DNA mini-machines may lead to molecular computers

Scientists built simple machines out of DNA, which switch reversibly between two different shapes and could be used to make a molecular computer Washington, June 26: Scientists have built simple machines out of DNA, which switch reversibly between two different shapes and could be used to make nanotech sensors, amplifiers and even a molecular computer. The DNA machines can relay discrete bits of information through space or amplify a signal, said Yonggang Ke, an assistant professor from Georgia Institute of Technology in the US.

“In the field of DNAbased computing, the DNA contains the information, but the molecules are floating around in solution,” Mr Ke said. “What’s new here is that we are linking the parts together in a physical machine,” he said.

Similarly, several laboratories have already made nanotech machines such as tweezers and walkers out of DNA. Mr Ke said that the work sheds light on how to build structures with more complex, dynamic behaviours. The arrays’ structures look like retractable security gates. Extending or contracting one unit pushes nearby units to change shape as well, working like a domino cascade whose tiles are connected.

The arrays’ units get their stability from the energy gained when DNA double helices stack up. To be stable, the units’ four segments can align as pairs side by side in two different orientations. By leaving out one strand of the DNA at the edge of an array, the engineers create an external trigger. When that strand is added, it squeezes the edge unit into changing shape.

To visualise the DNA arrays, the engineers used atomic force microscopy. They built rectangular 11x4 and 11x7 arrays, added trigger strands and could observe the cascade propagate from the corner unit to the rest of the array. The arrays’ cascades can be stopped or resumed at selected locations by designing break points into the arrays. The units’ shape conversions are modulated by temperature or chemical denaturants.

For reference, the rectangular arrays are around 50 nanometres wide and a few hundred nanometres long slightly smaller than a HIV or influenza virion. To build the DNA array structures, the engineers used both origami (folding one long “scaffold” strand with hundreds of “staple” strands) and modular brick approaches.

Both types of arrays selfassemble through DNA strands finding their complimentary strands in solution.

The origami approach led to more stable structures in conditions of elevated temperature or denaturant. Researchers showed that they could build rectangles and tubes of array units.

They also include a cuboid that has three basic conformations, more than the two-dimensional array units with two conformations.