Base pairs

Each step of the DNA ladder rises 0.34 nm, and ten steps make one full turn of 3.4 nm.

A twisted ladder

NHGRI compares DNA to a ladder twisted into a spiral. The two side rails are chains of alternating sugar and phosphate, and each rung is two bases holding on to each other. Bases do not pair at random. Adenine always pairs with thymine, and guanine always pairs with cytosine. So if one strand reads ATGC, the strand across from it must read TACG. Knowing one side is enough to write down the other.

Why these pairs? The bases come in two shapes. Adenine and guanine are purines, with two rings joined together. Cytosine and thymine are pyrimidines, with a single ring. Every rung has one purine and one pyrimidine, so every rung is the same length and the helix keeps the same width all the way along. The two partners are held by hydrogen bonds, weak attractions that are easy to break one at a time but strong together. A and T share two hydrogen bonds; G and C share three. Turn on Part names in the model and tap a rung to see the bonds.

The numbers of the helix

OpenStax Biology gives the dimensions used in the model. The helix is 2 nm across. Each base pair sits 0.34 nm above the one below it, and one full turn is 3.4 nm tall, so there are 3.4 ÷ 0.34 = 10 base pairs per turn. A nanometre is a millionth of a millimetre. The 27 base pairs in the model are 27 × 0.34 = 9.18 nm long, a little under three turns.

The two strands also run in opposite directions. Chemists number the carbon atoms of the sugar, and one end of a strand ends at the 5′ carbon while the other ends at the 3′ carbon. Across the rungs, the 5′ end of one strand sits next to the 3′ end of the other. This is called antiparallel. Because the backbones are not exactly opposite each other, the twist leaves a wide groove and a narrow groove running around the helix, which proteins use as places to grab and read the bases.

Pairing is how DNA copies itself

When a cell gets ready to divide, the helix splits down the middle into two single strands. Each strand then serves as a template. An A is added wherever there is a T, a C wherever there is a G, and so on, until every base has a partner again. The result is two double helices, each one an exact copy of the original. In each copy one strand is old and one is newly built, which is why biologists call replication semi-conservative. In the model, the old strands are beige and the new ones are blue, so you can follow them.