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Base Pairing and the Double Helix

Two strands, twisted into a helix, held together by a strict pairing rule: A with T, G with C. This is the shape that makes copying possible.

Two strands, one rule

DNA is almost never a lone strand. It is two strands clasped together and twisted into the famous double helix — a shape like a spiral ladder. What holds the two strands together is base pairing, and it follows one strict rule: A always pairs with T, and G always pairs with C. No other combinations form a stable rung.

Why those exact pairs? Partly the size rule from the last guide: a large purine (A or G) must pair with a small pyrimidine (T or C) so every rung is the same width. And within that constraint, A and T form two stabilising hydrogen bonds, while G and C form three. Each base pair is a rung; the two sugar-phosphate backbones are the ladder's rails.

Complementary strands

Because the pairing rule is strict, the two strands are not independent: each is the mirror-image partner of the other, called the complementary strand. If you know one strand, you automatically know the other. Wherever one strand has A, the partner must have T; wherever one has G, the partner must have C. This is the single most important consequence of base pairing.

Given one strand, write its complement by the rule A-T, G-C:

  Strand 1 (given):   5'- A T G C G T A C -3'
                          | | | | | | | |
  Strand 2 (built):   3'- T A C G C A T G -5'

Check each rung:
  A:T   T:A   G:C   C:G   G:C   T:A   A:T   C:G   ->  all valid

Notice: knowing strand 1 was enough to write all of strand 2.
Building the complementary strand from a known strand using the pairing rule.

Chargaff's hint

Before the helix was known, the chemist Erwin Chargaff measured the bases in DNA from many species and found something puzzling: the amount of A always equalled the amount of T, and the amount of G always equalled C. These Chargaff's rules were a riddle at the time, but they fall straight out of base pairing — if every A sits opposite a T, the totals must match.