Base-stacking is not well-studied in double-stranded DNA. Credit: KTSDESIGN/SPL/Getty Images
Researchers have provided new insights into how bases in a single DNA strand stack on top of each other1.
This may open up possibilities for building complex nanodevices and deciphering fundamental aspects of DNA structure, say researchers at the Indian Institute of Science in Bengaluru.
Base-pairing – interaction between bases on opposite strands – is widely known in double-stranded DNA. However, base-stacking – interaction between bases in the same strand – is not well studied.
So a team led by Mahipal Ganji probed 16 possible base-stacking combinations. They imaged the random binding and unbinding of two artificial DNA strands in a buffer solution at room temperature.
The researchers, who included Abhinav Banerjee, tagged one of the strands with a molecule that emits light during binding and then tested stacking this strand on another. A fluorescence microscope revealed that adding just one base-stacking interaction to a DNA strand increased its stability up to 250-fold.
They also discovered that each nucleotide pair has its unique stacking strength. Knowing this meant the researchers were able to design a highly efficient three-armed DNA nanostructure. It could be converted into a vehicle for targeting specific disease markers and delivering targeted therapies.
The team say their findings can be used to study the fundamental properties of single- and double-stranded DNA molecules and their repair mechanisms. This knowledge will be important, as failure to repair leads to many diseases including cancer, they add.
