IACS team designs logic devices for DNA-based computation

Sixteen combinations of different enzymes were used to make up the desired outputs

Scientists at the Indian Association for the Cultivation of Science (IACS), Kolkata, have been successful in designing DNA-based logic devices that would find application in DNA-based computation. They have designed reusable YES and INHIBIT logic systems by using a small molecule that serves as a fluorescent probe and binds to both a four-stranded DNA structure (G-quadruplex) present in human telomeres and nucleic acid cleaving enzymes (nucleases).

Fluorescence

The fluorescent probe — carbazole ligand — selectively binds to the G-quadruplex over other DNA structures present in the human genome. Once it binds to the DNA (G-quadruplex), the small molecule inhibits certain enzymes (nuclease S1 and exonucleases) from degrading the DNA. However, certain other enzymes (DNase I and T7 endonuclease I) can degrade the DNA even when bound by the small molecule.

While the small molecule by itself shows weak emission at 373 nm and 530 nm, the fluorescence intensity gets enhanced 14-fold at 530 nm once it binds to the DNA. Similarly, the small molecule bound to the DNA exhibits different fluorescence behaviour in the presence of different enzymes and this has been taken advantage of by the team led by Prof. Jyotirmayee Dash from the Department of Organic Chemistry to design conceptually novel logic devices. The results were published in the journal ACS Synthetic Biology.

Computation

For instance, DNase I enzyme degrades the DNA-bound small molecule and so when both the DNA the DNase I enzyme are used as inputs the fluorescence at 530 nm weakens. The output is therefore taken as zero. On the other hand, nuclease S1 enzyme does not degrade the DNA bound by the small molecule and so when both DNA and nuclease S1 enzyme are used as inputs the fluorescence at 530 nm does not get affected. The output is taken as one.

“So the INHIBIT logic gate is constructed using DNA and DNase I as inputs while the inputs of DNA and nuclease S1 form a YES logic gate,” says Prof. Dash.

Once the DNA is degraded by the DNase I enzyme, the logic system can be reused by supplying heat to deactivate the enzyme. “The logic system can be recycled for three cycles by adding a heat deactivation step. After three consecutive cycles, the efficiency of the system decreases by only 33%,” says Prof. Dash.

The team went a step further to design combinatorial logic systems (individual logic gates integrated into one another such as INHIBIT−INHIBIT and NOR−OR) by using different combinations of four nucleases (enzymes) as inputs.

16 combinations

The researchers were able to get 16 different combinations by adding one, two, three or four enzymes (nuclease S1, Exo I, T7 Endo I and DNase I) to the DNA-bound small molecule. The different combinations of the four enzymes are taken as inputs and the fluorescence response at 530 nm is taken as the output.

Of the 16 combinations, only four combinations are fluorescent (output taken as 1) and 12 are non-fluorescent (output taken as zero). The square numbers (1, 4, 9, 16) are assigned as fluorescent combinations, whereas the rest are assigned as non-fluorescent combinations. “So by suitable programming we can modulate the system to carry out complex calculations (for example, identification of square numbers up to 16) by varying the inputs,” she says.

“We hope that these DNA logic gates will provide the ability to not only create more complicated, sequential DNA computations but also create interfaces between silicon and DNA-based computers. The DNA-based nanodevice could be useful for diagnostic sensors and other biomolecular machines,” Prof. Dash says.

Source: The Hindu