Opening image: The dimeric β subunit of E. coli DNA Polymerase III. During replication, the β-clamp remains bound to the DNA duplex, sliding along the DNA at a rate of 500 to 1000 base pairs per second. The β-dimer requires an accessory protein to crack open the dimer to load around DNA. The central opening of the dimer is about 35 Å in diameter and is lined with conserved positive and polar residues. These residues make water-mediated contact with the DNA duplex. Water-mediated hydrogen bonds are quite mobile in an aqueous environment, allowing the β-clamp to slide freely along the DNA double helix for millions of base pairs during genome replication.

Introduction

Molecular recognition is dominated by shape and electronic complementarity. There is no finer example of molecular complementarity than the Watson-Crick base pairs. The purine and pyrimidine bases are planar heterocyclic molecules which contain both hydrogen bond acceptors and donor substituents around the edges of the aromatic rings. In planar base pairs the bases are arranged like jigsaw puzzle pieces; steric fit and hydrogen bonding between the bases specify the matching rules between adjacent pieces.

Nucleotides

Adenosine monophosphate (AMP), often referred to as adenylate.

Nucleotides have three components: a pyrimidine or purine base, a sugar, and phosphate. In a ribonucleoside the base is connected by a β-glycosidic bond to the anomeric (C1′) carbon of D-ribose.

The major purine bases found in nucleic acids are adenine (A) and guanine (G).

The "primed" numbers (n′) refer to the atoms of the sugar. Note that the amino group and purine ring are coplanar. The nitrogen atom is sp² hybridized. The lone pair electrons on nitrogen occupy its p orbital, and these electrons take part in the π-bonding system.

A ribonucleoside that is phosphorylated at its 5′-hydroxyl is called a ribonucleotide ("tied" to phosphate). A nucleotide is always assumed to be a 5′-phosphate ester unless otherwise designated.

The major pyrimidine bases are:

• Cytosine (C): DNA and RNA. What is the hybridization of the nitrogen atom in the amino group?
• Thymine (T): DNA only
• Uracil (U): RNA only

All our descriptions of ribonucleosides and ribonucleotides also apply to the components of DNA. The principle difference between RNA and DNA is the presence of D-2-deoxyribose as the sugar in DNA instead of the D-ribose found in RNA.

Another key difference is the presence of thymine in DNA instead of uracil. Thymine is simply uracil with a methyl group. We use the prefix "d-" to distinguish deoxyribonucleotides from ribonucleotides; the four deoxynucleotides in DNA are: dAMP, dGMP, dCMP, and dTMP.