27 January 2023
A tandem technique for resolving RNA structures
Published online 26 July 2022
Combining computational and experimental methods generates atomic-level insights into 3D RNA structures.
RNA strands fold into complex shapes that inform their functions. Researchers, led by Serdal Kirmizialtin at New York University Abu Dhabi and Lois Pollack at Cornell University, have developed an effective strategy for mapping these higher-order structures in unprecedented detail.
Basic information about the size and shape of RNA is obtained using a technique called small-angle X-ray scattering (SAXS). But it only provides a superficial perspective on RNA three-dimensional structure—also known as its tertiary structure. Researchers have attempted to address this with molecular dynamics algorithms that simulate atomic-scale RNA behaviour, but these are not accurate enough.
Kirmizialtin and Pollack devised a two-pronged approach to tackle this problem. They use a method known as wide-angle X-ray scattering (WAXS), an alternative to SAXS that is better suited for capturing higher-resolution structural information, to analyze a given RNA sequence. In parallel, they perform molecular dynamics simulations of the same RNA, and use the WAXS measurements to iteratively guide the modeling process towards results that best describe the experimental data.
They initially demonstrated this approach with RNA duplexes: simple double helical structures analogous to those typically seen with DNA. But then they focused on tertiary structures known as RNA triplexes, in which a third RNA strand interacts strongly with an existing duplex. “RNA triple helices were discovered more than 60 years ago, but their diverse biological activities have been explored only recently,” says Kirmizialtin. For example, these structures can enhance the activity of catalytic RNA molecules or boost gene expression levels.
Their analytical strategy generated a host of new insights. First, the researchers identified nucleotide sequence features that play a pivotal role in the formation of RNA triplexes, and which could even be used to predict such structures in newly identified RNAs. They also determined the nature of the physical interactions between the RNA duplex and the third strand that lead to triplex formation, and showed how positively charged ions in the surrounding solution help stabilize this triple helical structure.
Kirmizialtin is encouraged by this initial demonstration. “Our methodology provides an accurate description of RNA under physiological conditions,” he says. “This information can pave the way for developing drugs that target RNA molecules.” The strategy should also be broadly applicable, and he and Pollack plan to study various other poorly characterized RNA species with important biological functions.
Chen, Y.-L. et al. Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations. Cell Reports Physical Science 3,100971 (2022).