How does DNA polymerase link nucleotides to form a new strand, using an existing strand as a template?

Sourav PanNovember 8, 2024

Answered

DNA polymerase is a vital enzyme responsible for synthesizing new DNA strands during replication. It links nucleotides to form a new strand by using an existing strand as a template through a series of well-defined steps.

Mechanism of Nucleotide Linking by DNA Polymerase

1. Template Recognition: DNA polymerase begins the process by recognizing the template strand of DNA. This strand has exposed bases that will pair with incoming nucleotides. The pairing follows the rules of complementary base pairing: adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).
2. Nucleotide Addition: DNA polymerase can only add nucleotides to the 3′ end of an existing strand. It utilizes the free hydroxyl (-OH) group at this 3′ end as a nucleophile to initiate the addition of new nucleotides. The incoming nucleotide, which is in the form of a deoxyribonucleoside triphosphate (dNTP), has three phosphate groups attached.
3. Phosphodiester Bond Formation: When DNA polymerase catalyzes the reaction, the 3′ -OH group attacks the alpha phosphate of the incoming dNTP, leading to the formation of a phosphodiester bond. This reaction releases pyrophosphate (PPi), which provides the energy necessary for forming the bond between nucleotides. The overall reaction can be summarized as:
   (dNMP)n+dNTP→(dNMP)n+1+PPi
4. Directionality of Synthesis: As a result of this mechanism, DNA synthesis occurs in a 5′ to 3′ direction, meaning that while DNA polymerase moves along the template strand in a 3′ to 5′ direction, it elongates the new strand in a 5′ to 3′ direction . This antiparallel orientation is crucial for maintaining the structural integrity of the double helix.
5. Role of Primase: Before DNA polymerase can begin adding nucleotides, an RNA primer synthesized by primase provides a starting point with a free 3′ -OH group. This primer is essential because DNA polymerase cannot initiate synthesis without an existing nucleotide chain.
6. Error Checking: DNA polymerase also has proofreading capabilities. After adding a nucleotide, it undergoes conformational changes that allow it to check whether the newly added nucleotide correctly pairs with the template base. If there is an incorrect pairing, the enzyme can remove and replace it before continuing synthesis