Wikipedia

Polymerase

Ribbon diagram representation of Taq DNA polymerase

In biochemistry, a polymerase is an enzyme (EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using base-pairing interactions or half ladder replication.

A DNA polymerase from the thermophilic bacterium, Thermus aquaticus (Taq) (PDB 1BGX, EC 2.7.7.7), is used in the polymerase chain reaction, an important technique of molecular biology.

A polymerase may be template-dependent or template-independent. Poly-A-polymerase is an example of template independent polymerase. Terminal deoxynucleotidyl transferase is also known to have template independent and template dependent activities.

By function

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Classes of Template dependent polymerase
Produces DNA Produces RNA
Template is DNA DNA-dependent DNA polymerase (DdDp)
or common DNA polymerases 		DNA-dependent RNA polymerase (DdRp)
or common RNA polymerases
Template is RNA RNA-dependent DNA polymerase (RdDp)
or Reverse transcriptase (RT) 		RNA-dependent RNA polymerase (RdRp)
or RNA-replicase

By structure

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Polymerases are generally split into two superfamilies, the "right hand" fold (InterPro: IPR043502) and the "double psi beta barrel" (often simply "double-barrel") fold. The former is seen in almost all DNA polymerases and almost all viral single-subunit polymerases; they are marked by a conserved "palm" domain.[2] The latter is seen in all multi-subunit RNA polymerases, in cRdRP, and in "family D" DNA polymerases found in archaea.[3][4] The "X" family represented by DNA polymerase beta has only a vague "palm" shape, and is sometimes considered a different superfamily (InterPro: IPR043519).[5]

Primases generally don't fall into either category. Bacterial primases usually have the Toprim domain, and are related to topoisomerases and mitochondrial helicase twinkle.[6] Archae and eukaryotic primases form an unrelated AEP family, possibly related to the polymerase palm. Both families nevertheless associate to the same set of helicases.[7]

  • Right hand structure of Bacteriophage RB69, a family B DdRP.
    Right hand structure of Bacteriophage RB69, a family B DdRP.

Modification of activity

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Scientists have modified the activity of nucleic acid polymerases in many ways, from rational design to directed evolution, to achieve changes from incremental tweaks like higher speed/accuracy/thermostability or major shifts such as conversion of template and product types.

Nucleic acid types

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All known natural reverse transcriptases evovled from an ancestor that has no proofreading ability, causing a low fidelity. In 2016, scientists successfully used directed evolution to modify the proofreading Thermococcus kodakarensis DNA-directed DNA polymerase into what they call a reverse transcribing xenotranscriptase (RTX). This new enzyme is able to copy from and proofread with RNA and DNA templates. It is expected to improve the accuracy in RNA sequencing and other forms of RT-PCR.[8] It was commercialized some time before April 2018.[9]

In 2022, selective mutagenesis converted a Kod DNA polymerase into one that produces α-l-threofuranosyl nucleic acid or threose nucleic acid (TNA).[10] This result has been improved in 2024 and 2025 using HR-accelerated directed evolution, yielding several enzymes with near-natural speed and fidelity.[11]

In 2025, scientists used directed evolution, accelerated by homologous recombination (HR), to change a DNA polymerase into an RNA polymerase. It is able to perform transcription quickly (3 nt/s) and accurately (>99%). It is also a somewhat "universal" polymerase, being also capable of RNA-directed DNA production (reverse transcription) and chimeric DNA–RNA amplification.[12]

See also

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References

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  1. ^ Loc'h J, Rosario S, Delarue M (September 2016). "Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination". Structure. 24 (9): 1452–63. doi:10.1016/j.str.2016.06.014. PMID 27499438.
  2. ^ Hansen JL, Long AM, Schultz SC (August 1997). "Structure of the RNA-dependent RNA polymerase of poliovirus". Structure. 5 (8): 1109–22. doi:10.1016/S0969-2126(97)00261-X. PMID 9309225.
  3. ^ Cramer P (February 2002). "Multisubunit RNA polymerases". Current Opinion in Structural Biology. 12 (1): 89–97. doi:10.1016/S0959-440X(02)00294-4. PMID 11839495.
  4. ^ Sauguet L (September 2019). "The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution". Journal of Molecular Biology. 431 (20): 4167–4183. doi:10.1016/j.jmb.2019.05.017. PMID 31103775.
  5. ^ Salgado PS, Koivunen MR, Makeyev EV, Bamford DH, Stuart DI, Grimes JM (December 2006). "The structure of an RNAi polymerase links RNA silencing and transcription". PLOS Biology. 4 (12): e434. doi:10.1371/journal.pbio.0040434. PMC 1750930. PMID 17147473.
  6. ^ Aravind L, Leipe DD, Koonin EV (September 1998). "Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins". Nucleic Acids Research. 26 (18): 4205–13. doi:10.1093/nar/26.18.4205. PMC 147817. PMID 9722641.
  7. ^ Iyer LM, Koonin EV, Leipe DD, Aravind L (2005). "Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members". Nucleic Acids Research. 33 (12): 3875–96. doi:10.1093/nar/gki702. PMC 1176014. PMID 16027112.
  8. ^ Ellefson, JW; Gollihar, J; Shroff, R; Shivram, H; Iyer, VR; Ellington, AD (24 June 2016). "Synthetic evolutionary origin of a proofreading reverse transcriptase". Science (New York, N.Y.). 352 (6293): 1590–3. doi:10.1126/science.aaf5409. PMID 27339990.
  9. ^ "WarmStart® RTx Reverse Transcriptase | NEB". www.neb.com.
  10. ^ Nikoomanzar, A; Vallejo, D; Yik, EJ; Chaput, JC (17 July 2020). "Programmed Allelic Mutagenesis of a DNA Polymerase with Single Amino Acid Resolution". ACS synthetic biology. 9 (7): 1873–1881. doi:10.1021/acssynbio.0c00236. PMID 32531152.
  11. ^ Hajjar, Mohammad; Maola, Victoria A.; Lee, Joy J.; Holguin, Manuel J.; Quijano, Riley N.; Nguyen, Kalvin K.; Ho, Katherine L.; Medina, Jenny V.; Botello-Cornejo, Elionel; Barpuzary, Bhawna; Chim, Nicholas; Chaput, John C. (19 December 2025). "Directed evolution of a TNA polymerase identifies independent paths to fidelity and catalysis". Nature Communications. doi:10.1038/s41467-025-67652-1.
  12. ^ Medina, EL; Maola, VA; Hajjar, M; Ko, GK; Ho, EJ; Horton, AR; Chim, N; Chaput, JC (7 January 2026). "Rapid evolution of a highly efficient RNA polymerase by homologous recombination". Nature chemical biology. doi:10.1038/s41589-025-02124-7. PMID 41501182.
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