RNA operates in many capacities; structural scaffolding, gene regulation, enzymatic catalysis even though it is built from just four nucleotide bases. A recent study from Pennsylvania State University researchers Philip Bevilacqua, offers a potential clue to this versatility. It identifies an uncommon RNA pairing; what researchers term a “shifted wobble”that may underlie RNA’s functional diversity and even present a useful drug target.
Saon, M. S., Douds, C. A., Veenis, A. J., Pearson, A. N., Yennawar, N. H., & Bevilacqua, P. C. (2025). Identification and characterization of shifted G•U wobble pairs resulting from alternative protonation of RNA. Nucleic Acids Research, 53(14). https://doi.org/10.1093/nar/gkaf575
Typically, a GU “wobble” in RNA places the uracil in the major groove side of the helix. What this new study shows is a variant: the guanine adopts that groove position instead; making it a “shifted” wobble. Such a shift implies altered bonding geometry and potentially different biochemical behavior.
Researchers combed through a database of more than 3,000 high-resolution RNA structures. They applied cheminformatics; formulated in chemical terms of bond angles and distances; to flag shifted G–U pairs. From over a thousand initial findings, 41 unique cases passed quality filters for further analysis.
Philip Bevilacqua, distinguished professor at Eberly College of Science at Penn State University stated,
“Although it’s a close relative of DNA, RNA can do much more than carry genetic information.”
To confirm these computational hits, they tested reactions with dimethylsulfate (DMS) in living cells. Normally, DMS reacts with adenine and cytosine; but in the shifted GU pairs, uracil also reacted. That offers direct in vivo evidence that the shifted wobble exists.
Noncanonical base pairs, including standard GU wobbles, are already recognized as central to RNA’s 3D structure and function; they help form loops, junctions, and binding sites not seen in DNA. They represent around one-third of functional RNA pairings.
Tools that can locate non-standard conformations from structures are emerging as powerful approaches. The Bevilacqua lab, where this study originated, continues to advance RNA modeling and high-throughput probing methods that expand our understanding of RNA dynamics.
Because shifted GU pairs are more common in bacteria and chloroplasts than in human RNA or archaea, they may serve as selective drug targets. Chemicals designed to bind or disrupt these conformations could affect bacterial RNA without disturbing human RNA; potentially a path to new antibiotics.
Engineers designing RNA sensors, ribozymes, or therapeutics need to account not just for standard base pairing, but also for subtler, context-dependent arrangements like shifted wobbles. Such shifts could influence folding paths, binding specificity, or kinetics in unpredictable ways.
This study opens the door for further exploration: how widespread are shifted wobbles? Do they play regulatory roles in ribosome function or RNA-mediated sensing? Can they be engineered as molecular switches? Methods used here; combining structural mining and targeted chemistry; offer a blueprint for investigating noncanonical pairings across nucleic acids.
- RNA can include shifted G–U base pairs where guanine occupies the major-groove side.
- Researchers found 41 validated examples using cheminformatics and in vivo DMS reactivity.
- These shifted wobbles are more prevalent in bacteria, suggesting potential for selective drug targeting.
- Uncommon conformations like these are important for RNA-based design and understanding function.
Adrian graduated with a Masters Degree (1st Class Honours) in Chemical Engineering from Chester University along with Harris. His master’s research aimed to develop a standardadised clean water oxygenation transfer procedure to test bubble diffusers that are currently used in the wastewater industry commercial market. He has also undergone placments in both US and China primarely focused within the R&D department and is an associate member of the Institute of Chemical Engineers (IChemE).
