A fragment of double-stranded DNA. Credit: Vcpmartin/Wikimedia/CC BY-SA 4.
People often picture DNA as a string-like double Helix structure. The double DNA helix found in cells is actually supercoiled and constrained to loops. Although looping and supercoiling have been shown to affect every aspect of DNA activity it is not clear how.
A study published in Nature Communications by Baylor College of Medicine reveals that looping and supercoiling can transmit mechanical stresses along the DNA backbone. The stress can lead to the separation of the strands from the double helix at distant sites. This may expose the DNA bases and facilitate repair, replication, or other aspects of DNA function.
According to Dr. Lynn Zechiedrich (Kyle and Josephine Morrow Chairs in molecular microbiology and molecular virus research at Baylor), DNA stores the genetic information of a cell in a safe and secure form that is easily accessible by the cell. This seemingly paradoxical goal is achieved by supercoiled loops storing DNA. We investigated how looping and supercoiling affect DNA activity in the current study.
Zechiedrich began with small pieces of supercoiled, DNA. These are the same as those found in living cells. They started with a small, linear DNA double-helix and then twisted it in either the opposite direction (positive supercoiling), or in the same direction (negative supercoiling). They connected the ends to form a loop.
Zechiedrich, who is a Baylor Comprehensive Cancer Center member, said that in a previous study we had examined the 3D structures supercoiled minicircles using electron cryotomography. (cryoET) an imaging technique that produces high resolution 3D views large molecules. We were surprised at the variety of minicircle shapes that we observed, depending on the supercoiling level. Many of the shapes that we saw contained DNA that was sharply bent. This was a surprising observation.
This was surprising because models indicated that supercoiled DNA circles behave more like a twisted rubberband.
Zechiedrich stated, "We discovered that supercoiled looped DNA, rather than gently bending," suddenly pops out sharp edge that causes a disruption in double helix. The openings expose the particular DNA code and make it available to proteins searching for specific sequences to interact or repair it.
Dr. Jonathan M. Fogg (senior staff scientist at the Zechiedrich laboratory) said that another important discovery was the notion of "action at a distant". The supercoiling stress can be transmitted along a DNA backbone from one location of the loop to another. If one site is bent in a sharp way, the effects of supercoiling stress at another site can be transmitted along the DNA backbone to a distant site. This phenomenon cannot be captured by studying linear DNA, but supercoiled minicircles can reveal the dynamic properties of DNA as found in cells.
These results offer a new view on the regulation of DNA activities. The current theory is that specialized proteins interact to DNA to create a new perspective on how DNA activities are regulated.
Zechiedrich stated, "Here we demonstrated that no protein is required to access DNA. It can make itself accessible by itself."
Allison Judge, a graduate student at the Department of Pharmacology and Chemical Biology, said that "our cells have created many complicated processes to store and use DNA and that the shape of DNA affects all of these."
Erik Stricker (graduate student in pediatrics-oncology), co-author. "Our findings provide new insight into what governs DNA form." "We suggest that variations in these new DNA shapes could have potential applications for nanotechnology, such as gene therapy."
Co-author Hilda Chan is a graduate student in the Medical Scientist Training Program. "Our study rebrandsDNA from a passive biomolecule into an active one," she said. "Our findings encourage future research on how DNA shapes may be used to control access to specific sequences in a range of situations like when it responds to drugs, infection, or points in the cell's cycle."
More information: Nature Communications (2021): Looping and supercoiling promote DNA base accessibility, coordination among distant sites and coordination Information from Nature Communications: Nature Communications Supercoiling, looping promote DNA bases accessibility and coordination among distant locations (2021). DOI: 10.1038/s41467-021-25936-2
