Scientists from the Indian Institute of Science’s Department of Biochemistry have used an imaging method to identify how DNA building blocks stack on a single strand — paving the way for constructing intricate DNA nanodevices and uncovering essential insights into the structure of DNA.

DNA serves as the foundational blueprint for every living cell, carrying the essential information for growth, functioning, and reproduction. Typically, each DNA strand comprises four nucleotide bases: Adenine (A), Guanine (G), Thymine (T), and Cytosine (C). These bases on one strand pair up with their counterparts on the opposing strand to form double-stranded DNA (A pairs with T, and G pairs with C).

The stability of DNA’s double helix structure relies on two types of interactions: base-pairing — interaction between bases on different strands — is well-known, while base-stacking (interaction between bases on the same strand) has remained less explored, according to the researchers.

“Base-stacking interactions are typically stronger than base-pairing interactions,” said Mahipal Ganji, Assistant Professor at the Department of Biochemistry, IISc, and corresponding author of the paper published in Nature Nanotechnology.

To study all 16 possible base-stacking combinations, the researchers used DNA-PAINT (Point Accumulation in Nanoscale Topography).

“DNA-PAINT is an imaging technique that works on the principle that two artificially designed DNA strands, each ending on a different base, when put together in a buffer solution at room temperature, will bind and unbind to each other randomly for a very short time,” said the team.

For this, one strand (imager strand) was tagged with a fluorophore that would emit light during binding, and we tested the stacking of this strand on top of another docked strand. The binding and unbinding of different strand combinations (based on the end bases) were captured as images under a fluorescence microscope.

Through this process, it was discovered that incorporating an additional base-stacking interaction into a DNA strand can amplify its stability by up to 250 times.

Additionally, each nucleotide pair exhibited distinct stacking strengths. This insight enabled the design of an efficient three-armed DNA nanostructure, potentially forming a polyhedron-shaped vehicle for biomedical applications, including targeted disease marker identification, and precision therapy delivery.

Using the data obtained from DNA-PAINT, the researchers built a model that linked the timing of binding and unbinding with the strength of interaction between the stacked bases, noted Abhinav Banerjee, first author and PhD student at the Department of Biochemistry.

However, work is ongoing to improve the DNA-PAINT technique itself. By leveraging stacking interactions, the team plans to design novel probes that would expand the potential application of DNA-PAINT, Banerjee said.

Beyond imaging and nanotechnology, the research draws broader implications. Ganji envisions these findings contributing to the study of fundamental properties in single and double-stranded DNA, potentially shedding light on DNA repair mechanisms, disruptions of which are implicated in various diseases, including cancer.