Topoisomerases are a type of isomerase enzyme that modify the topology of deoxyribonucleic acid (DNA), causing its reluctance as both winding and supercoiling.


These enzymes have a specific role in the removal of torsional stresses in DNA so that important processes such as its replication, transcription of DNA into messenger ribonucleic acid (mRNA) and DNA recombination occur.

Topoisomerase enzymes are present in both eukaryotic and prokaryotic cells. Its existence was predicted by scientists Watson and Crick, when evaluating the limitations presented by the DNA structure to allow access to its information (stored in its nucleotide sequence).

To understand the functions of topoisomerase, it should be recognized that DNA has a stable structure of the double helix, with its chains rolling from one to the other. These linear chains are formed by 2-deoxyribes joined by phosphodiester bonds 5′-3′, and nitrogenous bases in their interior, like the steps of a spiral staircase.

Topological studies of DNA molecules have shown that they can assume several conformations depending on their stress tension: from a state of rest, to various states of twisted states that allow their condensation.

DNA molecules containing different molecules are called topoisomers. Thus, we can conclude that topoisomerases I and II can increase or decrease the stress tension of DNA molecules, forming their separate topoisomerases.

Among the possible DNA topoisomers, the most common conformation is supercoiling, which is very compact. However, the double helix of DNA must be unfolded by topoisomerase during many molecular processes.


general mechanism of action

Some topoisomerases can only relax the negative DNA supercoil, or both DNA supercoils: positive and negative.

If circular double-stranded DNA is open on its longitudinal axis and turns left-handed (clockwise), it is said to be negatively supercoiled. If the turning is clockwise (counter-clockwise), it is positively super-coiled.

Basically, topoisomerases can:

Facilitate the passage of one strand of DNA through a cut in the opposite strand (topoisomerase type I).

Facilitate the passage of a complete double helix through a split in itself, or through a split into another separate double helix.

In summary, topoisomerases act through cleavage of phosphodiester bonds, in one or both strands that make up DNA. Then modify the winding position of the strands with a double helix (topoisomerase I) or two double helices (topoisomerase II), to finally bind or lining the excised ends.

Topoisomerases and the cell cycle

Although topoisomerase I is an enzyme that exhibits maximum activity during S phase (DNA synthesis), it is not known to be dependent on a phase of the cell cycle.

Whereas topoisomerase II activity is more active during the logarithmic phase of cell growth and in rapidly growing tumor cells.


Alteration of genes encoding topoisomerase is lethal to cells, indicating the importance of these enzymes. Among the processes in which topoisomerase participate are:

Compact storage of genetic material

Topoisomerases facilitate the storage of genetic information in a compact way, as they generate DNA coiling and supercoiling, allowing relatively small amounts of large amounts of information.

access to genetic information

If there were no topoisomerases and their unique characteristics, it would be impossible to access the information stored in DNA. This is because topoisomerases periodically release tension by twisting that occurs in the double helix of DNA, during its reluctance, in the processes of replication, transcription and recombination.

If the tension is not released due to the torsion produced during these processes, it can produce a defective gene expression, blockage of circular DNA or chromosomes, even causing cell death.

regulation of gene expression

Changes (in a three-dimensional structure) of the DNA molecule expose specific regions to extrinsic, which can interact with DNA-binding proteins. These proteins have a positive function of gene expression (positive or negative).

Thus, the air state of DNA, generated by the action of topoisomerases, affects the regulation of gene expression.

Specifications of topoisomerase II

Topoisomerase II is required for the assembly of chromatids, the condensation and dissolution of chromosomes, and the separation of daughter DNA molecules during mitosis.

This enzyme is also a structural protein and one of the main components of the matrix of the cell nucleus during interphase.

Types of Topoisomerases

There are two main types of toisomerase depending on whether they are capable of carrying one or two DNA strands.

-topoisomerases type I


Type I topoisomerases are monomers that reduce the negative and positive supercoils, resulting from the movement of the fork during transcription, and during the processes of replication and gene recombination.

Type I topoisomerase can be subdivided into type 1a and type 1b. The latter are found in humans, and are responsible for relaxing supercoiled DNA.

Tyrosine in its active site

Topoisomerase 1B (Top1B) consists of 765 amino acids divided into 4 distinct domains. One of these domains contains a highly conserved region containing the active site with a tyrosine (Tyr7233). All toriosomerase present in their active site is a tyrosine with a fundamental role in the entire catalytic process.

mechanism of action

The tyrosine from the active site forms a covalent bond with the 3′-phosphate end of the DNA strand, cutting it and binding it to the enzyme, while passing another strand of DNA through excision.

The passage of the other strand of DNA through the excited strand is achieved thanks to a change of the enzyme, which produces the opening of the DNA double helix.

Then topoisomerase I returns to its initial conformation and is terminated again. This occurs by a process opposite to the break of the DNA chain in the catalytic site of the enzyme. Finally, the topoisomerase releases the DNA strand.

The DNA ligation rate is higher than the axis rate, which ensures the stability of the molecule and the integrity of the genome.

In summary, topoisomerase type I catalyzes:

  1. A bit of an excuse.
  2. The passage of the second strand through the split.
  3. The compulsion of partition ends.

-topoisomerases type II


Type II topoisomerases are dimeric enzymes that cleave both strands of DNA, thus relaxing the supercoils that arise during transcription and other cellular processes.

mg dependency ++ and atp

These enzymes require magnesium (Mg ++ ) and also the energy that comes from the breakdown of ATP triphosphate links, which they take advantage of thanks to ATPase.

Tyrosine with two active sites

Human topoisomerases II are similar to yeast ( Saccharomyces cerevisiae ), which is composed of two monomers (subfragments A and B). Each monomer contains an ATPase domain, and a subfragment containing the tyrosine active site 782, to which DNA can bind. Therefore, two strands of DNA may be involved in topoisomerase II.

mechanism of action

The mechanism of action of topoisomerase II is the same as that described for topoisomerase I, given that two DNA chains are cleaved and only one.

In the active site of topoisomerase II, a fragment of the protein is immobilized (via covalent binding with tyrosine). The double helix of DNA, called “piece G”. This fragment is cleaved and bound to the active site by covalent bonds.

Then, the enzyme allows another piece of DNA, called the “T fragment”, to pass through the fragment “G”, thanks to a conformational change of the enzyme, which is dependent on the hydrolysis of ATP.

Topoisomerase II binds to the two ends of “piece G” and recovers its initial position, releasing “fragment” at the end. Then, the DNA relaxes the torsional tension, which leads to the processes of replication and transcription.

-human topoisomerases

There are five topoisomerases in the human genome: top1, top3α, top3β (type I); and top2α, top2β (type II). The most relevant are the human topoisomerase top 1 (topoisomerase type IB) and 2α (topoisomerase type II).

topoisomerase inhibitors

Topoisomerases as a target for chemical attack

Because the processes catalysed by topoisomerase are essential for the survival of cells, these enzymes are good targets of attack to affect malignant cells. For this, topoisomerase is considered important in the treatment of many human diseases.

Drugs that interact with topoisomerase are currently widely studied as chemical agents against cancer cells (in various parts of the body) and pathogenic microorganisms.

– type of barrier

Topoisomerase activity inhibitory drugs can:

  • Eat DNA.
  • Affect topoisomerase enzymes.
  • Interleave a molecule near the active site of the enzyme while the DNA-topoisomerase complex is stabilized.

Stabilization of the transient complex formed by binding of DNA to tyrosine at the catalytic site of the enzyme prevents the association of the excited fragments, which can lead to cell death.

-inhibitors of topoisomerase

Among the compounds that inhibit topoisomerase are the following.

Antitumor antibiotics

Antibiotics are used against cancer because they inhibit the growth of tumor cells, usually by interfering with their DNA. They are often called antineoplastic antibiotics (against cancer). For example, actinomycin D affects topoisomerase II and is used for Wilm’s tumor and rhabdomyosarcomas in children.


Among anthracycline antibiotics, the most effective are anticancer drugs and broad-spectrum. They are used in the treatment of cancer of the lung, ovary, uterus, stomach, bladder, breast, leukemia and lymphadia. It is known to affect topoisomerase II by intercalation into DNA.

Daunorubicin was the first anthracycline ( Streptomyces peusetius ) isolated from actinobacteria. Later, doxorubicin was synthesized in the laboratory, and epirubicin and idarubicin are now used.


Anthraquinones or anthracanadienes are compounds similar to anthracyclines, which affect the activity of topoisomerase II by intercalation in DNA. They are used for metastatic breast cancer, non-Hodgkin’s lymphoma (NHL) and leukemia.

These drugs were found in the pigments of some insects, plants (Fenungula, senna, rhubarb), lichens and fungi; As well as in Hoelita, which is a natural mineral. Depending on their dosage, they can be carcinogenic.

Among these compounds, we have mitoxantrone and its analog losoxantrone. These stop the proliferation of malignant tumor cells, binding irreversibly to DNA.


Podophyllotoxins, such as epidophylotoxin (VP-16) and teniposide (VM-26), form a complex with topoisomerase II. They are used against cancer of the lung, testis, leukemia, lymphoma, ovarian cancer, breast carcinoma and malignant intracranial tumours. They are isolated from the plants Podophyllum notatum and P. peltatum.

Camptopsin Analogs

Campotekins are compounds that inhibit topoisomerase I, and among them are irinotecan, topotecan and difluometecan.

These compounds have been used against colon, lung and breast cancers, and are naturally derived from the bark and leaves. Camptotheca acuminata Chinese peach and Tibet K.

natural prohibition

Structural changes of topoisomerases I and II can also occur completely naturally. This can happen during certain events that affect its catalytic process.

Among these changes, we can mention the formation of pyrimidine dimers, mismatch of nitrogenous bases and other phenomena caused by oxidative stress.