DNA, the genetic blueprint for all living cells, is made up of four nucleotide bases: Adenine (A), Guanine (G), Thymine (T), and Cytosine (C). These bases form pairs, with A pairing with T and G with C, creating the double-stranded structure of DNA. The stability of this double helix is maintained through two types of interactions: base-pairing and base-stacking. According to Mahipal Ganji, an Assistant Professor at the Department of Biochemistry, IISc, base-stacking interactions, which are generally stronger than base-pairing, can be compared to the teeth of a zipper, ensuring a secure connection.
To study the 16 possible
base-stacking combinations, researchers used a novel imaging technique called
DNA-PAINT (Point Accumulation in Nanoscale Topography). This method involves
the random binding and unbinding of two artificially designed DNA strands in a
buffer solution at room temperature. Each strand ends with a different base and
is tagged with a fluorophore that emits light when binding occurs. The binding
and unbinding events were captured as images under a fluorescence microscope.
FIG: Patterned DNA nanostructures (cyan) as imaged using DNA-PAINT super-resolution technique enabled for studying strength of base-stacking interactions (pink).
The researchers found that the
time required for the strands to bind and unbind increased with stronger
base-stacking interactions. Using this data, they developed a model that links
the timing of binding and unbinding with the strength of the interaction
between stacked bases. This innovative technique provided new insights into
base-stacking. For example, adding just one more base-stacking interaction to a
DNA strand could increase its stability by up to 250 times. Additionally, each
nucleotide pair showed unique stacking strengths, allowing the design of highly
efficient three-armed DNA nanostructures.
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