Science & Technology, India (Commonwealth Union) – In a recent study, scientists from the Indian Institute of Science’s Department of Biochemistry have harnessed an innovative imaging technique to precisely determine the degree of stacking between adjacent bases – the foundational components of DNA – within a single strand. This breakthrough revelation holds promise for constructing intricate DNA nanodevices and unraveling fundamental aspects of DNA’s structural nature.
At the core of every functioning cell resides DNA, the carrier of genetic information governing growth, operation, and reproduction. Typically, a DNA strand comprises four nucleotide bases – Adenine (A), Guanine (G), Thymine (T), and Cytosine (C). The bases on one strand align with their counterparts on the opposing strand to form the double-stranded DNA structure (A pairs with T, and G pairs with C).
DNA’s double helix arrangement is stabilized through two distinct interactions. Base-pairing, which involves interactions between bases on different strands, is relatively well-known. In contrast, base-stacking, which pertains to interactions between bases within the same strand, remains less explored. Think of base-pairing as the zipper securing the two strands, while base-stacking functions like the teeth of the zipper, providing a firm and snug connection. Notably, base-stacking interactions tend to be more robust than base-pairing interactions, as indicated by Mahipal Ganji, Assistant Professor at the Department of Biochemistry, IISc, as well as the principal author of the research article that appeared in Nature Nanotechnology.
To delve into all possible combinations of base-stacking (16 in total), the researchers harnessed DNA-PAINT (Point Accumulation in Nanoscale Topography). This imaging technique capitalizes on the concept that when two synthetically designed DNA strands – each culminating with a distinct base – are combined within a buffer solution at room temperature, they will intermittently bind and disengage from each other in rapid succession. The team labeled one of these strands (the “imager strand”) with a fluorophore designed to emit light upon binding. They then explored the stacking of this strand onto another docked strand. The binding and unbinding events across various strand pairings (determined by their terminal bases) were captured as images through a fluorescence microscope.
The duration required for the attachment and detachment of the DNA strands exhibited an extension when the interaction between the stacked bases demonstrated greater strength. Abhinav Banerjee, a PhD student at the Department of Biochemistry and the primary author, elucidated this correlation. Consequently, utilizing the insights garnered from DNA-PAINT, the researchers formulated a model that established a connection between the timing aspects of binding and unbinding and the potency of interaction between the stacked bases.
With the aid of this methodology, the team unearthed intriguing revelations concerning base-stacking phenomena. For instance, the addition of just one more base-stacking interaction to a DNA strand appears to remarkably enhance its stability by up to 250 times. Additionally, the investigation unveiled that each pair of nucleotides possessed its distinct stacking strength. Armed with this knowledge, the researchers devised an exceedingly efficient three-pronged DNA nanostructure that holds the potential to be structured into a polyhedral vehicle, bearing relevance to biomedical applications such as targeting specific disease markers and facilitating targeted therapeutic interventions.
Furthermore, the team is diligently working on refining the DNA-PAINT technique itself. Banerjee disclosed plans to capitalize on stacking interactions to create novel probes, thereby broadening the spectrum of potential applications for DNA-PAINT.
The implications of this research extend beyond the realms of imaging and nanotechnology, as posited by the scientists. Ganji expressed the aspiration that these findings could be harnessed to scrutinize the core attributes of single and double-stranded DNA, subsequently illuminating the mechanisms of DNA repair. Failures in these mechanisms are implicated in various diseases.
DNA repair has been a key area of interest among researchers where some researchers have indicated the significance of components of the cell strongly influencing DNA damage and repair.
