Topoisomerases are enzymes that manage the complex topological challenges of DNA’s double-helical structure. They control DNA winding and unwinding, preventing tangles and relieving mechanical stress that can impede cellular processes. Without topoisomerases, cellular genetic material would become unmanageable.
The DNA Challenge
The DNA molecule, a long, coiled double helix, faces constant structural challenges within a cell. During DNA replication and transcription, DNA strands must temporarily unwind and separate. This unwinding creates torsional stress in adjacent DNA regions, leading to supercoiling.
Supercoiling can manifest in two forms: positive and negative. Positive supercoils occur when DNA becomes overwound, tightening the helix and hindering molecular machinery. Conversely, negative supercoils involve DNA underwinding, making strand separation easier for processes requiring genetic code access. Unresolved supercoiling impedes enzyme movement, making genetic information difficult to access and utilize.
Topoisomerase Binding Sites
Topoisomerases initiate action by interacting with the DNA molecule. These enzymes bind to the phosphate backbone of DNA, rather than recognizing specific nucleotide sequences. This allows them to act broadly across the genome, addressing topological issues wherever they arise.
The initial interaction varies between the two main types of topoisomerases. Type I topoisomerases introduce a transient break in only one DNA strand. Type II topoisomerases create a temporary break in both DNA strands simultaneously. A transient covalent bond forms between a tyrosine residue within the topoisomerase and a phosphate group on the DNA backbone during this process.
The Action After Binding
Following binding and DNA cleavage, topoisomerase proceeds through its catalytic cycle. The enzyme forms a transient phosphodiester bond with DNA, creating a break in the strand(s). Through this opening, the enzyme facilitates the passage of another DNA segment, either a single strand or a double helix, depending on the topoisomerase type.
After strand passage, the topoisomerase re-ligates the broken DNA strands, sealing the gap. This process relieves torsional stress, untangles DNA, and resolves knots without permanent damage. Type I enzymes operate without external energy, while Type II topoisomerases utilize ATP hydrolysis to power conformational changes and facilitate strand passage. The enzyme is then regenerated for multiple cycles of DNA manipulation.
Cellular Importance of Topoisomerase Binding
Topoisomerase binding and action are important for numerous cellular processes. During DNA replication, these enzymes resolve supercoils ahead of the replication fork, allowing DNA helicase to continue unwinding. They also untangle newly replicated daughter chromosomes, a process called decatenation, necessary for proper cell division.
In transcription, topoisomerases relieve torsional stress generated by RNA polymerase as it moves along the DNA template. This ensures gene expression proceeds efficiently without hindrance from overwound or underwound DNA regions. Topoisomerases are targets for certain therapeutic drugs, particularly in cancer treatment. Interfering with their binding or action can induce DNA damage and prevent the proliferation of rapidly dividing cells.