I know that the pyrophosphate of a NTP is hydrolysed so that it can create enough energy for the synthesis of DNA. But if we want to get specific we can know for sure that the 3' end of the DNA strand has got one phosphate because the phosphate is having a bond with another nucleotide. But what could be the reason for the 5' end to have only one phosphate and not 3? Could it be the energy providing or that the structure has to be consistent or something else that I can't think of?

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    $\begingroup$ You need to think about how DNA synthesis starts. Genomes or chromosomes are replicated (from replication origins). Read about that and I think it will answer your question. $\endgroup$ – David Mar 2 at 14:17

The DNA polymerase can only extend a primer and therefore almost all lifeforms have a primase (which is a type of RNA polymerase) that synthesizes RNA primers at the replication origins that the DNA polymerase can extend.

As you guessed, the 5' end would indeed have a triphosphate.

Organism            Template Sequence        Primer Synthesized

Herpes simplex-1 3′-GPyPy pppPuPu T4 3′-TTG pppAC T7 3′-CTG pppAC E. coli 3′-GTC pppAG S. aureus 3′-ATPy pppAPu S. aureus 3′-ATPy pppAPu A. aeolicus 3′-CCC, CCG, CGC pppGG, pppGC, pppCG B. stearothermophilus 3′-ATPy pppAPu Human 3′-PyNN pppPuNN Calf 3′-PyNN pppPuNN
Initiation sites used by primase from different sources. Pu = purine, Py = pyrimidine, N = any base ppp = the triphosphate on the 5′-end of the primer. Those bases that are required but do not code for a base in the primer (“cryptic” nucleotides) are underlined and in bold.

Kuchta and Stengel (2010)

In the final stages of replication, these RNA primers are removed by RNAseH and DNA polymerase I in bacteria and the gaps are filled by the latter (Cooper (2000) The Cell). In eukaryotes, the primer is removed by the action of Fen1 and Dna2 exonucleases and the gaps are filled by DNA polymerase δ (Burgers 2009).

In PCR, it is quite straightforward: the product will have whatever 5' modifications the primers have (usually none).


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