Tailoring Plasmonic Metamaterials for DNA Molecular Logic Gates

Structural and functional information encoded in DNA combined with unique properties of nanomaterials could be of use for the construction of novel biocomputational circuits and intelligent biomedical nanodevices. However, at present their practical applications are still limited by either low reproducibility of fabrication, modest sensitivity, or complicated handling procedures. Here, we demonstrate the construction of label-free and switchable molecular logic gates that use specific conformation modulation of a guanine- and thymine- rich DNA, while the optical readout is enabled by the tunable alphabetical metamaterials, which serve as a substrate for surface enhanced Raman spectroscopy (MetaSERS). By computational and experimental investigations, we present a comprehensive solution to tailor the plasmonic responses of MetaSERS with respect to the metamaterial geometry, excitation energy, and polarization. Our tunable MetaSERS-based DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions.

Taking Baby Steps in Molecular Logic-based Computation

Molecular logic-based computation is a broad umbrella covering molecular sensors at its simplest level and logic gate arrays involving steadily increasing levels of parallel and serial integration. The fluorescent PET(photoinduced electron transfer) switching principle remains a loyal servant of this entire field. Applications arise from the convenient operation of molecular information processors in very small spaces.

Building pH Sensors into Paper-based Small-molecular Logic Sys-tems for Very Simple Detection of Edges of Objects

Genetically-engineered bacteria and reactive DNA networks detect edges of objects, as done in our retinas and as also found within computer vision. We now demonstrate that simple molecular logic systems (a combination of a pH sensor, a photo acid generator and a pH buffer spread on paper) without any organization can achieve this relatively complex computational goal with good-fidelity. This causes a jump in the complexity achievable by molecular logic-based computation and extends its applicability. The molecular species involved in light dose-driven 'off-on-off' fluorescence is diverted in the ‘on’ state by proton diffusion from irradiated to unirradiated regions where it escapes a strong quencher, thus visualizing the edge of a mask.

Small molecular logic systems can draw the outlines of objects via edge visualization

The recently-discovered ability of small logical molecules to recognize edges is exploited to achieve outline drawing from binary templates. Outlines of arbitrary curvature, several colours and thicknesses down to 1 mm are drawn in around 30 min or less by employing a common laboratory two-colour ultraviolet lamp. The outlines and the light dose-driven XOR logic with fluorescence output or ‘off-on-off’ action which is observed in the irradiated regions are modelled by combining foundational principles of photochemistry, acid-base neutralization and diffusion.

From Sensing to Molecular Logic: A Journey

A personal account of the establishment of luminescent PET (photoinduced electron transfer) sensing and its development into molecular logic is given. Several applications of these two research areas, e.g. blood electrolyte diagnostics, ‘lab-on-amolecule’ systems and molecular computational identification (MCID) are illustrated.

Tailoring Plasmonic Metamaterials for Ultrasenstive Detection of Mercury Trace Contaminants via Molecular Logic Gates

Structural and functional information encoded in DNA combined with unique properties of nanomaterials could be of use for the construction of novel biocomputational circuits and intelligent biomedical nanodevices. However, at present their practical applications are still limited by either low reproducibility of fabrication, modest sensitivity, or complicated handling procedures. Here, we demonstrate the construction of label-free and switchable molecular logic gates (AND, INHIBIT, and OR) that use specific conformation modulation of a guanine- and thymine-rich DNA, while the optical readout is enabled by the tunable metamaterials which serve as a substrate for surface enhanced Raman spectroscopy (MetaSERS). Our MetaSERS-based DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions down to 2×10-4 ppb, which is four orders of magnitude lower than the exposure limit allowed by United States Environmental Protection Agency

Fluorescent Logic Systems for Sensing and Molecular Computation: Structure-Activity Relationships in Edge-Detection

Molecular logic-based computation continues to throw up new applications in sensing and switching, the newest of which is the edge detection of objects. The scope of this phenomenon is mapped out by the use of structure-activity relationships, where several structures of the molecules and of the objects are examined. The different angles and curvatures of the objects are followed with good-fidelity in the visualized edges, even when the objects are in reverse video.

Molecular Computational Elements Encode Large Populations of Small Objects

Since the introduction of molecular computation1, 2, experimental molecular computational elements have grown3, 4, 5 to encompass small-scale integration6, arithmetic7 and games8, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size9 (about 1 nm) and large 'on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100 m) used for synthesis of combinatorial libraries10, 11. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a 'wash and watch' protocol12. Our focus on converting molecular science into technology concerning analog sensors13, 14, turns to digital logic devices in the present work.

Metallosupramolecular Materials for Electronic Applications: Molecular Boolean Computation

It is an exciting era for molecular computation because molecular logic gates are being pushed in new directions. The use of sulfur rather than the commonplace nitrogen as the key receptor atom in metal ion sensors is one of these directions; plant cells coming within the jurisdiction of fluorescent molecular thermometers is another, combining photochromism with voltammetry for molecular electronics is yet another. Two-input logic gates benefit from old ideas such as rectifying bilayer electrodes, cyclodextrin-enhanced room-temperature phosphorescence, steric hindrance, the polymerase chain reaction, charge transfer absorption of donor–acceptor complexes and lectin–glycocluster interactions. Furthermore, the concept of photo-uncaging enables rational ways of concatenating logic gates. Computational concepts are also applied to potential cancer theranostics and to the selective monitoring of neurotransmitters in situ. Higher numbers of inputs are also accommodated with the concept of functional integration of gates, where complex input–output patterns are sought out and analysed. Molecular emulation of computational components such as demultiplexers and parity generators/checkers are achieved in related ways. Complexity of another order is tackled with molecular edge detection routines.

Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate

Cyclooxygenase 2 (COX2), a key regulatory enzyme of the prostaglandin/eicosanoid pathway, is an important target for anti-inflammatory therapy. It is highly induced by pro-inflammatory cytokines in a Nuclear factor kappa B (NFκB)-dependent manner. However, the mechanisms determining the amplitude and dynamics of this important pro-inflammatory event are poorly understood. Furthermore, there is significant difference between human and mouse COX2 expression in response to the inflammatory stimulus tumor necrosis factor alpha (TNFα). Here, we report the presence of a molecular logic AND gate composed of two NFκB response elements (NREs) which controls the expression of human COX2 in a switch-like manner. Combining quantitative kinetic modeling and thermostatistical analysis followed by experimental validation in iterative cycles, we show that the human COX2 expression machinery regulated by NFκB displays features of a logic AND gate. We propose that this provides a digital, noise-filtering mechanism for a tighter control of expression in response to TNFα, such that a threshold level of NFκB activation is required before the promoter becomes active and initiates transcription. This NFκB-regulated AND gate is absent in the mouse COX2 promoter, most likely contributing to its differential graded response in promoter activity and protein expression to TNFα. Our data suggest that the NFκB-regulated AND gate acts as a novel mechanism for controlling the expression of human COX2 to TNFα, and its absence in the mouse COX2 provides the foundation for further studies on understanding species-specific differential gene regulation.

New tools for self-organised pattern formation

Position-dependent gene expression is a critical aspect of the development and behaviour of multicellular organisms. It requires a complex series of interactions to occur between different cell types in addition to intracellular signalling cascades. We used Escherichia coli to study the properties of an artificial signalling system at the interface between two expanding cell populations. We genetically engineered one population to produce a diffusible acyl-homoserine lactone (AHL) signal, and another population to respond to it. Our experiments demonstrate how such a signal can be used to reproducibly generate simple visible patterns with high accuracy in swimming agar. The producing and responding cassettes of two such signalling systems can be linked to produce a symmetric interface for bidirectional communication that can be used to visualise molecular logic. Intracellular feedback between these two cassettes would then create a framework for self-organised patterning of higher complexity. Adapting the experiments of Basu et al. (Basu et al., 2005) using cell motility, rather than a differential response to AHL concentrations as a way to define zones of response, we noted how the interaction of sender and receiver cell populations on a swimming plate could lead to complex pattern formation. Equipping highly motile strains such as E. coli MC1000 with AHL-mediated auto-inducing systems based on Vibrio fischeri luxI/luxR and Pseudomonas aeruginosa lasI/lasR cassettes would allow the amplification of a response to an AHL signal and its propagation. We designed and synthesised codon-optimised auto-inducing luxI/R and lasI/R cassettes as optimal gene expression is crucial for the generation of robust patterns. We still have to complete and test the entire genetic circuitry, although by modelling the system we were able to demonstrate its feasibility. © 2007 The Institution of Engineering and Technology.

2010: A Small Space Odyssey with Luminescent Molecules

The road to molecular logic and computation in Belfast, Northern Ireland started with chemical sensors in Colombo, Sri Lanka. This journey is mapped out with reference to design principles, such as those for luminescent PET (photoinduced electron transfer) sensing. Applications such as those for blood electrolyte diagnostics, "lab-on-a-molecule" systems, and molecular computational identification (MCID) are also met along the way.