For example, polynucleotide synthesis reaction requires dATP which gives H on 3'end and synthesizes polynucleotide. For this reaction can I use ATP because I knew that ddNTPs are used so that ATP cannot be worked but I searched about it and found this,

"The unfavorable thermodynamics of the hypothetical dehydration reaction shown in Figure 4.6 leads us to ask: If polynucleotides cannot be synthesized in vivo by the direct elimination of water, how are they actually made? The answer is that their synthesis involves the energy-rich nucleoside or deoxynucleoside triphosphates. Although the process as it occurs in cells is quite complex, the basic reaction is simple. Instead of the dehydration reaction of Figure 4.6, what happens in living cells is the reaction shown in Figure 4.7. The nucleoside monophosphate being added to the growing chain is presented as a nucleoside triphosphate, like ATP or deoxy ATP (dATP), and pyrophosphate is released in the reaction. We can calculate the free energy change for this reaction by noting that it can be considered the sum of two reactions—hydrolysis of a nucleoside triphosphate and formation of a phosphodiester link by the elimination of water... The coupled reaction is favorable because the net delta G is negative. The reaction is further favored because the hydrolysis of the pyrophosphate product to orthophosphate, or inorganic phosphate, has a delta G = -19kJ>mol. Thus, the pyrophosphate is readily removed, driving the synthesis reaction even further to the right and yielding an overall Delta G of -25 kJ>mol. Polynucleotide synthesis is an example of a principle we emphasized in Chapter 3—the use of favorable reactions to drive thermodynamically unfavorable ones."[1]

So can nucleotide synthesize can be done with ATP in vitro? If yes, how? Also what kind of ATP required reactions can be replaced with dATP?


1)[Christopher K. Mathews, Kensal E. van Holde, Dean R. Appling, Spencer J. Anthony-Cahill - Biochemistry (2012, Pearson)]

  • $\begingroup$ It's not clear what you are asking about. ATP is already a nucleotide. I would advise you to read the chapter in your text on enzymes and substrate specificity to discover why what you seem to be suggesting is nonsense. $\endgroup$
    – David
    Oct 2, 2020 at 22:21
  • 1
    $\begingroup$ @user1136 — All very interesting (although I don’t subscribe to the “great men of history” idea, especially in its “great women” revival) but we are dealing here with a chemist, who understands Gibbs Free Energy changes, but apparently has forgotten about activation energy of reactions, and hasn’t yet encountered enzymes. $\endgroup$
    – David
    Oct 3, 2020 at 19:27


Browse other questions tagged .