The nucleases They are enzymes that are responsible for degrading nucleic acids. They do this by hydrolysis of the phosphodiester bonds that hold nucleotides together. For this reason, they are also known in the literature as phosphodiesterases. These enzymes are found in almost all biological entities and play fundamental roles in DNA replication, repair and other processes..
In general, we can classify them depending on the type of nucleic acids that they cleave: nucleases whose substrate is RNA are called ribonucleases, and those of DNA are known as deoxyribonucleases. There are some non-specific ones capable of degrading both DNA and RNA.
Another widely used classification depends on the action of the enzyme. If it does its job progressively, starting at the ends of the nucleic acid chain, they are called exonucleases. In contrast, if the break occurs at an interior point in the chain, they are called endonucleases..
Currently, certain endonucleases are widely used in recombinant DNA technology in molecular biology laboratories. These are invaluable tools for the experimental manipulation of nucleic acids..
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Nucleases are biological molecules of a protein nature and with enzymatic activity. They are capable of hydrolyzing the bonds that join nucleotides in nucleic acids.
They act through a general acid-base catalysis. This reaction can be divided into three fundamental steps: the nucleophilic attack, the formation of a negatively charged intermediate and, as a final step, the breaking of the bond..
There is a type of enzyme called polymerases, responsible for catalyzing the synthesis of both DNA (in replication) and RNA (in transcription). Some types of polymerases exhibit nuclease activity. Like polymerases, other related enzymes also exhibit this activity..
Nucleases are an extremely heterogeneous set of enzymes, where there is little relationship between their structure and mechanism of action. That is, there is a drastic variation between the structure of these enzymes, so we cannot mention any structure common to all of them..
There are multiple types of nucleases and also different systems to classify them. In this article, we will discuss two main classification systems: according to the type of nucleic acid they degrade and according to the way the enzyme is attacked..
If the reader is interested, they can look for a third more extensive classification based on the function of each nuclease (see Yang, 2011).
It is necessary to mention that nucleases also exist in these enzyme systems that are not specific to their substrate and can degrade both types of nucleic acids..
There are two types of nucleic acids that are virtually ubiquitous to organic beings: deoxyribonucleic acid, or DNA, and ribonucleic acid, RNA. The specific enzymes that degrade DNA are called deoxyribonucleases, and RNA, ribonucleases.
If the nucleic acid chain is attacked endolytically, that is, in internal regions of the chain, the enzyme is called an endonuclease. The alternative attack occurs gradually at one end of the chain and the enzymes that carry it out are exonucleases. The action of each enzyme results in different consequences.
Since exonucleases separate nucleotides step by step, the effects on the substrate are not very drastic. On the contrary, the action of endonucleases is more pronounced, since they can cleave the chain at different points. The latter can change even the viscosity of the DNA solution.
Exonucleases were crucial elements in elucidating the nature of the bond that held nucleotides together..
The specificity of the endonuclease cleavage site varies. There are some types (such as the enzyme deoxyribonuclease I) that can cut at nonspecific sites, generating relatively random cuts with respect to the sequence.
In contrast, we have very specific endonucleases that only cut at certain sequences. Later we will explain how molecular biologists take advantage of this property.
There are some nucleases that can act as both endo and exonucleases. An example of this is the so-called microconic nuclease.
Nucleases catalyze a series of reactions essential for life. Nuclease activity is an essential element of DNA replication, since they help the removal of the primer or first and participate in the correction of errors.
In this way, two important processes such as recombination and DNA repair are mediated by nucleases..
It also contributes to generating structural changes in DNA, such as topoisomerization and site-specific recombination. For all these processes to take place, a temporary breakdown of the phosphodiester bond is necessary, carried out by nucleases..
In RNA, nucleases also participate in fundamental processes. For example, in the maturation of the messenger and in the processing of interfering RNAs. In the same way, they are involved in the processes of programmed cell death or apoptosis..
In unicellular organisms, nucleases represent a defense system that allows them to digest foreign DNA that enters the cell.
Molecular biologists take advantage of the specificity of certain nucleases called specific restriction nucleases. Biologists had noticed that bacteria were able to digest foreign DNA that was introduced through techniques in the laboratory.
Investigating further into this phenomenon, scientists discovered restriction nucleases - enzymes that cut DNA at certain nucleotide sequences. They are a kind of "molecular scissors" and we find them produced for sale.
Bacteria DNA is "immune" to this mechanism, since it is protected by chemical modifications in the sequences that promote degradation. Each species and strain of bacteria has its specific nucleases.
These molecules are very useful, since they ensure that the cut will always be made in the same place (4 to 8 nucleotides in length). They are applied in recombinant DNA technology.
Alternatively, in some routine procedures (such as PCR) the presence of nucleases negatively affects the process, since they digest the material that needs to be analyzed. For this reason, in some cases it is necessary to apply inhibitors of these enzymes..
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