scholarly journals The A-Rule and Deletion Formation During Abasic and Oxidized Abasic Site Bypass by DNA Polymerase θ

2017 ◽  
Vol 12 (6) ◽  
pp. 1584-1592 ◽  
Author(s):  
Daniel J. Laverty ◽  
April M. Averill ◽  
Sylvie Doublié ◽  
Marc M. Greenberg
Keyword(s):  
Dna Polymerase ◽  
Abasic Site ◽  
Deletion Formation ◽  
Oxidized Abasic Site

scholarly journals Biotinylation of Deoxyguanosine at the Abasic Site in Double-Stranded Oligodeoxynucleotides

2016 ◽  
Vol 2016 ◽  
pp. 1-4
Author(s):  
Chun Wu
Keyword(s):  
Dna Polymerase ◽  
Click Reaction ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Sequencing Analysis ◽  
Abasic Site ◽  
Nylon Membrane ◽  
Abasic Sites ◽  
Polymerase Chain ◽  
Dna Sequencing Analysis ◽  
Endonuclease Digestion

Biotinylation of deoxyguanosine at an abasic site in double-stranded oligodeoxynucleotides was studied. The biotinylation of deoxyguanosine is achieved by copper-catalyzed click reaction after the conjugation of the oligodeoxynucleotide with 2-oxohex-5-ynal. The biotinylation enables visualization of the biotinylated oligodeoxynucleotides by chemiluminescence on a nylon membrane. In order to investigate the biotinylated site, the biotinylated oligodeoxynucleotides were amplified by the DNA polymerase chain reaction. Replacement of guanine opposing the abasic site with adenine generated by the activity of the terminal deoxynucleotidyl transferase of DNA polymerase was detected by DNA sequencing analysis and restriction endonuclease digestion. This study suggests that 2-oxohex-5-ynal may be useful for the detection of the unpaired deoxyguanosine endogenously generated at abasic sites in genomic DNA.

scholarly journals Error-prone bypass of certain DNA lesions by the human DNA polymerase κ

2000 ◽  
Vol 14 (13) ◽  
pp. 1589-1594 ◽  
Author(s):  
Eiji Ohashi ◽  
Tomoo Ogi ◽  
Rika Kusumoto ◽  
Shigenori Iwai ◽  
Chikahide Masutani ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
High Frequency ◽  
Dna Lesions ◽  
Human Homolog ◽  
Abasic Site ◽  
Thymine Dimer ◽  
Human Dna

The Escherichia coli protein DinB is a newly identified error-prone DNA polymerase. Recently, a human homolog of DinB was identified and named DINB1. We report that the DINB1gene encodes a DNA polymerase (designated polκ), which incorporates mismatched bases on a nondamaged template with a high frequency. Moreover, polκ bypasses an abasic site andN-2–acetylaminofluorene (AAF)-adduct in an error-prone manner but does not bypass a cis–syn or (6-4) thymine–thymine dimer or a cisplatin-adduct. Therefore, our results implicate an important role for polκ in the mutagenic bypass of certain types of DNA lesions.

scholarly journals MSH2–MSH6 stimulates DNA polymerase η, suggesting a role for A:T mutations in antibody genes

2005 ◽  
Vol 201 (4) ◽  
pp. 637-645 ◽  
Author(s):  
Teresa M. Wilson ◽  
Alexandra Vaisman ◽  
Stella A. Martomo ◽  
Patsa Sullivan ◽  
Li Lan ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Base Excision Repair ◽  
Somatic Hypermutation ◽  
Excision Repair ◽  
Cytidine Deaminase ◽  
Abasic Site ◽  
Cell Extracts ◽  
Activation Induced Cytidine Deaminase ◽  
Base Excision

Activation-induced cytidine deaminase deaminates cytosine to uracil (dU) in DNA, which leads to mutations at C:G basepairs in immunoglobulin genes during somatic hypermutation. The mechanism that generates mutations at A:T basepairs, however, remains unclear. It appears to require the MSH2–MSH6 mismatch repair heterodimer and DNA polymerase (pol) η, as mutations of A:T are decreased in mice and humans lacking these proteins. Here, we demonstrate that these proteins interact physically and functionally. First, we show that MSH2–MSH6 binds to a U:G mismatch but not to other DNA intermediates produced during base excision repair of dUs, including an abasic site and a deoxyribose phosphate group. Second, MSH2 binds to pol η in solution, and endogenous MSH2 associates with the pol in cell extracts. Third, MSH2–MSH6 stimulates the catalytic activity of pol η in vitro. These observations suggest that the interaction between MSH2–MSH6 and DNA pol η stimulates synthesis of mutations at bases located downstream of the initial dU lesion, including A:T pairs.

Effects of the C4‘-Oxidized Abasic Site on Replication inEscherichia coli. An Unusually Large Deletion Is Induced by a Small Lesion†

Biochemistry ◽  
2004 ◽  
Vol 43 (43) ◽  
pp. 13621-13627 ◽  
Author(s):  
Kelly M. Kroeger ◽  
Jaeseung Kim ◽  
Myron F. Goodman ◽  
Marc M. Greenberg
Keyword(s):  
Large Deletion ◽  
Small Lesion ◽  
Inescherichia Coli ◽  
Abasic Site ◽  
Oxidized Abasic Site

scholarly journals Photochemical generation of C4′-oxidized abasic site containing oligonucleotide and its amine modification reaction

2006 ◽  
Vol 50 (1) ◽  
pp. 169-170
Author(s):  
Kazuteru Usui ◽  
Mariko Aso ◽  
Yukiko Toguchi ◽  
Yoshie Kakihara ◽  
Tsuyoshi Goromaru ◽  
...  
Keyword(s):  
Abasic Site ◽  
Photochemical Generation ◽  
Amine Modification ◽  
Oxidized Abasic Site

Protein interactions in T7 DNA replisome inhibit the bypass of abasic site by DNA polymerase

Mutagenesis ◽  
2019 ◽  
Author(s):  
Zhenyu Zou ◽  
Tingting Liang ◽  
Zhongyan Xu ◽  
Jiayu Xie ◽  
Shuming Zhang ◽  
...  
Keyword(s):  
Dna Replication ◽  
Dna Synthesis ◽  
Dna Polymerase ◽  
Protein Interactions ◽  
Accessory Proteins ◽  
Abasic Site ◽  
Traditional Concept ◽  
Translesion Dna Synthesis ◽  
Dna Lesion ◽  
Translesion Dna

Abstract Abasic site as a common DNA lesion blocks DNA replication and is highly mutagenic. Protein interactions in T7 DNA replisome facilitate DNA replication and translesion DNA synthesis. However, bypass of an abasic site by T7 DNA replisome has never been investigated. In this work, we used T7 DNA replisome and T7 DNA polymerase alone as two models to study DNA replication on encountering an abasic site. Relative to unmodified DNA, abasic site strongly inhibited primer extension and completely blocked strand-displacement DNA synthesis, due to the decreased fraction of enzyme–DNA productive complex and the reduced average extension rates. Moreover, abasic site at DNA fork inhibited the binding of DNA polymerase or helicase onto fork and the binding between polymerase and helicase at fork. Notably and unexpectedly, we found DNA polymerase alone bypassed an abasic site on primer/template (P/T) substrate more efficiently than did polymerase and helicase complex bypass it at fork. The presence of gp2.5 further inhibited the abasic site bypass at DNA fork. Kinetic analysis showed that this inhibition at fork relative to that on P/T was due to the decreased fraction of productive complex instead of the average extension rates. Therefore, we found that protein interactions in T7 DNA replisome inhibited the bypass of DNA lesion, different from all the traditional concept that protein interactions or accessory proteins always promote DNA replication and DNA damage bypass, providing new insights in translesion DNA synthesis performed by DNA replisome.

Identification of the C4′-Oxidized Abasic Site as the Most Abundant 2-Deoxyribose Lesion in Radiation-Damaged DNA Using a Novel HPLC-Based Approach

2014 ◽  
Vol 181 (2) ◽  
pp. 131 ◽  
Author(s):  
Marina Roginskaya ◽  
Reza Mohseni ◽  
Terence J. Moore ◽  
William A. Bernhard ◽  
Yuriy Razskazovskiy
Keyword(s):  
Abasic Site ◽  
Oxidized Abasic Site ◽  
Damaged Dna

In Vitro Replication and Repair of DNA Containing a C2‘-Oxidized Abasic Site†

Biochemistry ◽  
2004 ◽  
Vol 43 (48) ◽  
pp. 15217-15222 ◽  
Author(s):  
Marc M. Greenberg ◽  
Yvonne N. Weledji ◽  
Kelly M. Kroeger ◽  
Jaeseung Kim
Keyword(s):  
Abasic Site ◽  
In Vitro Replication ◽  
Oxidized Abasic Site
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