Why is DNA negatively charged?

Phosphate group in DNA is the reason for negative charge
The presence of phosphate groups in nucleotides.
A nucleotide consists of a sugar phosphate backbone and a nitrogenous base.
More details on DNA structure is here.
In DNA double helix, the two strands are joined together by hydrogen bond between nitrogenous bases.

What is phosphodiester bond?
 phosphodiester bond
Adjacent nucleotides are joined by phosphodiester bond. One phosphoric acid molecule joins with the hydroxyl group of two sugar molecules of two nucleotides forming ester linkage.
In the figure you can see  that the first ester linkage (C-O bond in red color) is at the third position of sugar molecule (3’ OH position) and the second ester linkage is at the fifth position of second sugar molecule of the incoming nucleotide (5’ CH2OH). Thus two ester bonds are formed and called as phosphodiester bond.

Why phosphates in DNA?
In DNA, the nucleotides are joined through phosphate forming phosphodiester bond. The characteristics of phosphate that makes it a perfect molecule for bonding include:
  • The negative charge of the DNA is due to phosphodiester bond that keeps the nucleotides and DNA within the nuclear membrane. Negatively charged molecules are insoluble in lipids therefore DNA cannot move across lipid made nuclear membrane.
  • Phosphate groups can from linked bonds.
  • The bonds formed from phosphates are ester bonds that are stable. At the same  time theses bonds can be easily hydrolysed by enzymes.

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