Question

Explain the 5’-to-3’ directional activity of DNA polymerase.

Please give an explanation for the inability of this enzyme to synthesize DNA in opposite direction (3’-to-5’).

Answer 1

DNA polymerase recruits the free dNTPs and forms a covalent phosphodiester bond with the previous nucleotide of the same strand. the energy required for the formation of the phosphodiester bond comes from dNTPs. dNTP is made up of the deoxyribose sugar, nitrogenous base, and the phosphate group.

so DNA polymerase adds a free nucleotide (dNTP)to the 3' end of DNA strand and elongates the strand 5' to 3' direction. DNA polymerase cannot synthesize the strand on its own it adds the free nucleotide to the 3' OH group. To join the 3'OH group with the phosphate of the new nucleotide, to form the covalent bond one oxygen has to be removed from this phosphate group. this oxygen attached to two phosphates, and phosphate attached to mg++. this mg++ pull up the electrons from the oxygen and weaken the bond and nucleophilic attack of the oxygen from 3' OH group form the phosphodiester bond. which lead to extension from 5' to 3'.

DNA polymerase can not synthesize 3' to 5' because if we try the add the dNTPs 3'OH group to the 5' phosphate of new nucleotide then the energy required to weaken the bond between oxygen connected to 5' phosphorus is very high which makes the nucleophilic attach harder because there is no good pyrophosphate leaving group.