Tag Archives: molecular

The 2016 Nobel Prize in chemistry awarded to trio of molecular machine pioneers

The 2016 Nobel Prize in chemistry has been awarded to┬áJean-Pierre Sauvage from the University of Strasbourg, Sir J. Fraser Stoddart affiliated with Northwestern University, and Bernard L. Feringa from the University of Groningen for their work on molecular machines — nano-scale mechanisms capable of performing various tasks.

Molecular machines are teeny-tiny assemblies with the potential to spark a huge revolution. In essence, their purpose is to do the same things machines do for us today — transport, crafting, repairs — but on the molecular scale. And, just as you can’t make a car without first making some wheels, they need to be built from even smaller parts.

The trio’s work led to the creation of the most advanced such parts we’ve yet put together. Sauvage created the first molecular chain — or “catenane” — in 1983. Stoddart designed a “rotaxane”, a molecular ring around an axle. Feringa created the first molecular motor by coaxing a blade to spin in only one direction. Just remember, we’re talking about molecules here — far from the solid pieces of steel we use to build our machines in the macroscopic world, these molecular machines are subjected to the same rules as other molecules, such as Brownian motion.

Building on their work, chemists have designed muscles, elevators, and even cars, on an incredibly small scale. At the conference announcing the prize, committee member Sara Snogerup Linse asked if the audience wanted to see some molecular machines. She pulled away a black cylinder to reveal the items with a “Ta-da!” but there was nothing there.

“I’m sorry,” she said. “You can’t see them. They are more than a thousand times smaller than a human hair.”

Committee member Olof Ramstrom went on to present diagrams showcasing how the devices are built and their functionality. Sauvage, professor emeritus at the University of Strasbourg in France, developed a chain-linking process using a copper ion to hold two molecules in place. A third is added to complete the second link, and the copper ion is removed — allowing the two rings to move freely while still staying connected. Stoddart, Board of Trustees Professor of Chemistry at Northwestern University, used the attraction between an electron-starved ring and an electron-rich rod to thread the ring, forming an axle. The loop is then closed, to complete the assembly. Feringa, Jacobus Van’t Hoff Distinguished Professor of Molecular Sciences at the University of Groningen in the Netherlands, coaxed a spinning rotor blade to move in a single direction by driving it with pulses of light.

“They really are very tiny,” Ramstrom agreed.

The trio’s work has “opened this entire field of molecular machinery,” he added. There’s enormous potential in these tiny cogs and gears, as the Nobel Prize website explains:

“2016’s Nobel Laureates in Chemistry have taken molecular systems out of equilibrium’s stalemate and into energy-filled states in which their movements can be controlled. In terms of development, the molecular motor is at the same stage as the electric motor was in the 1830s, when scientists displayed various spinning cranks and wheels, unaware that they would lead to electric trains, washing machines, fans and food processors. Molecular machines will most likely be used in the development of things such as new materials, sensors and energy storage systems.”

The three scientists share the prize equally. A summary of their research can be read here. A technical explanation is available here.

 

Scientists create the first molecular transistor

Researchers from Yale University succeeded in what seemed to be an impossible task: they’ve created a transistor from a single molecule. In case you don’t know, a transistor is a “semiconductor device commonly used to amplify or switch electronic signals” (via wikipedia).

power_transistor

The team showed that using a single benzene molecule attached to gold contacts is just as good as the regular silicone transistor. Also, by modifying the voltage applied through the contacts, they were able to control the current that was going through the molecule.

“We were able to allow current to get through when it was low, and stopping the current when it was high,” says Mark Reed, Professor of Engineering & Applied Science at Yale.

The importance of this discovery should not be underestimated; it could prove to be very useful, especially in computer circuits, because common transistors are not feasible at such small scales, and this may very well be another step towards the next generation of computers. However, researchers underlined the fact that fast molecular computers are probably decades away.

“We’re not about to create the next generation of integrated circuits,” he said. “But after many years of work gearing up to this, we have fulfilled a decade-long quest and shown that molecules can act as transistors.”

3D structure of humans finally decoded

dna_500

It’s quite obvious that genetics is the most important step in our evolution that we have to take and although the molecular structure of DNA has been discovered more than half a century ago, its three dimensional structure remained a mystery. However, recently a team led by researchers from Harvard University, the Broad Institute of Harvard and MIT and the University of Massachusetts Medical School managed to solve this puzzle, paving the way for new insights into genomic functions and greatly expanding our understanding limits.

In order to accomplish this task, they employed a novel technology they call Hi-C and found out how DNA folds; the goal was to find out how our cells can somehow store three billion base pairs of DNA without having any of its functions blocked or impaired.

“We’ve long known that on a small scale, DNA is a double helix,” says co-first author Erez Lieberman-Aiden, a graduate student in the Harvard-MIT Division of Health Science and Technology and a researcher at Harvard’s School of Engineering and Applied Sciences and in the laboratory of Eric Lander at the Broad Institute. “But if the double helix didn’t fold further, the genome in each cell would be two meters long. Scientists have not really understood how the double helix folds to fit into the nucleus of a human cell, which is only about a hundredth of a millimeter in diameter. This new approach enabled us to probe exactly that question.”

It has to be said, this Hi-C technology is almost as amazing as the discovery itself, at least from where I’m standing. To be able to go to such a level that allows assessment of the three dimensional interactions between DNA is just amazing. Regarding the importance of ‘decoding’ the structure, it basically means scientists will be able to find out how to turn most genes on and off:

“Cells cleverly separate the most active genes into their own special neighborhood, to make it easier for proteins and other regulators to reach them,” says Job Dekker, associate professor of biochemistry and molecular pharmacology at UMass Medical School and a senior author of the Science paper.

At an even finer scale, scientists had to reach out for mathematics, because DNA takes a shape of what is called in mathematics a ‘fractal‘. The specific architecture they found was named a ‘fractal globule’ that allows the cell to pack DNA unbelievable tightly. Just so you can make an idea, the density of information stored there is trillions and trillions of times bigger than that of the world’s best computer chip.

fractal-dna

“Nature’s devised a stunningly elegant solution to storing information — a super-dense, knot-free structure,” says senior author Eric Lander, director of the Broad Institute, who is also professor of biology at MIT, and professor of systems biology at Harvard Medical School.

The idea of such a structure has in fac been suggested a while back, but it was as good as any guess at the moment, with no proof to back it up. However, thanks to this new kind of technology, the amazing truth was observed and scientists were able to solve the puzzle.

“By breaking the genome into millions of pieces, we created a spatial map showing how close different parts are to one another,” says co-first author Nynke van Berkum, a postdoctoral researcher at UMass Medical School in Dekker’s laboratory. “We made a fantastic three-dimensional jigsaw puzzle and then, with a computer, solved the puzzle.”