American researchers open the way for new, potential applications

Mar 19, 2012 12:48 GMT  ·  By
Because methyl groups discourage hydrogen bonding, methylated uracil should be incapable of proton transfer. But after ionization of methylated uracil dimers, a proton moves by a different route
   Because methyl groups discourage hydrogen bonding, methylated uracil should be incapable of proton transfer. But after ionization of methylated uracil dimers, a proton moves by a different route

A group of scientists led by experts at the US Department of Energy's (DOE) Lawrence Berkeley National Laboratory (Berkeley Lab) announces the discovery of a new type of proton transfer taking place between molecules.

This finding could pave the way for the creation of new technologies in the fields of environmental sciences, biology and green chemistry. Experts say that the bare nucleus of a hydrogen atom is made up of a single proton.

Until now, it was widely believed among physicists that protons can transfer from one molecule to another, or within the same atom, solely through the formation of a hydrogen bond. These conduits are known as proton wires, and they can connect in ways that change the very properties of molecules.

These bonds are absolutely critical for complex molecular constructs, including DNA and RNA. Inside these nucleic acids, they bind all four base pairs that make up genetic material, and also map the structure of proteins.

What was extremely interesting for scientists to find in the new study was that proton transfers can occur even when the hydrogen bonds are blocked. The research was carried out at the Berkeley lab Advanced Light Source (ALS).

Details about how this occurs are published in the latest issue of the top scientific journal Nature Chemistry. The team was led by Berkeley Lab Chemical Sciences Division (CSD) senior scientist Musahid Ahmed.

A group of experts from the University of Southern California (USC), headed by researcher Anna Krylov, was also involved in this investigation. The discovery was made while the scientists were analyzing computer models of paired, ring-shaped uracil molecules, which are one of the four nucleobases of RNA.

It also represents one of the main differences between RNA and DNA. While the former is made up of adenine, cytosine, guanine and uracil, the latter contains thymine instead of uracil. In the new study, experts used a form of uracil called 1,3-dimethyluracil to block the usual hydrogen bonds.

The group found that uracil could still connect to the RNA structure, but this time through pi bonds, explains CSD investigator, Amir Golan.

“Uracils could be joined by hydrogen bonds or by pi bonds, but these uracils had been methylated to block hydrogen bonds. So what we expected to see when we ionized them was that if they were bonded, they would have to be stacked on top of each other,” he concludes.