RNA priming

• No new DNA starts:  Deoxynucleotides can only be added to 3'-end of a pre-existing strand of DNA (or RNA). There are no enzymes capable of initiating the synthesis of a DNA-templated DNA molecule at the level of a single nucleotide. This makes necessary to use an indirect priming procedure.
  
  
• RNA primers:  A variety of enzymes are capable of initiating new DNA-templated RNA synthesis (as in transcription). New DNA synthesis is primed with a short segment of RNA that is later removed
  
  
• Primase:  A separate enzyme in the initiation complex called primase synthesizes a short RNA primer each time that new DNA synthesis begins, including all new starts in the discontinuous pattern of synthesis described below.

Leading and lagging strands

• Unidirectional synthesis of antiparallel DNA:  The inability to synthesize new chains in a 3' to 5' direction adds a major complication to the replication of antiparallel double-stranded DNA. At any replication fork, one of the template strands has a 3' to 5' orientation, which is what is needed for synthesis of a new complementary strand in a 5' to 3' direction. Synthesis on that template is primed and starts very quickly. However, the other template strand has a 5' to 3' orientation and is thus unable to support synthesis beginning at the origin and moving away from it in a 3' to 5' direction. Because of this, the 5' to 3' template strand accumulates in a single stranded configuration until there is a sufficient length so that synthesis of its complementary antiparallel strand can be primed and initiated in a 5'-to-3' direction ("backward" toward the origin of replication). The strand whose synthesis begins immediately is called the "leading" strand, and the one whose synthesis is delayed is called the "lagging" strand.
  
  
• Discontinuous synthesis -- Okazaki fragments:  As synthesis of the leading strand continues, more and more of the single stranded DNA of the lagging strand is unwound. Each time that a sufficient length is reached, synthesis of a new segment of the complementary strand begins. If the replicating DNA is denatured (separated into individual strands) before the newly synthesized pieces of the lagging strand have been ligated together, a number of relatively small fragments of newly synthesized DNA will be recovered, together with the much longer strands produced by continuous synthesis in the leading strand. The small fragments are called "Okazaki fragments", named for the person who first discovered them.

DNA polymerase III

Template DNA synthesis:  After the RNA primer has reached an adequate length, DNA polymerase III begins synthesis of DNA, which proceeds to completion in the leading strand, and proceeds until the 5'-end of the previous primer is encountered in the lagging strand.

• DNA polymerase III holoenzyme:  DNA polymerase III is a highly complex dimeric aggregate, consisting of 20 or more protein subunits. The alpha subunits perform the actual DNA synthesis, but operate in conjunction with multiple accessory proteins.
  
  
• Simultaneous synthesis of leading and lagging strands:  There is yet another complicating factor in DNA synthesis. It is now generally believed that the leading and lagging strands are synthesized simultaneously by a single dimeric DNA polymerase III complex. This requires formation of a looped structure with the leading and lagging strands so positioned that their synthesis can occur side by side in the same orientation, despite the fact that the newly synthesized chains are growing in opposite directions relative to the overall DNA that is being replicated. A similar looping also appears to occur in eukaryotic DNA replication.
  
  
• Clamping function of beta subunits: The beta subunits appear to have a clamping function that keeps the leading and lagging strands appropriately aligned with the catalytically active alpha subunits.
  
  
• Replisome complex:  The entire DNA-synthesizing complex at each replication fork, which also includes topoisomerase, helicase, and primase, is sometimes referred to as a replisome.