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NCBI Activity 2009: Exploring the stability of Taq Polymerase by Keats Shwab and Jason Harris

Topic:

We are invstigating a very well used enzyme, Taq polymerase. We wish to understand the structural characteristics which make it ideal for high temperature activity. We we also would like to see how related its peptide sequence is to non thermophillic polymerases.

Content:

All DNA polymerases have a similar structure that is related to their function, yet they differ in the details which comprise this uniform structure. This structure is analogous to that of a cupped right hand with the palm, fingers, and thumb being the domains of the complex (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=polymerase,dna&rid=stryer.section.3769#3770, a NCBI Book reference 27.2.1. All DNA Polymerases Have Structural Features in Common)

If the structures of polymerases are so remarkably conserved and no mention is made of taq, a very popular DNA polymerase, then it seems safe to assume that it falls into this generalization. In order for it to maintain its DNA binding and polymerizing structure at thermophyllic temperatures, the details of its composition are expected to vary from that of other lower temperature operating polymerases.

The referenced book above was searched for in the NCBI BOOK database using the term ‘taq polymerase’. This query resulted in several books about polymerases, but none specifically on taq polymerase. It did however provide a generalized overview of DNA polymerases.

Taq polymerase is a DNA-dependent DNA polymerase derived from the themophilic bacterium Thermus aquaticus, which is found in hot springs and geothermal vents. This enzyme is widely used in polymerase chain reactions (PCR) because of its ability to catalyze DNA synthesis at high temperatures, with an optimal temparature between 72-80 C. Taq polymerase is not ideal for PCR, however, as it lacks 5′-3′ exonuclease proofreading activity that results in occasional errors in DNA synthesis. Other “High-fidelity” DNA polymerases with this proofreading activity have been isolated from other thermophilic bacteria and archaea, such as the archean Pyrococcus furiosus (Pfu polymerase).

References:

Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus.

A Chien, D B Edgar, and J M Trela

Journal of bacteriology 127 (3), 1550-7 (Sep 1976)

Molecular diversity and catalytic activity of Thermus DNA polymerases.

Moreland Gibbs et al.

Extremophiles : life under extreme conditions, (12 Jul 2009)

info:pmid/19597696 | info:doi/10.1007/s00792-009-0269-8

DNA polymerases: structural diversity and common mechanisms.

T A Steitz

The Journal of biological chemistry 274 (25), 17395-8 (18 Jun 1999)

Search: We searched for “Taq polymerase,” “Polymerase thermostability,” and “Taq polymerase structure.”

Tips:

You can find 3-dimensional protein structures in the “Structure” section of NCBI.

Questions:

There seems to be limited information of specifically what properties allow certain polymerases to be more thermostable than others.

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