Endonuclease-Based Logic Gates and Sensors Using Magnetic Force-Amplified Readout of DNA Scission on Cantilevers

Recognition of Bimolecular Logic Operation Pattern Based on a Solid-State Nanopore

Nanopores have a unique advantage for detecting biomolecules in a label-free fashion, such as DNA that can be synthesized into specific structures to perform computations. This method has been considered for the detection of diseased molecules. Here, we propose a novel marker molecule detection method based on DNA logic gate by deciphering a variable DNA tetrahedron structure using a nanopore. We designed two types of probes containing a tetrahedron and a single-strand DNA tail which paired with different parts of the target molecule. In the presence of the target, the two probes formed a double tetrahedron structure. As translocation of the single and the double tetrahedron structures under bias voltage produced different blockage signals, the events could be assigned into four different operations, i.e., (0, 0), (0, 1), (1, 0), (1, 1), according to the predefined structure by logic gate. The pattern signal produced by the AND operation is obviously different from the signal of the other three operations. This pattern recognition method has been differentiated from simple detection methods based on DNA self-assembly and nanopore technologies.

Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation

Nucleic acids have attracted widespread attention due to the simplicity with which they can be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of DNA/RNA nanotechnology offer numerous opportunities for in-cell and in-vivo applications, and the technology holds great promise to advance the growing field of synthetic biology. Many elegant examples have revealed the potential in integrating nucleic acid nanostructures in cells and in vivo where they can perform important physiological functions. In this Review, we summarize the current abilities of DNA/RNA nanotechnology to realize applications in live cells and then discuss the key problems that must be solved to fully exploit the useful properties of nanostructures. Finally, we provide viewpoints on how to integrate the tools provided by DNA/RNA nanotechnology and related new technologies to construct nucleic acid nanostructure-based molecular circuitry for synthetic biology.

Blood Droplet-Based Cancer Diagnosis via Proteolytic Activity Measurement in Cancer Progression

Matrix metalloproteinase (MMP) is a key marker and target molecule for cancer diagnosis, as MMP is able to cleave peptide chains resulting in degradation of extracellular matrix (ECM), a necessary step for cancer development. In particular, MMP2 has recently been recognized as an important biomarker for lung cancer. Despite the important role of detecting MMP molecules in cancer diagnosis, it is a daunting task to quantitatively understand a correlation between the status of cancer development and the secretion level of MMP in a blood droplet. Here, we demonstrate a nanoscale cancer diagnosis by nanomechanical quantitation of MMP2 molecules under cancer progression with using a blood droplet of lung cancer patients. Specifically, we measured the frequency dynamics of nanomechanical biosensor functionalized with peptide chains mimicking ECM in response to MMP2 secreted from tumors in lung with different metastasis level. It is shown that the frequency shift of the biosensor, which exhibits the detection sensitivity below 1 nM, enables the quantitation of the secretion level of MMP2 molecules during the progression of cancer cells or tumor growth. More importantly, using a blood droplet of lung cancer patients, nanomechanical biosensor is shown to be capable of depicting the correlation between the secretion level of MMP2 molecules and the level of cancer metastasis, which highlights the cantilever-based MMP2 detection for diagnosis of lung cancer. Our finding will broaden the understanding of cancer development activated by MMP and allow for a fast and point-of-care cancer diagnostics.

G-quadruplex-based logic gates for HgII and AgI ions employing a luminescent iridium(iii) complex and extension of metal-mediated base pairs by polymerase

We report herein the synthesis of a series of cyclometallated iridium(iii) complexes as luminescent G-quadruplex-selective probes to construct AND, OR and INHIBIT logic gates for the detection of Hg^II and Ag^I ions.

Construction of DNA logic gates utilizing a H+/Ag+ induced i-motif structure

A simple technology to construct diverse DNA logic gates (OR and INHIBIT) has been designed utilizing a H(+) and/or Ag(+) induced i-motif structure. The logic gates are easily controlled and also show a real time response towards inputs. The research provides a new insight for designing DNA logic gates using an i-motif DNA structure.

Non-covalent monolayer-piercing anchoring of lipophilic nucleic acids: preparation, characterization, and sensing applications

Functional interfaces of biomolecules and inorganic substrates like semiconductor materials are of utmost importance for the development of highly sensitive biosensors and microarray technology. However, there is still a lot of room for improving the techniques for immobilization of biomolecules, in particular nucleic acids and proteins. Conventional anchoring strategies rely on attaching biomacromolecules via complementary functional groups, appropriate bifunctional linker molecules, or non-covalent immobilization via electrostatic interactions. In this work, we demonstrate a facile, new, and general method for the reversible non-covalent attachment of amphiphilic DNA probes containing hydrophobic units attached to the nucleobases (lipid-DNA) onto SAM-modified gold electrodes, silicon semiconductor surfaces, and glass substrates. We show the anchoring of well-defined amounts of lipid-DNA onto the surface by insertion of their lipid tails into the hydrophobic monolayer structure. The surface coverage of DNA molecules can be conveniently controlled by modulating the initial concentration and incubation time. Further control over the DNA layer is afforded by the additional external stimulus of temperature. Heating the DNA-modified surfaces at temperatures >80 °C leads to the release of the lipid-DNA structures from the surface without harming the integrity of the hydrophobic SAMs. These supramolecular DNA layers can be further tuned by anchoring onto a mixed SAM containing hydrophobic molecules of different lengths, rather than a homogeneous SAM. Immobilization of lipid-DNA on such SAMs has revealed that the surface density of DNA probes is highly dependent on the composition of the surface layer and the structure of the lipid-DNA. The formation of the lipid-DNA sensing layers was monitored and characterized by numerous techniques including X-ray photoelectron spectroscopy, quartz crystal microbalance, ellipsometry, contact angle measurements, atomic force microscopy, and confocal fluorescence imaging. Finally, this new DNA modification strategy was applied for the sensing of target DNAs using silicon-nanowire field-effect transistor device arrays, showing a high degree of specificity toward the complementary DNA target, as well as single-base mismatch selectivity.

Enzymatic cleavage of nucleic acids on gold nanoparticles: a generic platform for facile colorimetric biosensors

The enzymatic cleavage of nucleic acids (DNA or DNA with a single RNA linkage) on well-dispersed gold nanoparticles (AuNPs) is exploited in the design of facile colorimetric biosensors. The assays are performed at salt concentrations such that DNA-modified AuNPs are barely stabilized by the electrostatic and steric stabilization. Enzymatic cleavage of DNA chains on the AuNP surface destabilizes the AuNPs, resulting in a rapid aggregation driven by van der Waals attraction, and a red-to-purple color change. Two different systems are chosen, DNase I (a DNA endonuclease) and 8-17 (a Pb(2+)-depedent RNA-cleaving DNAzyme), to demonstrate the utility of our assay for the detection of metal ions and sensing enzyme activities. Compared with previous studies in which AuNP aggregates are converted into dispersed AuNPs by enzymatic cleavage of DNA crosslinkers, the present assay is technically simpler. Moreover, the accessibility of DNA to biomolecular recognition elements (e.g. enzymes) on well-dispersed AuNPs in our assay appears to be higher than that embedded inside aggregates. This biosensing system should be readily adaptable to other enzymes or substrates for detection of analytes such as small molecules, proteases and their inhibitors.

A light-controlled reversible DNA photoligation via carbazole-tethered 5-carboxyvinyluracil

We describe a light-controlled template-directed reversible DNA photoligation via carbazole-tethered 5-carboxyvinyluracil. Carbazole-tethered 5-carboxyvinyl-2'-deoxyuridine-containing oligodeoxynucleotide (ODN) can be ligated by irradiation at 366 nm in the presence of template ODN, and the ligated ODN can be split by irradiation at 366 nm in the absence of template ODN.

Part II: coordinated biosensors--development of enhanced nanobiosensors for biological and medical applications

In this review, we summarize recent developments in nanobiosensors and their applications in biology and potential in medical diagnostics. We first highlight the concept of coordinated nanobiosensors, which integrate desirable properties of the individual components: protein machinery for sensitivity and specificity of binding, peptide or nucleic acid chemistry for aligning the various electron-transducing units and the nanoelectrodes for enhancing sensitivity in electronic detection. The fundamental basis of coordinated nanobiosensing is in applying the precise 3D atomic resolution structural information to rationally design and fabricate biosensors with high specificity and sensitivity. Additionally, we describe several biosensors developed for detecting biologically relevant compounds, including those for hydrogen peroxide, dopamine, glucose, DNA and cytochrome C. Results from these systems highlight the potential advantages of using nanoscale biosensors and how further developments in this area will change biomedical diagnostics and treatments drastically.

Towards biomedical applications for nucleic acid nanodevices

DNA and RNA can be used to construct artificial nanodevices with strong potential for future biomedical applications. DNA nanodevices can function as biosensors, which detect and report the presence of proteins and naturally occurring nucleic acids, such as mRNA or microRNAs. Complex sensors can be realized by supporting DNA devices with DNA-based information processing. Artificial DNA-based reaction networks can be created that amplify molecular signals or evaluate logical functions to report the simultaneous presence of several disease-related molecules. Other applications for DNA nanodevices are found in controlled release and drug delivery. DNA can be used to build nanocontainers for drugs or switchable hydrogels, which can trap and release compounds. For in vivo applications of DNA nanodevices, techniques for efficient packaging and delivery have been developed and the first examples of intracellular RNA-based nanodevices have already been demonstrated.

Part I: recent developments in nanoelectrodes for biological measurements

Biosensors are a type of analytical device that use biological molecules to monitor biorecognition events and interactions. Coupled with the progress in nanotechnologies over recent years, the development of a nanobiosensor based on individual nanoelectrodes and nanoelectrode arrays or nanoelectrode ensembles offers unprecedented avenues for screening and detection at ultrahigh sensitivities. These capabilities provide the basis for a paradigmatic change in biomedical diagnostics and treatment. In this review, we highlight recent developments in nanoelectrode platforms and their suitability for integrating with biological components for the fabrication of ultrasensitive nanobiosensors.

Phosphate-Mediated Molecular Memory Driven by Two Different Protein Kinases as Information Input Elements

There is increasing interest in studying molecular-based devices that perform Boolean logic operations whose output state (0 or 1) depends on the input conditions (0/0, 1/0, 0/1, or 1/1). So far, great efforts have been devoted to establish molecular-scaled logic gates activated by chemical, physical, and biological inputs. We herein describe the design and synthesis of a tandem protein kinase substrate peptide acting as a phosphate-mediated molecular memory. The molecular-based memory system is comprised of two different phosphorylatable substrate regions joined in series and a spiropyran derivative at the N-terminus. We also demonstrated three basic "AND", "OR", and "NOR" logic operations on the basis of alterations in the spiropyran-to-merocyanine (SP-to-MC) thermocoloration properties of the spiropyran moiety in the peptide upon kinase-catalyzed phosphorylation. The three logic functions were successfully performed by adding ionic polymers as programming elements with preset thresholds of a signal intensity in a microplate format. Throughout this study, information was recorded on the substrate peptide by protein kinase-catalyzed phosphorylation, stored stably as phosphoesters, read according to the extent of the SP-to-MC thermocoloration, and erased by phosphatase-catalyzed dephosphorylation, resulting in the peptide returning to the initial recordable state. Thus, the proof-of-concept experiments described herein could be used to provide clues for developing practical molecular-based processing and computing.

Chemical Approaches to Molecular Logic Elements for Addition and Subtraction

Molecular and supramolecular logic gates are candidates for computation at the nanoscale level. Nowadays all common logic operations can be mimicked with molecular devices based on chemical approaches. One step further towards molecular systems with increased logic capabilities is the addition or subtraction of binary digits. This Minireview describes recent developments to attain this goal, including bioinspired systems based on DNA and enzymes. Furthermore, chemical molecular logic gates are discussed and compared critically with regard to alternative concepts.

Encoded and enzyme-activated nanolithography of gold and magnetic nanoparticles on silicon

A C18 monolayer-functionalized Si surface is electrochemically patterned to yield a carboxylic acid-terminated pattern. Tyramine is covalently linked to the pattern to yield an encoded nanostructure for the enzyme tyrosinase. The biocatalytic oxidation of the tyramine residues yields catechol moieties that control the assembly of boronic acid-functionalized Au nanoparticles (NPs) or magnetic NPs. The different NPs are linked to the patterns by the formation of complexes between the boronic acid residues or Fe3+ ions and the catechol ligands.

Biomolecule–nanoparticle hybrid systems for bioelectronic applications

Recent advances in nanobiotechnology involve the use of biomolecule-nanoparticle (NP) hybrid systems for bioelectronic applications. This is exemplified by the electrical contacting of redox enzymes by means of Au-NPs. The enzymes, glucose oxidase, GOx, and glucose dehydrogenase, GDH, are electrically contacted with the electrodes by the reconstitution of the corresponding apo-proteins on flavin adenine dinucleotide (FAD) or pyrroloquinoline quinone (PQQ)-functionalized Au-NPs (1.4 nm) associated with electrodes, respectively. Similarly, Au-NPs integrated into polyaniline in a micro-rod configuration associated with electrodes provides a high surface area matrix with superior charge transport properties for the effective electrical contacting of GOx with the electrode. A different application of biomolecule-Au-NP hybrids for bioelectronics involves the use of Au-NPs as carriers for a nucleic acid that is composed of hemin/G-quadruplex DNAzyme units and a detecting segment complementary to the analyte DNA. The functionalized Au-NPs are employed for the amplified DNA detection, and for the analysis of telomerase activity in cancer cells, using chemiluminescence as a readout signal. Biomolecule-semiconductor NP hybrid systems are used for the development of photoelectrochemical sensors and optoelectronic systems. A hybrid system consisting of acetylcholine esterase (AChE)/CdS-NPs is immobilized in a monolayer configuration on an electrode. The photocurrent generated by the system in the presence of thioacetylcholine as substrate provides a means to probe the AChE activity. The blocking of the photocurrent by 1,5-bis(4-allyldimethyl ammonium phenyl)pentane-3-one dibromide as nerve gas analog enables the photoelectrochemical analysis of AChE inhibitors. Also, the association CdS-NP/double-stranded DNA hybrid systems with a Au-electrode, and the intercalation of methylene blue into the double-stranded DNA, generates an organized nanostructure of switchable photoelectrochemical functions. Electrochemical reduction of the intercalator to the leuco form, -0.4 V vs. SCE, results in a cathodic photocurrent as a result of the transfer of photoexcited conduction-band electrons to O(2) and the transport of electrons to the valance-band holes by the reduced intercalator units. The oxidation of the intercalator, E 0 V (vs. SCE), yields in the presence of triethanolamine, TEOA, as sacrificial electron donor, an anodic photocurrent by the transport of conduction-band electrons, through intercalator units, to the electrodes, and filling the valance-band holes with electrons supplied by TEOA. The systems reveal potential-switchable directions of the photocurrents, and reveal logic gate functions.

Photonic Boolean logic gates based on DNA aptamers

We designed a pair of DNA-based logic gates that sense single-stranded DNAs and aptamer ligands to produce fluorescence outputs according to Boolean logic functions AND and OR.

A New Redox-Resettable Molecule-Based Half-Adder with Tetrathiafulvalene

A new redox molecule-based half-adder with tetrathiafulvalene (TTF) was reported for the first time. This half-adder employs electrochemical and chemical oxidations (NOPF6) as input signals and absorbances at 350 and 435 nm as output signals. It is interesting to note that this new molecule-based half-adder shows reset capability by making use of the unique redox behaviors of TTF.

Logic Gates and Elementary Computing by Enzymes

Different selected enzymes, glucose oxidase (GOx), catalase (Cat), glucose dehydrogenase (GDH), horseradish peroxidase (HRP), and formaldehyde dehydrogenase (FDH), are used alone or coupled to construct eight different logic gates. The added substrates for the respective enzymes, glucose and H(2)O(2), act as the gate inputs, while the biocatalytically generated gluconic acid or NADH are the output signals that follow the operation of the gates. Different enzyme-based gates are XOR, INHIBIT A, INHIBIT B, AND, OR, NOR, Identity and Inverter gates. By combining the AND and XOR or the XOR and INHIBIT A gates, the half-adder and half-subtractor are constructed, respectively, opening the way to elementary computing by the use of enzymes.

A Molecular Full-Adder and Full-Subtractor, an Additional Step toward a Moleculator

Over the past decade, there has been remarkable progress in the development of molecular logic and arithmetic systems, which has brought chemists closer to the realization of a molecular scale calculator (a Moleculator). This paper describes a significant step in this direction. By integrating past and new approaches for molecular logic reconfiguration, we were able to load advanced arithmetic calculations onto a single molecular species. Exchanging chemical inputs, monitoring at several wavelengths simultaneously, as well as using negative logic for the transmittance mode significantly increase the input and output information channels of the processing molecule. Changing the initial state of the processor is an additional approach used for altering the logical output of the device. Finally, introducing degeneracy to the chemical inputs or, alternatively, controlling their interactions to form identical chemical states minimizes the complexity of realizing three-bits addition and subtraction at the molecular scale. Consequently, using a commercially available fluorescein molecule, acid and base chemical inputs, and a simple UV-vis measurement setup, integration of a full-adder and, for the first time, a full-subtractor is now possible within individual molecules.

Luminescent logic function of a surfactant-encapsulated polyoxometalate complex

We have fabricated a novel organic/inorganic hybrid material consisting of multifunctional surfactant-encapsulated polyoxometalloeuropate which functions as a luminescent logic gate with dual output operated by light and metal ion as inputs.