sensitivity. The exponential amplification of nucleic acids has become a core technology in medical diagnostics and has been widely used for the construction of DNA sensor, DNA nanomachine and DNA sequencing. It would be of great interest to develop DNA-based logic systems with exponential amplification for the output signal. In the present study, a series of three-input DNA logic gates with the cycle isothermal amplification based on nicking endonuclease (NEase) are designed. Very low concentrations of the analytes were sufficient to initiate an autocatalytic cascade, achieving a significant improvement of the detection limit, 100-fold improvement compared to the non-autocatalytic system. This was achieved by engineering a simple and flexible biological circuit designed to initiate a cascade of events to detect and amplify a specific DNA sequence. This procedure has the potential to greatly simplify the logic operation because amplification can be performed in “one-pot”.     

Multi/infinite dimensional neural networks, multi/infinite dimensional logic theory

A mathematical model of an arbitrary multi-dimensional neural network is developed and a convergence theorem for an arbitrary multi-dimensional neural network represented by a fully symmetric tensor is stated and proved. The input and output signal states of a multi-dimensional neural network/logic gate are related through an energy function, defined over the fully symmetric tensor (representing the connection structure of a multi-dimensional neural network). The inputs and outputs are related such that the minimum/maximum energy states correspond to the output states of the logic gate/neural network realizing a logic function. Similarly, a logic circuit consisting of the interconnection of logic gates, represented by a block symmetric tensor, is associated with a quadratic/higher degree energy function. Infinite dimensional logic theory is discussed through the utilization of infinite dimension/order tensors.     

Design and analysis of a robust genetic Muller C-element

This paper presents results on the design and analysis of a robust genetic Muller C-element. The Muller C-element is a standard logic gate commonly used to synchronize independent processes in most asynchronous electronic circuits. Synthetic biological logic gates have been previously demonstrated, but there remain many open issues in the design of sequential (state-holding) logic operations. Three designs are considered for the genetic Muller C-element: a majority gate, a toggle switch, and a speed-independent implementation. While the three designs are logically equivalent, each design requires different assumptions to operate correctly. The majority gate design requires the most timing assumptions, the speed-independent design requires the least, and the toggle switch design is a compromise between the two. This paper examines the robustness of these designs as well as the effects of parameter variation using stochastic simulation. The results show that robustness to timing assumptions does not necessarily increase reliability, suggesting that modifications to existing logic design tools are going to be necessary for synthetic biology. Parameter variation simulations yield further insights into the design principles necessary for building robust genetic gates. The results suggest that high gene count, cooperativity of at least two, tight repression, and balanced decay rates are necessary for robust gates. Finally, this paper presents a potential application of the genetic Muller C-element as a quorum-mediated trigger.