Wobble pairs make RNA more reactive

The wealth of information contained in a strand of genetic material boils down to sequences of matched pairs of nucleotides that cellular machinery decodes to construct proteins.

Writing in The Proceedings of the National Academy of Sciences, a University of Wisconsin-Madison bacteriologist reveals that mispaired nucleotides in transfer RNA actually make the molecule more adroit, enhancing its ability to build proteins. The paper also illustrates the dynamic nature of genetic material, which is not flat, like an illustration in a textbook, but twists and bends as it interacts with cellular machinery.

The mispairs, also called "wobble pairs," do not bind together as tightly as matched pairs bind, making transfer RNA "a compressed spring ready to be sprung," according to William McClain, a professor of bacteriology in the UW-Madison's College of Agricultural and Life Sciences and the author of the PNAS paper. He notes that specific transfer RNA mispairs, which likely originally arose through natural mutation, are highly conserved across all kingdoms of life, providing evidence that they play an important role in making the molecule more reactive.

Genetic information is encoded in DNA, which is made up of matched base pairs of adenine and thymine, and guanine and cytosine - commonly denoted with the letters A, T, G and C. Cellular machinery transcribes the information from DNA into RNA - where the base uracil replaces thymine - and then translates the coded data into proteins, which form the building blocks of life.

Scientists have long known that transfer RNA - which adds amino acids to a growing chain during protein synthesis - holds a surprising secret when it comes to its base pairs: occasionally, instead of the expected A-U or G-C pairs, there exists instead a mispair of A-C or G-U. However, the role and importance of mispairs has never been well understood, says McClain.

McClain, who has spent his career investigating how transfer RNA selects specific amino acids during protein synthesis, was curious about how mispairs affect the function of RNA. In the study reported in PNAS, he altered the position of a G-U mispair in a bacterial plasmid - by literally moving the mispair up and down the molecule's cloverleaf structure - and demonstrated that the mutation increases the ability of the RNA to accept amino acids and improves its efficiency at moving through the ribosome, the cellular organelle where translation occurs. In fact, removing the mispair or repairing it to make it a correct matched pair inactivated the molecule completely.

"The wobble pairs fit together at an angle and the bonds are much less stable than matched pairs," McClain explains. "This makes the molecule more likely to come undone, and therefore more reactive."

This is crucial because DNA and RNA molecules are not the static, flat images that are depicted in textbooks, McClain notes. "They flex, move and come apart all the time," he says. "And mispairs promote this movement. My interpretation is that nature conserves these mispairs because they enhance protein synthesis."

McClain adds that he views his work as both an intellectual challenge as well as "tremendous fun."

"What biologists want to do is understand a cell in terms of all of its workings," he says, "just as when you take your car to a mechanic they have to know how it's made. I want to know how a molecule is made, and how its parts come together."