DNA, the molecule carrying life’s blueprint, is a long thread that must be coiled to fit within a cell. This coiling of the DNA helix upon itself is DNA supercoiling. Like a twisted rubber band, DNA undergoes this higher-order coiling to manage its structure and accessibility. The process is fundamental to how genetic information is stored and used.
The Need for DNA Compaction
The need for DNA supercoiling arises from a space problem. A human cell contains about two meters of DNA that must fit inside a nucleus only 5 to 10 micrometers in diameter. This packaging challenge requires compacting the DNA by a factor of hundreds of thousands. If a cell nucleus were the size of a basketball, the DNA inside would stretch for miles.
This condensation is a hierarchical process with supercoiling as a foundational step. The DNA is first wound around proteins, like thread on a spool, and these structures are then folded. Supercoiling introduces twists into the DNA, causing it to contort, which reduces its volume and allows genetic information to be stored in an organized way.
Positive and Negative Supercoiling
The twisting of the DNA helix can occur in two directions, resulting in two types of topological strain. In its relaxed state, the DNA double helix completes a turn about every 10.5 base pairs. When additional twists are introduced in the same direction as the helix, it becomes overwound, a state known as positive supercoiling. This tightens the DNA structure, making it more compact but also more difficult for the two strands to be separated.
Conversely, removing twists makes the DNA underwound, leading to negative supercoiling. This creates tension that makes opening the double helix easier. Because this is advantageous for cellular processes, most organisms’ DNA is negatively supercoiled. An underwound helix stores energy that helps drive reactions requiring strand separation, like reading a gene.
The structural result of this strain is often a plectoneme, where the helix twists back on itself. In eukaryotic cells, DNA can also wrap around protein cores in a toroidal, or spiral, form. These structures are dynamic and change in response to cellular needs, managed by specific enzymes.
Enzymes That Regulate Supercoiling
Enzymes called topoisomerases manage the topological state of DNA. They act as molecular machines that cut, pass, and reseal DNA strands to introduce or remove supercoils, controlling the level of strain. This regulation is a controlled activity that prevents the DNA from becoming tangled.
Topoisomerases are classified into two main types. Type I topoisomerases create a temporary break in a single DNA strand, allowing the other strand to pass through the gap before the break is resealed. This action changes the number of twists in the DNA, relaxing supercoils to relieve torsional stress. This process does not require the energy molecule ATP.
Type II topoisomerases perform a more complex operation by cutting both strands of the DNA double helix, creating a gate for another DNA segment to pass through. After passage, the enzyme reseals the break. A well-known bacterial example is DNA gyrase, which actively introduces negative supercoils into DNA at the expense of ATP. This process is important for bacterial DNA replication.
Functional Impact on Cellular Processes
Beyond packaging, DNA supercoiling directly impacts gene expression and DNA replication. Because negatively supercoiled DNA is easier to separate, it is more accessible to the proteins that read genes. This means changes in supercoiling can influence whether a gene is turned on or off.
Processes like DNA replication and repair also rely on the unwinding of the double helix. As the replication machinery moves along the DNA, it generates positive supercoils ahead of it and negative supercoils behind it. Both types of supercoils must be resolved by topoisomerases to prevent the process from stalling.
Therapeutic Targeting of Supercoiling
The machinery controlling DNA supercoiling is a therapeutic target for bacterial infections and cancer. Because topoisomerases are required for cell division, inhibiting them can halt the proliferation of unwanted cells. This approach exploits a process that rapidly multiplying cells rely on to survive.
For instance, quinolone antibiotics, including ciprofloxacin, target bacterial DNA gyrase and topoisomerase IV. These drugs stabilize the complex formed between the enzyme and the cut DNA, preventing the strands from being resealed. This leads to an accumulation of lethal double-strand breaks in the bacterial chromosome but does not affect human cells, which lack DNA gyrase.
Similarly, many chemotherapy drugs are topoisomerase inhibitors. Agents like etoposide target human topoisomerase II, while others like topotecan target topoisomerase I. These drugs trap the enzyme on the DNA after it cuts, leading to DNA breaks in rapidly dividing cancer cells and triggering cell death. This highlights the importance of regulating DNA supercoiling.