New RNA sequencing method reveals molecular structures at single-molecule resolution

Researchers at A*STAR Genome Institute of Singapore have developed a new method for studying individual RNA molecules, giving scientists a clearer understanding of how gene regulation influences health and disease.

The technology, known as sm-PORE-cupine, allows researchers to examine how RNA molecules fold into different shapes and how those structures affect their behaviour inside cells. The breakthrough could support future advances in antiviral treatments, drug discovery and precision medicine.

New insight into RNA structure

RNA is widely recognised for its role in carrying genetic instructions from DNA to produce proteins. However, scientists say RNA also performs a range of other functions because of its ability to bend, fold and interact with surrounding molecules.

These varying shapes can determine how efficiently proteins are produced, how long RNA molecules survive and how diseases develop, including viral infections.

RNA is widely recognised for its role in carrying genetic instructions from DNA to produce proteins

Until now, researchers have struggled to study RNA structures in detail because the molecules are highly flexible and constantly changing. Existing techniques typically provide only an averaged view across large numbers of RNA molecules, making it difficult to identify structural differences between individual molecules from the same gene.

The team at A*STAR GIS said its new sm-PORE-cupine method overcomes these limitations by combining chemical labelling with direct RNA sequencing technology.

Reading RNA molecules individually

The technique works by using specially optimised chemical compounds to mark non-paired RNA bases, which are areas of the molecule that remain more exposed. These chemical markers act as indicators that help scientists determine how the RNA molecule is folded.

Researchers then used nanopore direct RNA sequencing to read full-length RNA molecules in detail. Advanced computational analysis enables the team to interpret the signals at single-molecule resolution. This reveals how RNAs from the same gene can fold and behave differently.

The technique works by using specially optimised chemical compounds to mark non-paired RNA bases, which are areas of the molecule that remain more exposed

Using the technology, the researchers saw that RNA molecules can adopt a variety of structures, with these differences directly linked to how efficiently proteins are produced and how quickly RNA molecules degrade.

Scientists say this is significant because protein production and RNA stability are central to gene regulation. Problems in these processes are associated with a range of diseases.

“At ASTAR GIS, we pursue deep scientific understanding to enable better solutions for health and disease,” said Dr Wan Yue, Executive Director at ASTAR GIS and lead author of the study. ”By uncovering how RNA molecules adopt different structures and how these structures influence gene regulation, this work lays the foundation for more precise approaches to diagnosis and treatment.”

Potential for future therapies

The new findings could help identify RNA-based therapeutic targets and contribute to the development of antiviral medicines, antifungal treatments and RNA-targeted therapies.

In the longer term, the researchers said the technology could improve disease diagnostics and support more personalised approaches to medicine by helping scientists better understand the relationship between RNA structure and disease.

In the longer term, the researchers said the technology could improve disease diagnostics and support more personalised approaches to medicine

“By leveraging direct RNA sequencing using nanopores we now have a unique capability to study the dynamics of how RNAs shape-shift,” said co-lead author Dr Niranjan Nagarajan. ”This work builds on A*STAR GIS’ significant strengths in nanopore sequencing-based analytics.”