The individual components:

The nucleosides are connected by esterifying a phosphate to the 5'-position of one sugar, and then to the 3'-OH of another, producing a 3'-5' phosphodiester linkage.

• Nucleic acid chains are unsymmetrical: they have a free 3' and a free 5' end (similarly, proteins have a free amino at one end and a free carboxyl at the other)

• By convention, structural abbreviations are assumed to read in the 5' to 3' direction

• The sequence of bases reading in that direction is the primary structure of the nucleic acid

• In writing a shorthand sequence, the phosphate is represented as "p", and the sugar as "d" or "r" (deoxy ribose or ribose)

• The picture presents pdApdC, or just AC if the reference to DNA is clear

• The phosphates are shown as charged since they have a pK of about 2; thus nucleic acids are polyanions under physiological conditions

Erwin Chargaff demonstrated in 1950 that in DNA, A and T are present in equimolar amounts, as are C and G.

• The ratio of (A+T) to (C+G) varies widely from organism to organism, depending on the closeness of the species

• However the ratio of purines to pyrimidines is always 1:1

The model of DNA proposed by Watson and Crick in 1953 [Nature, 1953, 171, 737] explained Chargaff's observations by suggesting:

• DNA is double stranded

• The bases on one strand hydrogen bond to complementary bases on the other

  Here is a video of Watson explaining the base pairing idea:

  The Watson-Crick Model

• Such a structure requires that the two strands run antiparallel to each other

The complementarity is a crucial idea: it means that each strand can serve as a template for the other.

• In a lovely understatement, Watson and Crick wrote in their paper:

  "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."

The picture above suggests some similarities to a ladder, with the phosphate-sugar chains forming the side rails, and the paired bases the rungs.

• This structure leaves the charged phosphates exposed to the aqueous environment, and places the more lipophilic bases in the interior.

• An alternative structure, with the phosphates inside, would be destabilized by electrostatic interactions between the phosphate chains

The twist into a helical conformation is produced by the interactions between the bases of one "rung" and the next; the stacking of the bases in parallel planes allows attractive van der Waals interactions between them.

This structure is "plectonemic", meaning that the two chains wind around each other

• the alternative is "paranemic": one helix simply slipped into the other one

• being plectonemic creates problems in copying which we address later

The location of the sugar-phosphate backbones on the outside of the molecule (an exoskeleton?), coupled with the twist, produces two grooves on the surface of the double helix:

B-DNA (ACACTACAATGTTG; 3bse)

The larger one is the major groove, the smaller, the minor groove.

• In an aqueous environment, the grooves are filled with water molecules, hydrogen bonded to the phosphates and to exposed amino and carbonyl groups of the bases.

• The hydration averages about 20 molecules of water per base pair.

  B-DNA (The red spheres are water; 3bse)

(Read more about one of the great scientific discoveries of the 20^th century:

• James Watson, "The Double Helix: A Personal Account of the Discovery of the Structure of DNA"

• James Watson, "DNA: The Secret of LIfe"

• Brenda Maddox, "Rosalind Franklin: The Dark Lady of DNA"

• Thomas Hager, "Force of Nature: The Life of Linus Pauling"

• Horace Judson, "The Eighth Day of Creation: Makers of the Revolution in Biology"

• Robert Olby, "Francis Crick: Hunter of Life's Secrets")