A team of scientists looked at the three-dimensional structure of biologically active DNA in stunning detail, and discovered how DNA coils and uncoils to drive cell activity.
The iconic double-helical structure is actually an active form of DNA, instead the team looked at DNA minicircles, or "MiniVectors," containing only 336 base pairs, Baylor College of Medicine reported.
"Previous studies were on short fragments ([six to] 12 base pairs) of linear DNA, but human DNA is constantly moving around in your body - and it coils and uncoils. You can't coil linear DNA and study it, so we had to make circles so the ends would trap the different degrees of winding," said Lynn Zechiedrich, professor in the department of molecular virology and microbiology, and co-contributing author.
In the study, the researchers wound or unwound a single turn at a time the DNA double helix comprising their circles to see how the motion affected the circles' shape. They used the purified enzyme human topoisomerase II alpha to relieve the winding stress from the supercoiled minicircles. This means the circles must act like longer DNA that topoisomerases encounter in human cells.
"These enzymes don't do anything to linear DNA because it's not coiled up," said co-author Dr. Daniel J. Catanese, Jr., also of Baylor.
The researchers used the powerful microscopy technique cryo-electron tomography to reveal the three-dimensional structures of individual DNA molecules, and noticed the coiling caused a variety of shapes.
"Some of the circles had sharp bends, some were figure-8s, and others looked like racquets or sewing needles. Some looked like rods because they were so coiled," said Rossitza N. Irobalieva, the co-lead author on the publication, who is also at Baylor.
"Being able to observe individual DNA circles allows us to understand the different structures of biologically active DNA. Each of these different structures facilitates how DNA interacts with proteins, other DNA and RNA, and anticancer drugs, adapting to the cell processes required," continued Jonathan Fogg, the other lead author of the publication, also of Baylor College of Medicine.
The team expected to see an opening of base pairs when the DNA was underwound, so they were surprised to observe this type of opening for overwound DNA. They believe the disruption of base pairs causes flexible "hinges" that allow the DNA to sharply bend and potentially fit into cells.
"The next step is to start adding the other components of the cell or anticancer drugs to see how the DNA shapes change," Fogg concluded.
The findings were published in a recent edition of the journal Nature Communications.