The following points highlight the six main types of enzymes that are associated with enzymes and some of them plays a key role in replication. The types are: 1. The Nucleases 2. The Ligases 3. Restriction Enzymes 4. The Polymerases 5. The Swivelases 6. Unwinding Enzymes and Proteins.
Type # 1. The Nucleases:
Enzymes which catalyse the breakdown of particular bonds leading to fragmentation of nucleic acids are called nucleases. The enzyme DNase causes hydrolysis (addition of water) of the phosphodiester bonds that link nucleotides in a DNA molecule. Similarly RNase acts on the polynucleotide RNA.
The exonucleases are enzymes that attack a nucleic acid at its terminal nucleotide only. In the 3′ or the 5′ phosphodiester bonds an exonuclease will act on either the 3′ or the 5′ end of the linkage. The endonucleases react only with those bonds which occur in the interior of a chain.
They can cut a single polynucleotide chain into pieces. In the case of double stranded DNA, they can produce nicks (gaps) in a single strand. Due to this the helix remains intact and the free ends at the gaps serve as substrates for exonucleases. There are several types of nucleases known which can degrade a nucleic acid in different specific ways.
Type # 2. The Ligases:
These are enzymes which can join broken ends of two DNA chains by catalysing the synthesis of a phosphodiester bond between a 3′-hydroxyl group at the end of one chain and a 5′-phosphate group at the end of the other chain.
Type # 3. Restriction Enzymes:
In the 1970s a new class of endonucleases has been isolated from micro-organisms whose action is limited only to specified nucleotide sequences. They are known as restriction enzymes and will produce breaks only within sequences which have two identical bases in adjacent positions such as CCT, TTA, GGC, AAG.
Since at these positions the complementary strand also has identical bases (GGA, AAT, CCG, TTC), restriction enzymes act on both strands and produce a break. A number of different restriction enzymes have been isolated (such as Hind II, Hind III, Eco R 1 and others) which specifically break particular nucleotides. They are thus useful for breaking a DNA molecule into specific known type of smaller fragments.
Type # 4. The Polymerases:
Enzymes such as DNA polymerase and RNA polymerase are involved in the synthesis of nucleic acids by addition of bases to a growing nucleotide chain. DNA polymerase can also perform nuclease activity by removing bases from a DNA strand, but in the opposite direction (3′ 5′) to that in which it adds bases (5′ 3′). The details of polymerase function are described later.
Type # 5. The Swivelases:
The two helical strands of DNA are wound around each other as if two parallel strands had been coiled around a central axis. This is called plectonemic coiling and is revealed by X-ray diffraction data. This winding does not allow rotation or movement of helices about each other. DNA replication requires rotation at specific sites called swivels within the helical strands.
Swivels allow free rotation of one part of the molecule relative to the adjacent part. In this way only the DNA between the growth point and the nearest swivel would have to rotate during replication. Enzymes that produce transient swivels are known as swivelases. They have endonuclease action on one of the strands thus allowing free rotation within the DNA molecule. The site is then immediately scaled leaving an intact strand for replication.
Type # 6. Unwinding Enzymes and Proteins:
The unwinding of DNA during replication requires an endonuclease enzyme that makes a single break in a strand. This allows DNA to unwind in that region instead of the whole DNA molecule having to twist. The further opening up of local regions is aided by specific unwinding proteins which bind preferentially to single-stranded DNA, resulting in separation of strands.
The binding of one unwinding protein to a DNA strand promotes the binding of a second, so that the helix continues to unwind. Another class of proteins called strand separation proteins (SSP) have also been isolated from both prokaryotes and eukaryotes.