In dehydration synthesis of nucleotides, the hydrogen atom from the 3' carbon on the deoxyribose sugar of one nucleotide reacts with the hydroxyl group on the phosphate group of another nucleotide to form water. As the water molecule forms, a new covalent bond comes into existence between the two nucleotides.

Hydroxyl group can be in different positions within the phosphate group, for example:

Hydroxyl group on the left Hydroxyl group on the top Hydroxyl group at the bottom

I'm wondering if different positions of the hydroxyl group have an impact on the dehydration synthesis between nucleotide monomers. For example, when the hydroxyl group is at the bottom, will the dehydration synthesis occur at all? Also, when the hydroxyl group is on the left, does the spatial structure of the sugar-phosphate backbone have a spatial shape different from when the OH group is on the top?

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    $\begingroup$ No, because there are all interchangeable on a nanosecond timescale. These are just different 2D representations of an equilibrium situation. $\endgroup$ – Waylander Sep 9 '20 at 13:36

The phosphate ion is of vital importance in biological systems. Its molecular geometry is tetrahedral. Thus, based on the $\mathrm{pH}$ of the system, hydroxy groups are inter-changeable with $\ce{P=O}$ form and hence all three remaining $\ce{O}$s are equivalent (see Waylander's comment). Therefore no impact on the dehydration.

However, the stereochemistry of the hydroxy group on the 3'-carbon on the deoxyribose nucleus of the nucleotide has an impact on the enzymatic dehydration process. For instance, if you change the original $(S)$-orientation of 3'-hydroxy group to $(R)$-orientation, DNA-synthase would not pick that nucleotide to synthesize intended DNA sequence.


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