BIo Tech

 Primers

Though DNA polymerase can elongate a polynucleotide strand by adding new nucleotides, it cannot start a strand from scratch because it can only bond new nucleotides to a free sugar (3') end of a nucleotide chain. DNA polymerase requires the assistance of a primer, a previously existing short strand of DNA (or RNA) that is complementary to the first part of the DNA segment being copied.  This small strand of nucleotides anneals (binds) by complementary base pairing to the beginning of the area being copied.  With the primer in place, DNA polymerase is then able to continue adding the rest of the pairs of the segment until a new double strand of DNA is completed.  Primers are formed from free nucleotides in the cell by enzymes called DNA primases. 

 Replication occurs differently on antiparallel strands of DNA.

That nucleotides can be added only to the sugar or 3' end of the growing complementary chain presents no problem for the side of the DNA chain opening at its phosphate or 5' end.  The primer that binds to the first few exposed bases will end with a sugar (3') where the phosphate of a new nucleotide can be attached.  From there on, DNA polymerase can continuously synthesize the growing complementary strand.  This strand of DNA is called the leading strand.  A nice little animation of DNA synthesis on the leading strand can be seen at the Nobel Prize e-museum site at http://www.nobel.se/medicine/educational/dna/a/replication/replication_ani.html.

A different challenge faces DNA polymerase when the complementary side of the DNA molecule begins unzipping from its sugar (3') toward its phosphate (5') end.  A primer of complementary molecules attaching to the opening end of this chain would have a phosphate not a sugar at its exposed end so that new nucleotides could not be joined. To get around this problem, this strand is synthesized in small pieces backward from the overall direction of replication.  This strand is called the lagging strand.  The short segments of newly assembled DNA from which the lagging strand is built are calledOkazaki fragments. As replication proceeds and nucleotides are added to the 3' end of the Okazaki fragments, they come to meet each other.  The primer fragments are then booted out by enzymes and replaced by appropriate DNA nucleotides.  The whole thing is then stitched together by another enzyme called DNA ligase.  The Nobel e-museum also has an animation of this process at http://www.nobel.se/medicine/educational/dna/a/replication/lagging_ani.html .

Figure 2

 Replication occurs simultaneously at multiple places along a DNA strand.

Because human DNA is so very long (with up to 80 million base pairs in a chromosome) it unzips at multiple places along its length so that the replication process is going on simultaneously at hundreds of places along the length of the chain.  Eventually these areas run together to form a complete chain.  In humans, DNA is copied at about50base pairs per second. The process would take a month (rather than the hour it actually does) without these multiple places on the chromosome where replication can begin.

 DNA replication is extraordinarily accurate.

DNA polymerase makes very few errors, and most of those that are made are quickly corrected by DNA polymerase and other enzymes that "proofread" the nucleotides added into the new DNA strand.  If a newly added nucleotide is not complementary to the one on the template strand, these enzymes remove the nucleotide and replace it with the correct one.  With this system, a cell's DNA iscopied with less than one mistake in a billion nucleotides.  This is equal to a person copying 100 large (1000 page) dictionaries word for word, and symbol for symbol, with only one error for the whole process!