Base excision repair-inspired DNA motor powered by intracellular apurinic/apyrimidinic endonuclease

Nanoscale ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 1343-1350 ◽  
Author(s):  
Lidan Li ◽  
Na Li ◽  
Shengnan Fu ◽  
Yingnan Deng ◽  
Changyuan Yu ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Living Cells ◽  
Ap Endonuclease ◽  
Base Excision

A DNA motor was operated in living cells by endogenous AP endonuclease.

Studies on the base excision repair (BER) complex in Pyrococcus furiosus

2009 ◽  
Vol 37 (1) ◽  
pp. 79-82 ◽  
Author(s):  
Shinichi Kiyonari ◽  
Saki Tahara ◽  
Maiko Uchimura ◽  
Tsuyoshi Shirai ◽  
Sonoko Ishino ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Pyrococcus Furiosus ◽  
Excision Repair ◽  
Repair Process ◽  
Nuclear Antigen ◽  
Physical Interaction ◽  
Ap Endonuclease ◽  
Reading Frame ◽  
Base Excision

We have been studying the functions of PCNA (proliferating-cell nuclear antigen) for the assembly and reassembly of the replisome during replication fork progression. We have identified the functional interactions between PCNA and several proteins involved in DNA replication and repair from Pyrococcus furiosus. We recently reported that the activity of UDG (uracil–DNA glycosylase) in P. furiosus (PfuUDG) is stimulated by PCNA (PfuPCNA) in vitro, and identified an atypical PCNA-binding site, AKTLF, in the PfuUDG protein. To understand further the function of the complex in the BER (base excision repair) process, we investigated the AP (apurinic/apyrimidinic) endonuclease, which can process the BER pathway after uracil removal by UDG. Interestingly, one candidate ORF (open reading frame) for the AP endonuclease was found in the operon containing the gene encoding UDG in the P. furiosus genome. However, this ORF did not exhibit any activity. Instead, we identified the AP endonuclease activity from the other candidate gene products, and designated the protein as PfuAP. We discovered a physical interaction between PfuAP and PfuPCNA, suggesting the formation of a BER complex in one of the repair systems in P. furiosus.

scholarly journals A novel regulatory circuit in base excision repair involving AP endonuclease 1, Creb1 and DNA polymerase β

2010 ◽  
Vol 39 (8) ◽  
pp. 3156-3165 ◽  
Author(s):  
De-Sheng Pei ◽  
Xiao-Jie Yang ◽  
Wei Liu ◽  
Jeroen E. J. Guikema ◽  
Carol E. Schrader ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Dna Polymerase Β ◽  
Ap Endonuclease ◽  
Regulatory Circuit ◽  
Ap Endonuclease 1 ◽  
Base Excision

scholarly journals Spontaneous Mutagenesis Is Enhanced in Apex Heterozygous Mice

2004 ◽  
Vol 24 (18) ◽  
pp. 8145-8153 ◽  
Author(s):  
Jessica Huamani ◽  
C. Alex McMahan ◽  
Damon C. Herbert ◽  
Robert Reddick ◽  
John R. McCarrey ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Germ Line ◽  
Excision Repair ◽  
Spontaneous Mutant ◽  
Spermatogenic Cells ◽  
Ap Endonuclease ◽  
Repair Activity ◽  
Base Excision ◽  
Mutant Frequency

ABSTRACT Germ line DNA directs the development of the next generation and, as such, is profoundly different from somatic cell DNA. Spermatogenic cells obtained from young adult lacI transgenic mice display a lower spontaneous mutant frequency and greater in vitro base excision repair activity than somatic cells and tissues obtained from the same mice. However, spermatogenic cells from old lacI mice display a 10-fold higher mutant frequency. This increased spontaneous mutant frequency occurs coincidentally with decreased in vitro base excision repair activity for germ cell and testicular extracts that in turn corresponds to a decreased abundance of AP endonuclease. To directly test whether a genetic diminution of AP endonuclease results in increased spontaneous mutant frequencies in spermatogenic cell types, AP endonuclease heterozygous (Apex +/−) knockout mice were crossed with lacI transgenic mice. Spontaneous mutant frequencies were significantly elevated (approximately twofold) for liver and spleen obtained from 3-month-old Apex +/− lacI + mice compared to frequencies from Apex +/+ lacI + littermates and were additionally elevated for somatic tissues from 9-month-old mice. Spermatogenic cells from 9-month-old Apex +/− lacI + mice were significantly elevated twofold compared to levels for 9-month-old Apex +/+ lacI + control mice. These data indicate that diminution of AP endonuclease has a significant effect on spontaneous mutagenesis in somatic and germ line cells.

AP endonuclease and poly(ADP-ribose) polymerase-1 interact with the same base excision repair intermediate

DNA Repair ◽  
2004 ◽  
Vol 3 (6) ◽  
pp. 581-591 ◽  
Author(s):  
Cheryl Cistulli ◽  
Olga I Lavrik ◽  
Rajendra Prasad ◽  
Esther Hou ◽  
Samuel H Wilson
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Ap Endonuclease ◽  
Base Excision

scholarly journals The mechanism of gap creation by a multifunctional nuclease during base excision repair

2021 ◽  
Vol 7 (29) ◽  
pp. eabg0076
Author(s):  
Jungmin Yoo ◽  
Donghun Lee ◽  
Hyeryeon Im ◽  
Sangmi Ji ◽  
Sanghoon Oh ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Single Molecule ◽  
Excision Repair ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Ap Endonuclease ◽  
Base Excision ◽  
Polymerase I ◽  
Gap Creation ◽  
Ap Site

During base excision repair, a transient single-stranded DNA (ssDNA) gap is produced at the apurinic/apyrimidinic (AP) site. Exonuclease III, capable of performing both AP endonuclease and exonuclease activity, are responsible for gap creation in bacteria. We used single-molecule fluorescence resonance energy transfer to examine the mechanism of gap creation. We found an AP site anchor-based mechanism by which the intrinsically distributive enzyme binds strongly to the AP site and becomes a processive enzyme, rapidly creating a gap and an associated transient ssDNA loop. The gap size is determined by the rigidity of the ssDNA loop and the duplex stability of the DNA and is limited to a few nucleotides to maintain genomic stability. When the 3′ end is released from the AP endonuclease, polymerase I quickly initiates DNA synthesis and fills the gap. Our work provides previously unidentified insights into how a signal of DNA damage changes the enzymatic functions.

scholarly journals DNA polymerase β and PARP activities in base excision repair in living cells

DNA Repair ◽  
2009 ◽  
Vol 8 (11) ◽  
pp. 1290-1299 ◽  
Author(s):  
Aya Masaoka ◽  
Julie K. Horton ◽  
William A. Beard ◽  
Samuel H. Wilson
Keyword(s):  
Dna Polymerase ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Living Cells ◽  
Dna Polymerase Β ◽  
Base Excision
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