From molecular interactions to contact networks

New tool helps researchers unravel complex RNA and DNA interactions

Interactions involving RNA and DNA lie at the heart of many of life’s essential processes—from gene regulation and RNA splicing to translation and viral replication. But understanding exactly how these molecules interact can be difficult. RNA and DNA are flexible and constantly changing their shape. A new software tool, ProNA3D, developed by scientists at the Leibniz Institute of Virology (LIV) and recently published in the Computational and Structural Biotechnology Journal, could help researchers better explore these complex molecular interactions. The tool provides an interactive way to identify, visualize, and analyze where and how RNA, DNA and proteins interact with one another. It can also help researchers assess the confidence of interaction sites predicted by AI-based structure prediction methods.

“Until recently, if I wanted to look at how DNA interacts with DNA or how RNA interacts with a protein, I had to use different tools,” says Luca Genz, who recently completed her PhD in the Research Department of Integrative Virology at the Leibniz Institute of Virology and developed ProNA3D. “We wanted to bring these different types of interactions together in one place.”

ProNA3D combines several ways of exploring molecular interactions in a single environment. Researchers can investigate protein–RNA, protein–DNA, RNA–RNA, DNA–DNA, and RNA-DNA interactions, while also examining where interactions occur, how different interaction regions are organized, and how confidently the underlying structure can be interpreted. The software can analyze both experimentally determined structures and AI-based predictions. This is particularly useful for complexes containing DNA or RNA, for which the number of experimentally determined structures is still limited. AI-based methods such as AlphaFold3 can predict many more of these structures. But not every part of a predicted structure is equally reliable. ProNA3D uses AlphaFold3’s confidence information to show researchers not only where an interface is predicted to occur, but also how reliable that prediction is.

Understanding where molecules interact is an important first step, but molecular complexes can be more complicated. Molecules can interact with each other at several separate regions. When these regions are close together in space, they may be treated as one large interface by conventional approaches.

 “A unique feature of ProNA3D is that it can distinguish these separate contact regions, allowing researchers to examine each one individually in detail,” explains Prof. Maya Topf, head of the Research Department of Integrative Virology at the Leibniz Institute of Virology.

Additionally, ProNA3D offers two-dimensional connectivity plots that show which nucleotides or residues are in contact with one another.

“The connectivity can be thought of as a kind of social network,” says Luca. “Some nucleotides or residues have only one contact, while others interact with many different residues and therefore act more like hubs in the network. Such a nucleotide or residue with multiple contacts is referred to as having high connectivity.” 

These highly connected positions may be particularly interesting because they could play an important role in holding a molecular complex together or in its biological function. High connectivity does not prove that a position has a particular function, but it can point researchers towards areas worth investigating further.

In one example involving a complex between HIV-1 RNA and an antibody, ProNA3D identified a nucleotide with particularly high connectivity, highlighting it as a candidate for further investigation.

By combining interactive visualization, interface analysis, connectivity analysis and confidence information in a single package, ProNA3D provides researchers with a way to explore nucleic-acid-containing complexes and generate new hypotheses about their molecular interactions. The software is available as a plugin for ChimeraX, a widely used platform for 3D molecular visualization and analysis, as well as a command-line tool.

Original Publication

Genz LR, Topf M (2026) Comput. Struct. Biotechnol. J. ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces. doi/10.34133/csbj.0202