Molecule of the Month: DNA Polymerase
DNA polymerase makes an accurate copy of the cell's genome
The Secret of Life
Prisoners and Pedigrees
Of course, there is very little DNA in a dried drop of blood. This is where DNA polymerase enters the world of forensics. A small sample of DNA is multiplied using PCR (the polymerase chain reaction), creating a large sample that may be easily analyzed. The tiny sample is placed in a test tube, and DNA polymerase is added to make a copy. Then the sample is heated up momentarily, and the two strands of DNA separate. Then DNA polymerase builds a new double helix from each strand. These two copies are then heated, and duplicated, yielding four copies. After repeating this many times, many identical DNA strands are produced. Our own DNA polymerases, and those from most organisms, would be destroyed by the heating step in this process. But today, DNA polymerase from Thermus aquaticus, a bacterium that lives in hot springs, is used. This polymerase, shown in the picture here, is perfectly happy at 70 degrees centigrade, and may be used throughout all of the PCR heating and cooling steps. This enzyme may be found in the PDB in the file 1tau .
Three simple polymerases are pictured here, each with a tiny piece of DNA bound in the active site. In each picture, the template DNA strand is colored purple and the newly built strand is colored green. At upper left is DNA polymerase I from Escherichia coli, with PDB accession code 1kln . At upper right is human DNA polymerase, from the PDB file 1zqa . At bottom is a viral DNA polymerase, from the PDB file 1clq . They are quite different in size and shape, but notice how all wrap around the DNA, and enclosing the end of the DNA in a pocket in which the synthetic reaction is performed.
These illustrations were created with RasMol. You can create similar pictures by clicking on the accession codes and choosing one of the options for 3D viewing.
Exploring the Structure
DNA polymerase in action
Simple DNA polymerases are roughly shaped like a hand. PDB entry 1tau from Thermus aquaticus demonstrates this, where the template and synthesized strands snugly fit into the “palm” between the “thumb” and “fingers.” This enzyme has three active sites. The polymerase domain near the top (in green) synthesizes a new strand from the template strand. The 3’-5’ exonuclease (blue-green) is responsible for proofreading the synthesized strand for mistakes. However this domain is not functional in Thermus aquaticus, potentially due to its extremely hot environment performing this function. The 5’-3’ exonuclease domain (in blue) removes the small RNA fragments used to prime DNA replication.
Select the JSmol tab to explore these structures in an interactive view.
This JSmol was designed and illustrated by Ryan Nini.
March 2000, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2000_3