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Assembling the Double Helix: The Structure of DNA

Nucleotides are the true building blocks of DNA. There are three components of a single nucleotide: one deoxyribose sugar, one phosphate, and one of the four bases. To make a complete DNA molecule, single nucleotides join to make chains that come together as matched pairs and form long double strands. This article walks you through the assembly process.

DNA normally exists as a double-stranded molecule. In living things, new DNA strands are always put together using a preexisting strand as a pattern.

Starting with one: Weaving a single strand

Hundreds of thousands of nucleotides link together to form a strand of DNA. But they don't hook up haphazardly. Nucleotides are a bit like coins in that they have two "sides" — a phosphate side and a sugar side. Nucleotides can only make a connection by joining phosphates to sugars. The bases wind up parallel to each other (stacked like coins) and the sugars and phosphates run perpendicular to the stack of bases. A long strand of nucleotides put together in this way is called a polynucleotide strand (poly meaning many).

Because of the way the chemical structures are numbered, DNA has numbered "ends." The phosphate end is referred to as the 5' (5-prime) end, and the sugar end is referred to as the 3' (3-prime) end. The bonds between a phosphate and two sugar molecules in a nucleotide strand are collectively called a phosphodiester bond. This is a fancy way of saying that two sugars are linked together by a phosphate in between.

After they're formed, strands of DNA don't enjoy being single; they're always looking for a match. The arrangement in which strands of DNA match up is very, very important. A number of rules dictate how two lonely strands of DNA find their perfect matches and eventually form the star of the show, the molecule you've been waiting for — the double helix.

Doubling up: Adding the second strand

A complete DNA molecule has

  • Two side-by-side polynucleotide strands twisted together.
  • Bases attached in pairs in the center of the molecule.
  • Sugars and phosphates on the outside, forming a "backbone."

If you were to untwist a DNA double helix and lay it flat, it would look a lot like a ladder. The bases are attached to each other in the center to make the rungs, and the sugars are joined together by phosphates to form the sides of the ladder. It sounds pretty straightforward, but this ladder arrangement has some special characteristics.

If you were to separate the ladder into two polynucleotide strands, you'd see that the strands are oriented in opposite directions. The locations of the sugar and the phosphate give nucleotides heads and tails, two distinct ends. The heads-tails (or in this case, 5'-3') orientation applies here. This head-to-tail arrangement is called antiparallel, which is a fancy way of saying parallel and running in opposite directions. Part of the reason the strands must be oriented this way is to guarantee that the dimensions of the DNA molecule are even along its entire length. If the strands were put together in a parallel arrangement, the angles between the atoms would be all wrong, and the strands wouldn't fit together.

The molecule is guaranteed to be the same size all over because the matching bases complement each other, making whole pieces that are all the same size. Adenine complements thymine, and guanine complements cytosine. The bases always match up in this complementary fashion. Therefore, in every DNA molecule, the amount of one base is equal to the amount of its complementary base. This condition is known as Chargaff's rules.

An important result of the bases' complementary pairing is the way in which the strands bond to each other. Hydrogen bonds form between the base pairs. The number of bonds between the base pairs differs; G-C pairs have three bonds, and A-T pairs have only two. Every DNA molecule has hundreds of thousands of base pairs, and each base pair has multiple bonds, so the rungs of the ladder are very strongly bonded together.

When inside a cell, the two strands of DNA gently twist around each other like a spiral staircase. The antiparallel arrangement of the two strands is what causes the twist. Because the strands run in opposite directions, they pull the sides of the molecule in opposite directions, causing the whole thing to twist around itself.

Most naturally occurring DNA spirals clockwise. A full twist (or complete turn) occurs every ten base pairs or so, with the bases safely protected on the inside of the helix. The helical form is one way that the information that DNA carries is protected from damage that can result in mutation.

There are a few additional details about DNA that you need to know:

  • A DNA strand is measured by the number of base pairs it has.
  • The sequence of bases in DNA isn't random. The genetic information in DNA is carried in the order of the base pairs. In fact, the genes are encoded in the base sequences.
  • DNA uses a preexisting DNA strand as a pattern or template in the assembly process. DNA just doesn't form on its own. The process of making a new strand of DNA using a preexisting strand is called replication.
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