DNA bending is essential in biology as DNA must wrap around other structures or be packed into small volumes. Nam Ki Lee and co-workers, Pohang University of Science and Technology and IBS Center for Self-Assembly and Complexity, Pohang, South Korea, wanted to find out what exactly happens to short double-stranded DNS (dsDNA) when it is subject to bending stress from a compressive force.
The team constructed a D-shaped DNA nanostructure comprising dsDNA and a single-stranded (ss) DNA string (pictured), and used the alternating laser-excitation (ALEX) method to detect individual molecules. Two DNA conformers were observed when the bending force was applied: a fork (end-melting) and a kink (or strong bending). By introducing mismatched DNA sequences, the researchers were able to explain that the two conformers arise from local DNA melting either at the ends or the center of the DNA.
The dynamic behavior and interconversion of the two conformers were also investigated, and it was found that the transition from a fork to a kink is dominated by enthalpic contributions, whereas the transition in the other direction is dominated by entropic contributions. This insight into DNA bending under high stress could lead to further understanding of many biological processes.
- Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks,
Cheolhee Kim, O-chul Lee, Jae-Yeol Kim, Wokyung Sung, Nam Ki Lee,
Angew. Chem. Int. Ed. 2015.