title: Sensing domain and extension rate of a family B-type DNA polymerase determine the stalling at a deaminated base.
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.
authors.affiliation: Korea Ocean Research and Development Institute, Ansan P.O. Box 29, Seoul 425-600, Korea.
authors.forename: Yun Jae
authors.initials: YJ
authors.lastname: Kim
authors.forename: Sun-Shin
authors.initials: SS
authors.lastname: Cha
authors.forename: Hyun Sook
authors.initials: HS
authors.lastname: Lee
authors.forename: Yong Gu
authors.initials: YG
authors.lastname: Ryu
authors.forename: Seung Seob
authors.initials: SS
authors.lastname: Bae
authors.forename: Yona
authors.initials: Y
authors.lastname: Cho
authors.forename: Hyun-Soo
authors.initials: HS
authors.lastname: Cho
authors.forename: Sang-Jin
authors.initials: SJ
authors.lastname: Kim
authors.forename: Suk-Tae
authors.initials: ST
authors.lastname: Kwon
authors.forename: Jung-Hyun
authors.initials: JH
authors.lastname: Lee
authors.forename: Sung Gyun
authors.initials: SG
authors.lastname: Kang