The DNA molecule carries a negative charge because of the phosphate groups in its sugar-phosphate backbone. Under ordinary cellular conditions, the phosphate groups are deprotonated and contribute negative charges to each DNA strand.
Each nucleotide is built from a sugar, a nitrogen-containing base, and phosphate group(s). When nucleotides polymerize, phosphodiester bonds connect the 3′ carbon of one sugar to the 5′ phosphate of the next nucleotide. The resulting repeating backbone contains negatively charged phosphate groups, while the bases project inward and pair with one another.
This charge has important structural consequences. Positively charged proteins, especially histones, bind DNA and help compact it inside the nucleus. In laboratory procedures, DNA can move toward a positively charged electrode during gel electrophoresis, allowing fragments to be separated by size.
“Negative” describes DNA’s overall charge, not a claim that every atom or chemical group is negative. The bases contain different atoms and functional groups, and the exact charge can depend on chemical conditions. The negative backbone is also why salts and positively charged ions help shield repulsion between neighboring DNA strands and support stable folding and packaging.