DNA-based logic gates
It is believed that the electronics of the future must meet a number of conditions. Computing devices should be fast and economical, and their production should be environmentally friendly. Great hopes are pinned on the so-called molecular electronics, in particular, based on the use of biomolecules.
The creation of molecular logic elements is a bottleneck in the construction of molecular computing devices. One of the essential problems of logic elements based on ribozymes, enzymes or optical materials is the different nature of the incoming and outgoing signal, unlike electronic systems that use a common input and output signal (electron). Since the output of one molecular logic element is not applicable as an input for another, there are obvious problems with combining such elements into more or less complicated logic systems.
American researchers have tried to work around this problem by constructing logic gates based on DNA. First of all, they created the elements AND (and), OR (or) and XOR (exclusive or). DNA fragments about 24 nucleotides long are used as input for these elements; oligonucleotides are also used as output.
Let's take a closer look at the principle of operation of the AND element (Figure 1).
The logic element consists of two oligonucletides: this is a fluorescently labeled 28-nucleotide AND-pin (blue in the diagram), which does not glow for the time being, because it is connected to a fixed AND-stationary (tricolor). The blue section of the AND-station forms a double helix with an AND-terminal, and the white and red are in a single-stranded state and act as seedings for two possible AND-inputs. In this form, the AND element is ready to work.
AND-inputs consist of 24 nucleotides and are complementary to one or the other half of the AND-hospital. When adding any one AND-input, it first binds to the corresponding free end of the AND-stationary (white or red), and then partially displaces the AND-output from the complex with the AND-stationary. However, the AND-output still remains in the bound state, and fluorescence is not detected. If both AND-inputs are added, the AND-output is completely displaced from the complex with the AND-stationary, passes into the solution and begins to glow – thus, the AND logic element works correctly.
The OR and XOR elements are arranged similarly. In the case of OR, both the OR-stationary and the OR-output have free single-stranded ends. One of the OR-inputs is completely complementary to the OR-output, the second is OR–stationary. Thus, the addition of any of the OR inputs leads to the release of the OR output from the complex with the OR stationary (Figure 2, above).
For the correct operation of the XOR logic element, chains of 20 nucleotides complementary to each other have been added to the XOR inputs. Due to this, the XOR inputs added simultaneously form a double helix with each other, without displacing the XOR output from the XOR stationary (Figure 2, below).
Having demonstrated the work of logic elements, scientists began to design more complex logic systems. First of all, they created a semi-summator consisting of the elements XOR and AND (Figure 3).
A half–summator is a logic circuit that adds two binary digits and outputs zero, one, or a discharge transfer signal. To implement such a scheme, the authors mixed the components of the XOR and AND elements in one test tube, marking the conclusions for these elements with two different dyes. By adding one, two or both inputs and detecting the appearance of fluorescence, the researchers made sure that the half-summator was working correctly.
The following scheme was even more complicated: it consisted of two XOR elements and one OR, as shown in Figure 4.
Here the outputs of the XOR elements are passed as input for the OR element. It is easy to notice that the whole scheme works exactly the same as one XOR element; however, in this case it is important that the scheme worked correctly – that is, the possibility of creating more complex chains of logical elements based on DNA is shown.
The work "Sequence-Addressable DNA Logic" is published in Small.