Dinoflagellates often incorporate 5-hmU into their genome; does this modification cause issues with PCR, such that we'd need to use uracil-incorporating polymerases, or is a normal high fidelity polymerase sufficient?
I am not an expert in this field, but I am very interested and have researched to find an answer. I received some assistance from tlooto.com for this response. Could you please review the response below to see if it is correct?
5-Hydroxymethyl uracil (5-hmU) can indeed cause problems with PCR because it can interfere with DNA polymerase binding efficiency and fidelity. Dinoflagellates, which often incorporate 5-hmU into their genome, may face amplification challenges, leading to potential misincorporations or incomplete extensions [1][2]. While normal high fidelity polymerases may struggle with this modification, uracil-incorporating polymerases are specifically designed to handle uracil and its derivatives. These specialized polymerases would likely improve the accuracy and efficiency of PCR reactions involving templates with 5-hmU, ensuring more reliable amplification [3][4].
Reference
[1] Rae, P. (1976). Hydroxymethyluracil in eukaryote DNA: a natural feature of the pyrrophyta (dinoflagellates).. Science, 194 4269, 1062-4 .
[2] Verma, A., Barua, A., Ruvindy, R., Savela, H., Ajani, P., & Murray, S. (2019). The Genetic Basis of Toxin Biosynthesis in Dinoflagellates. Microorganisms, 7.
[3] Orr, R. J. S., Stüken, A., Murray, S., & Jakobsen, K. (2013). Evolution and Distribution of Saxitoxin Biosynthesis in Dinoflagellates. Marine Drugs, 11, 2814 - 2828.
[4] Hudson, D. A., & Adlard, R. (1995). PCR techniques applied to Hematodinium spp. and Hematodinium-like dinoflagellates in decapod crustaceans. Diseases of Aquatic Organisms, 20, 203-206.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA