DNA is a complex, twisted structure. This twisting, known as DNA supercoiling, plays an important role in how our genetic information is stored and accessed. This article focuses on positive supercoiling. Understanding this form of DNA coiling is fundamental to many cellular processes.
Understanding Positive Supercoiling
Positive supercoiling describes a state where the DNA double helix is overwound, meaning it has more twists per unit length than its relaxed form. Imagine twisting a rubber band or a phone cord until it coils upon itself; this extra coiling is analogous to positive supercoiling in DNA. In its normal, relaxed state, B-form DNA has one helical turn for approximately every 10.4 to 10.5 base pairs.
Positive supercoiling results in a more compact and tightened DNA structure, which can hinder the binding of enzymes and proteins to the DNA molecule. This contrasts with negative supercoiling, which occurs when DNA is underwound, leading to a looser structure with fewer twists. While negative supercoiling is prevalent in most organisms and promotes processes like replication and transcription by making DNA more accessible, positive supercoiling is a temporary condition that cells actively manage.
When Positive Supercoiling Occurs
Positive supercoiling naturally arises during various biological processes that require the unwinding of the DNA helix. DNA replication is a prime example, where the double-stranded DNA must separate to allow for the synthesis of new strands. As the replication machinery, including helicases, unwinds the DNA ahead of the replication fork, the region immediately in front of it becomes overwound, leading to the accumulation of positive supercoils. If not addressed, this torsional stress would impede the progression of the replication fork.
Transcription, the process of converting DNA into RNA, also generates positive supercoiling. As RNA polymerase moves along the DNA template, it unwinds the helix, creating positive supercoils ahead of the enzyme and negative supercoils behind it, a phenomenon known as the “twin-domain model”. These changes in DNA topology are a direct consequence of enzyme movement and resistance to DNA rotation. The accumulation of positive supercoils ahead of the RNA polymerase can slow down transcription elongation.
How Cells Manage Positive Supercoiling
Cells employ specialized enzymes called topoisomerases to manage the topological challenges posed by DNA supercoiling, including the relaxation of positive supercoils. These enzymes can alter DNA topology by transiently cutting and rejoining DNA strands. There are two main types of topoisomerases: Type I and Type II.
Type I topoisomerases create a transient single-strand break in the DNA, allowing one strand to pass through the other before resealing the break. In eukaryotes, Type I topoisomerases can relieve both positive and negative supercoils.
Type II topoisomerases, such as DNA gyrase in bacteria or human topoisomerase II, cleave both strands of the DNA duplex, pass another DNA segment through the break, and then rejoin the cut ends. This action changes the linking number of the DNA by two, and Type II topoisomerases are particularly effective at relaxing positive supercoils, especially those that accumulate ahead of replication forks.
The Critical Role of Supercoiling Regulation
The precise regulation of DNA supercoiling is important for cell survival and proper cellular function. Uncontrolled accumulation of positive supercoiling can lead to negative consequences for the cell. For example, excessive positive supercoiling can stall DNA replication forks, preventing the genetic material from being accurately copied. Similarly, it can inhibit transcription, thereby disrupting gene expression and the production of necessary proteins.
Beyond these immediate effects, unregulated supercoiling can contribute to chromosomal instability, potentially leading to errors in DNA segregation during cell division. Ultimately, these disruptions can result in cell death.
Supercoiling regulation is also important in antibiotic development. Many antibacterial drugs, such as fluoroquinolones, target bacterial Type II topoisomerases like DNA gyrase and topoisomerase IV. These drugs interfere with the enzymes’ ability to manage DNA topology, leading to the accumulation of DNA breaks and bacterial cell death. This highlights the vulnerability of this process in pathogens.