DNA is a nucleic-acid polymer built from deoxyribonucleotide residues joined into directional strands.

Sugar-phosphate backbone

Within one strand, the $3'$ hydroxyl of one deoxyribose is connected through phosphate to the $5'$ carbon of the next sugar. The resulting covalent linkage is a phosphodiester bond because one phosphate forms ester connections to two sugar groups.

Repeated phosphodiester linkages produce the DNA sugar-phosphate backbone.

A strand therefore has directionality:

• the $5'$ end is associated with the terminal side of the backbone at sugar carbon $5'$;
• the $3'$ end carries the terminal $3'$ hydroxyl side.

DNA sequences are conventionally written $5'\rightarrow3'$.

Bases project from the backbone

Each sugar carries one nitrogenous base: adenine (A), thymine (T), guanine (G) or cytosine (C). The sequence of these bases can vary while the repeating sugar-phosphate chemistry remains the same.

The phosphate-rich backbone is negatively charged and interacts strongly with water and counterions. The bases are attached to the sugars and project away from the backbone, where they can stack with neighboring bases and pair with bases on another strand.

Antiparallel double helix

In ordinary double-stranded DNA, two strands run in opposite directions: one is oriented $5'\rightarrow3'$ while the other runs $3'\rightarrow5'$ alongside it. The strands associate into a double helix with the sugar-phosphate backbones on the outside and paired bases in the interior.

The two strands are not covalently joined along their length. Their association depends on noncovalent interactions, especially base pairing and base stacking.

Hydrogen bonding contributes strongly to pairing specificity, while stacking interactions among neighboring bases contribute substantially to duplex stability. Solvent, ions, sequence and temperature all affect the stability of the double-stranded structure.

The next unit focuses on why the donor/acceptor geometry of the bases favors the complementary pairs A-T and G-C.