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Wang J, Zhu J, Wang C, Zhou G, Yu X, Fan H, An R, Komiyama M, Liang X. Thermus thermophilus DNA Ligase Connects Two Fragments Having Exceptionally Short Complementary Termini at High Temperatures. Biochemistry 2020; 59:400-406. [PMID: 31887028 DOI: 10.1021/acs.biochem.9b00866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thermus thermophilus DNA ligase (Tth DNA ligase) is widely employed for cloning, enzymatic synthesis, and molecular diagnostics at high temperatures (e.g., 65 °C). It has been long believed that the complementary ends must be very long (e.g., >30 bp) to place two DNA fragments nearby for the ligation. In the current study, the length of the complementary portion was systematically varied, and the ligation efficiency was evaluated using the high resolution melting (HRM) method. Unexpectedly, very short oligonucleotides (7-10 nt) were successfully ligated on the complementary overhang attached to a dsDNA at 70 °C. Furthermore, sticky ends with the overhang of only 4 nt long, available after scission with many restriction enzymes, were also efficiently ligated at 45-70 °C. The ligation yield for the 6-nt-long sticky ends was as high as 80%. It was concluded that Tth DNA ligase can be used as a unique tool for DNA manipulation that cannot be otherwise easily accomplished.
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Affiliation(s)
- Jing Wang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,CAS Key laboratory of Marine Ecology and Environmental Sciences , Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 , China
| | - Jianming Zhu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Chenru Wang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Guangqing Zhou
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xin Yu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Huijun Fan
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003 , China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003 , China
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Bauer NC, Corbett AH, Doetsch PW. The current state of eukaryotic DNA base damage and repair. Nucleic Acids Res 2015; 43:10083-101. [PMID: 26519467 PMCID: PMC4666366 DOI: 10.1093/nar/gkv1136] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/16/2015] [Indexed: 12/15/2022] Open
Abstract
DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair.
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Affiliation(s)
- Nicholas C Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
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