The Construction And Application Of DNA Logic Gates

Molecular computer or information processing on the molecular scale, is a promising substitute for the traditional silicon-based computer technologies, and it is necessary to flourish efficient and economic logic components for its development. Since nucleic acids exhibit many advantages that would rival silicon based computation in developing biologically relevant computation systems, such as structural simplicity, straight forward sequence-specific hybridization between complementary strands as well as the ability to capture certain target molecules such as metal ions, small molecules, and proteins in a highly specific manner. Thus far, considerable DNA logic gates have been achieved such as AND, OR, XOR, NOR, NAND, INHIBIT, XNOR. The paper engaged in the exploration and research of the construction of DNA logic gates as well as application. As reflected in the following two aspects:1. We report a series of novel metal-ion-mediated DNA logic gates (AND, NAND, NOR) based on electrochemical outputs for logical detection of Hg2+and Ag+. Utilizing the unique features that Ag+ions interact with the cytosine-cytosine(C-C) mismatch and Hg2+ions interact with the thymine-thymine(T-T) mismatch in DNA duplexes, an AND logic system is constructed based on the proximity dependent surface hybridization between a thiolated T-/C-rich DNA on gold electrode surface and another T-/C-rich DNA labeled with ferrocenecarboxylic acid (Fc), in which the Hg2+and Ag+ions are employed as inputs and the current of the Fc as output. Subsequently, a NAND logic gate is constructed based on the strand dissociation as well as the conformational switch of T-/C-rich DNA triggered by Ag+and Hg2+ions. In addition, we firstly find that the C-Ag+-C and T-Hg2+-T base pairs can trigger the structural conversion of multiple nucleic acid helices from triplexes to duplexes, which motivate us to fabricate another NOR logic gate. Hence, the development of DNA electrochemical logic gates, which can be fast, sensitive, simple, and reversible, overcome the shortcomings of the traditional optical logic gate with design complexity, complicated operation, which pave a way for logic detection metal ions.2. Here we report on the use of ion-dependent DNAzymes as functional nucleic acids for the construction of a series of DNA logic gates based entirely on colorimetric outputs. Two kinds of ion-dependent DNAzymes and tailored substrates enables the design of the logic gates (OR, AND, INHIBIT), using Pb2+and Cu2+as inputs, and then a three-inputs AND logic gate was developed utilizing the unique features that Hg+ions interact with the thymine-thymine (T-T). Firstly, the Pb2+-dependent DNAzyme and the Cu2+-dependent DNAzyme hybridize with the substrates, respectively. The substrates consist of the specific sequences that include each a ribonucleobase that allows the specific cleavage by the Pb2+-or Cu2+-dependent DNAzymes. Simultaneously, the substrates include two domains with the characteristic sequence of the horseradish peroxidase (HRP)-mimicking DNAzyme and regions that are complementary to the ions-dependent DNAzymes. Thus, hybridization of the two ion-dependent DNAzymes with the substrates prohibit the self-assembly of the HRP-mimicking DNAyzme consisting of the hemin/G-quadruplex structure. Treatment of the system with either Pb2+, or Cu2+results in the cleavage of the substrate at the respective ribonucleobases. The scission processes yield to nucleic acid fragments that lack further synergistic stabilization and thus are released from the complex, respectively. The released fragments consist of the HRP-mimicking DNAzyme sequences, and hence, they self-assemble in the presence of hemin to the biocatalytic DNAzyme that generates TMB+. That is, the DNAzyme is formed when the system is subjected to any of the ion inputs, Pb2+or Cu2+, or when the system is activated by the two ion-inputs. Inspired by the above OR logic gate, similarly, AND, INHIBIT, three-inputs AND logic gates were constructed based on the ion-dependent DNAzyme. We are able to recognize the logic output signals effortlessly by our naked eyes. It is a simple, economic and safe approach for the design of complex multiple input DNA logic molecular device.