Sensing domain and extension rate of a family B-type DNA polymerase determine the stalling at a deaminated base

Yun Jae Kim, Sun Shin Cha, Hyun Sook Lee, Yong Gu Ryu, Seung Seob Bae, Yona Cho, Hyun Soo Cho, Sang Jin Kim, Suk Tae Kwon, Jung Hyun Lee, Sung Gyun Kang

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Abstract

The uracil-sensing domain in archaeal family B-type DNA polymerases recognizes pro-mutagenic uracils in the DNA template, leading to stalling of DNA polymerases. Here, we describe our new findings regarding the molecular mechanism underpinning the stalling of polymerases. We observed that two successive deaminated bases were required to stall TNA1 and KOD1 DNA polymerases, whereas a single deaminated base was enough for stalling Pfu DNA polymerase, in spite of the virtually identical uracil-sensing domains. TNA1 and KOD1 DNA polymerases have a much higher extension rate than Pfu DNA polymerase; decreasing the extension rate resulted in stalling by TNA1 and KOD1 DNA polymerases at a single deaminated base. These results strongly suggest that these polymerases require two factors to stop DNA polymerization at a single deaminated base: the presence of the uracil-sensing domain and a relatively slow extension rate.

Original languageEnglish
Pages (from-to)1377-1385
Number of pages9
JournalJournal of microbiology and biotechnology
Volume18
Issue number8
Publication statusPublished - 2008 Aug 28

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Applied Microbiology and Biotechnology

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    Kim, Y. J., Cha, S. S., Lee, H. S., Ryu, Y. G., Bae, S. S., Cho, Y., Cho, H. S., Kim, S. J., Kwon, S. T., Lee, J. H., & Kang, S. G. (2008). Sensing domain and extension rate of a family B-type DNA polymerase determine the stalling at a deaminated base. Journal of microbiology and biotechnology, 18(8), 1377-1385.