Nonenzymatic Parallel DNA Logic Circuits

There is significant interest in exploring the possibilities of molecular-scale and biological computation. Many studies have investigated the use of biological molecules for carrying out various types of calculations and computations. Most studies on biological computing have focused on DNA-based systems. In such systems the underlying computational element is the specific hybridization of single-stranded DNA molecules to a complementary strand. The computational paradigm takes advantage of the huge number of available DNA molecules to carry out a parallel exhaustive search of the solution space. Logic gates are devices that perform the basic logic operations NOT, AND and OR, as well as their combinations, such as fulladder, which is a key digital logic element used in computer engineering. Constructing a full-adder with DNA molecules is a challenge for any novel computational paradigm. The function of this element is to take three binary inputs and add them together to produce two binary outputs, which are known as the “sum” and “carry”. DNA logic gates are crucial for the development of molecular-scale computing. Mao et al. have reported a one-dimensional algorithm based on the self assembly of DNA triple-crossover molecules that could be used to execute four steps of a logical (cumulative XOR) operation on a string of binary bits. Stojanovic et al. have developed several types of deoxyribozyme-based molecular logic gates, such as an AND gate, OR gate and full-adder, with two or three oligonucleotides (ODNs) as inputs and two independent fluorogenic-cleavage reactions as outputs. In these deoxyribozyme-based logic gates, the activities of deoxyribozymes were allosterically regulated by specific effectors, which were rationally designed ODNs that contained complementary sequences to target deoxyribozyme. The system, however, had the critical disadvantage that the input variables were restricted to only three or less. Therefore, more complex mathematical problems cannot be solved by using this system. Additional efforts are thus needed to create more broadly applicable methods that allow accurate, simple, paratactic and scalable DNA logic operations. Here, we report the construction of a photochemical logic circuit made entirely of DNA and implemented by using sequence-specific photocleavage (SSPC) of photocrosslinked sites in the gate strands. As an example, we demonstrate the performance of logic operations, which include NOT, AND, OR and full-adder, using SSPC. We have previously studied several artificial DNA bases as tools for photochemical DNA manipulation, for example 5-carboxyvinyl-2’-deoxyuridine (U). This method provides exact control over the location, dose and time at which an event occurs, and also facile automation as evidenced by application in different types of analytical equipment, such as high-performance liquid chromatography and capillary electrophoresis. Recently, we reported the catalytic repair of a thymine dimer incorporated in a DNA duplex with a carbazole nucleoside. The properties of carbazole derivatives enable them to be exploited as electron donors for the repair of thymine dimers in DNA. In a similar mechanism, thyminedimer analogues can be split by using carbazole-modified ODNs by irradiation at 366 nm (Figure 1A). This system allows a photocrosslinked site to be cleaved specifically. To investigate the photocleavage efficiency of the photocrosslinked site by irradiation at 366 nm in the presence of carbazole-modified ODN, the isolated photocrosslinked product was irradiated at 366 nm for 3 h at room temperature. The result showed the rapid disappearance of the photocrosslinked product and appearance of the two original ODNs (1 and 2), as evidenced by migration of the products on a denaturing PAGE gel (Figure 1B). Analysis of the ODNs formed by MALDITOF MS also indicated that these ODNs were ODN 1 and ODN 2 (Supporting Information). The time course of cleavage efficiency showed that the photocleavage reaction was complete after 3 h (Figure 1C). Next, we designed and prepared six photocrosslinked products (gate strands) and six carbazolemodified ODNs (input strands) to examine the sequence specificity of the SSCP reaction. The gate strands consisted of a 23-mer gate moiety that possessed the photocrosslinked site, an address sequence at the 5’ end and a biotin at the 3’ end for output detection by using streptavidine–Cy3. For the design of the 23-mer sequences, the following constraints were applied: similar GC content, thermodynamic uniform behaviour and no self complementarity. All gate strands and one input strand were mixed in a single test tube, and then photoirradiated at 366 nm by using a transilluminator. The results of the SSPC reaction were visualized by fluorescence imaging after sequence-specific hybridization between a probe attached to a DNA chip and the address sequence at the 5’ end of the gate moiety (Figure 2). The results show that fluorescence output was observed except for gates that matched the input sequence; this indicates that the SSPC reaction was robust (Supporting Information). Therefore, this system is like a NOT gate because fluorescence was not observed (output=0) in the presence of a matching input strand. Based on the results of the SSPC experiments we designed a photochemical AND gate. The AND gate was achieved by linear connection of the two gate moieties. In addition, we designed an OR logic gate, which was expressed by the sum of the inputs (Figure 3A). We initially converted the OR equation [a] S. Ogasawara, Y. Kyoi, Prof. Dr. K. Fujimoto School of Materials Science Japan Advanced Institute of Science and Technology Asahidai, Nomi, Ishikawa 923-1292 (Japan) Fax: (+81)761-51-1671 E-mail : kenzo@jaist.ac.jp Supporting information for this article is available on the WWW under http://www.chembiochem.org or from the author.