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Deoxyribozyme can be either in active or in inactive state. This enzyme can be made switch sensitive to an input DNA strand by adding a stem-loop structure to the molecule. In the stem-loop structure, the two substrate binding regions are complementary to each other, thus these regions hybridize to each other to form the stem component. These formed structures inhibit the substrates to bind to its recognition site in deoxyribozyme.

Figure 2.13 Mechanism to switch on deoxyribozyme logic gate.

The mechanism of controlling the catalytic activity of deoxyribozyme is shown in Figure 2.13. Deoxyribozyme logic gate can be switched on by addition of a single stranded short input DNA strand. This input oligonucleotide binds to the complementary single stranded loop region of deoxyribozyme. The hybridization leads to the destabilization of the stem-loop structure of deoxyribozyme. As a result, the stem-loop module opens up which permits the substrate to bind with deoxyribozyme. Thus, it can be concluded that the addition of the input oligonucleotides leads to the conformation change of the stemloop region of the enzyme which causes it is the catalytic activity. Following this method, the DNA logic gate can be switched on. This mechanism can also be applied for large DNA logic circuit. In this case, many different DNA oligonucleotides selectively bind to the specific corresponding stem-loop regions of deoxyribozyme. Thus, the activation of the logic circuit can be controlled by adding all inputs and enzymes in the same solution.

Now, in the next subsections, we will discuss the basic logic gates that can be constructed by using deoxyribozyme [6].