Multivalued logic gates based on DNA.

Binary logic is the basis of modern computers, in which every bit is coded by 0 or 1, corresponding to a low or high signal, respectively. Simple Boolean logic gates receive one or more binary (0, 1) input signals and produce a single binary output signal. The principles of binary logic can be applied to the signal transduction operated by molecular switches. In the past decade, molecular systems capable of performing Boolean logic operations have been attractive for the construction of molecular-level devices and machines. Various materials, such as organic molecules, protein, nucleic acids, enzymatic biochemical network, 14] supramolecular hydrogel, and polymer–ligand interactions have been used to process chemical signals, mimicking Boolean logic operations. These logic gates show great promise, but at the same time face substantial challenges. With the development of biological computing and quantum computing, the dominance of binary logic is challenged and multi-valued logic gates attract intense interest for research. Boolean binary logic has only two states that are true and false, or on and off. However, quite often, the logic gates suffer a certain degree of uncertainty and imprecision. In these cases, it is difficult to process information based on binary logic. Multi-valued logic is likely to play an increasingly important role in the conception and design of a molecular computer, since it would be able to deal with uncertain information. Multi-valued logic is defined as a nonbinary logic and involves the switching between more than two states. The number of distinguishable states increases, which allows for higher information densities. The common application of a multi-valued variable is coding. The Morse code, which uses three different symbols, is probably the best known. The more different symbols there are, the shorter the code words. A ternary or three-valued logic function is one that has two inputs that can assume three states (say 0, 1 and 2) and generates one output signal that can have one of these three states. Thus ternary logic is the extension of predominating binary logic. Recently, a multi-valued logic function was realized by using a nanofluidic diode based on conical nanopores functionalized with polyprotic acid chains. The low, medium, and high pH values constitute the inputs, and the conductance values constitute the outputs. Pischel s group has reported a tristable molecular fluorescent switch of the fluorophore1– spacer–receptor–spacer–fluorophore2 dyad. [21] A careful assignment of the logic operation yielded a ternary NOR logic gate. In addition, Cervera et al. reported a multi-valued XOR logic gate implemented with metallic nanoparticles and organic ligands. However, until now, the description of a ternary logic gate operation based on nucleic acids remains rare. Nucleic acids exhibit many advantages in comparison with organic molecules, such as easy synthesis with high reproducibility and purity, a simple operation, and high affinity with target molecules. Thus, DNA can be considered as a promising material for the development of a logic system. Various nucleic-acid-based binary logic gates such as AND, OR, XOR, NOR, NAND, INHIB, XNOR, and so on were realized. 23] Herein, we demonstrate the implementation of a ternary OR gate and an INH gate using nucleic acids immobilized on the surface of silica nanoparticles (SiNPs). The specificity of the Watson–Crick base pairing between complementary DNA strands enables the use of DNA as a functional material to construct structures and devices on a nanometer scale. As shown in Scheme 1, strand A was immobilized on the surface of silica nanoparticles. The 3’-extended DNA strand B, which contained 20 additional bases, was designed to form a duplex with strand A. Strand C could hybridize with the 3’-extended region of strand B. The three DNA strands could assemble into an ensemble. The gel electrophoresis image confirms the formation of DNA ensemble (see the Supporting Information, Figure S1). Stoichiometric mixing of the three strands leads to a low-mobility gel band. We designed ternary logic gates based on the DNA ensemble and the easy separation property of SiNPs. By observing the change of state of DNA ensemble on SiNPs, the multi-valued logic could be operated. In the experiments, the amino-decorated SiNPs were first synthesized by a modified reverse microemulsion method. Then, glutaraldehyde (GA) was used as a linker molecule for immobilization of amino-modified oligonucleotides (strand A) on the silica surface. Bovine serum albumin [a] Dr. F. Pu, Prof. Dr. J. Ren, X. Yang, Prof. Dr. X. Qu State Key Laboratory of Rare Earth State Resource Utilization and Laboratory of Chemical Biology Changchun Institute of Applied Chemistry Chinese Academy of Sciences, Changchun Jilin 130022 (P.R. China) and Graduate School of the Chinese Academy of Sciences Beijing, 100039 (P.R. China) Fax: (+86) 431-85262625 E-mail : jren@ciac.jl.cn xqu@ciac.jl.cn Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/chem.201101140.