scholarly journals Kinetic Investigation of Translesion Synthesis across a 3-Nitrobenzanthrone-Derived DNA Lesion Catalyzed by Human DNA Polymerase Kappa

2019 ◽  
Vol 32 (8) ◽  
pp. 1699-1706
Author(s):  
Kenneth K. Phi ◽  
Madison C. Smith ◽  
E. John Tokarsky ◽  
Zucai Suo
Keyword(s):  
Dna Polymerase ◽  
Translesion Synthesis ◽  
Kinetic Investigation ◽  
Dna Lesion ◽  
Human Dna

scholarly journals Translesion synthesis of the major nitrogen mustard-induced DNA lesion by human DNA polymerase η

2020 ◽  
Vol 477 (23) ◽  
pp. 4543-4558
Author(s):  
Hunmin Jung ◽  
Naveen Kumar Rayala ◽  
Seongmin Lee
Keyword(s):  
Dna Polymerase ◽  
Nitrogen Mustard ◽  
Alkylating Agents ◽  
Twist Angle ◽  
Translesion Synthesis ◽  
Major Groove ◽  
Dna Lesion ◽  
Human Dna ◽  
Interstrand Cross Links ◽  
A Site

Nitrogen mustards are among the first modern anticancer chemotherapeutics that are still widely used as non-specific anticancer alkylating agents. While the mechanism of action of mustard drugs involves the generation of DNA interstrand cross-links, the predominant lesions produced by these drugs are nitrogen half-mustard-N7-dG (NHMG) adducts. The bulky major groove lesion NHMG, if left unrepaired, can be bypassed by translesion synthesis (TLS) DNA polymerases. However, studies of the TLS past NHMG have not been reported so far. Here, we present the first synthesis of an oligonucleotide containing a site-specific NHMG. We also report kinetic and structural characterization of human DNA polymerase η (polη) bypassing NHMG. The templating NHMG slows dCTP incorporation ∼130-fold, while it increases the misincorporation frequency ∼10–30-fold, highlighting the promutagenic nature of NHMG. A crystal structure of polη incorporating dCTP opposite NHMG shows a Watson–Crick NHMG:dCTP base pair with a large propeller twist angle. The nitrogen half-mustard moiety fits snugly into an open cleft created by the Arg61–Trp64 loop of polη, suggesting a role of the Arg61–Trp64 loop in accommodating bulky major groove adducts during lesion bypass. Overall, our results presented here to provide first insights into the TLS of the major DNA adduct formed by nitrogen mustard drugs.

scholarly journals Bypass of the Major Alkylative DNA Lesion by Human DNA Polymerase η

Molecules ◽  
2019 ◽  
Vol 24 (21) ◽  
pp. 3928 ◽  
Author(s):  
Myong-Chul Koag ◽  
Hunmin Jung ◽  
Yi Kou ◽  
Seongmin Lee
Keyword(s):  
Dna Polymerase ◽  
Base Pair ◽  
Alkylating Agents ◽  
Dna Polymerases ◽  
Translesion Synthesis ◽  
Catalytic Site ◽  
Structural Basis ◽  
Dna Lesion ◽  
Human Dna ◽  
Wide Range

A wide range of endogenous and exogenous alkylating agents attack DNA to generate various alkylation adducts. N7-methyl-2-deoxyguanosine (Fm7dG) is the most abundant alkylative DNA lesion. If not repaired, Fm7dG can undergo spontaneous depurination, imidazole ring-opening, or bypass by translesion synthesis DNA polymerases. Human DNA polymerase η (polη) efficiently catalyzes across Fm7dG in vitro, but its structural basis is unknown. Herein, we report a crystal structure of polη in complex with templating Fm7dG and an incoming nonhydrolyzable dCTP analog, where a 2′-fluorine-mediated transition destabilization approach was used to prevent the spontaneous depurination of Fm7dG. The structure showed that polη readily accommodated the Fm7dG:dCTP base pair with little conformational change of protein and DNA. In the catalytic site, Fm7dG and dCTP formed three hydrogen bonds with a Watson–Crick geometry, indicating that the major keto tautomer of Fm7dG is involved in base pairing. The polη-Fm7dG:dCTP structure was essentially identical to the corresponding undamaged structure, which explained the efficient bypass of the major methylated lesion. Overall, the first structure of translesion synthesis DNA polymerase bypassing Fm7dG suggests that in the catalytic site of Y-family DNA polymerases, small N7-alkylguanine adducts may be well tolerated and form the canonical Watson–Crick base pair with dCTP through their keto tautomers.

Phenylalanine 171 is a molecular brake for translesion synthesis across benzo[a]pyrene-guanine adducts by human DNA polymerase kappa

2011 ◽  
Vol 718 (1-2) ◽  
pp. 10-17 ◽  
Author(s):  
Akira Sassa ◽  
Naoko Niimi ◽  
Hirofumi Fujimoto ◽  
Atsushi Katafuchi ◽  
Petr Grúz ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Translesion Synthesis ◽  
Human Dna ◽  
Guanine Adducts ◽  
Molecular Brake

scholarly journals DNA binding properties of human DNA polymerase η: implications for fidelity and polymerase switching of translesion synthesis

2004 ◽  
Vol 9 (12) ◽  
pp. 1139-1150 ◽  
Author(s):  
Rika Kusumoto ◽  
Chikahide Masutani ◽  
Shizu Shimmyo ◽  
Shigenori Iwai ◽  
Fumio Hanaoka
Keyword(s):  
Dna Binding ◽  
Dna Polymerase ◽  
Translesion Synthesis ◽  
Binding Properties ◽  
Human Dna ◽  
Dna Binding Properties

scholarly journals Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion

2012 ◽  
Vol 40 (18) ◽  
pp. 9193-9205 ◽  
Author(s):  
Lee Lior-Hoffmann ◽  
Lihua Wang ◽  
Shenglong Wang ◽  
Nicholas E. Geacintov ◽  
Suse Broyde ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Transfer Reaction ◽  
Catalytic Mechanism ◽  
Dna Lesion ◽  
Human Dna

scholarly journals Translesion Synthesis past Acrolein-derived DNA Adduct, γ-Hydroxypropanodeoxyguanosine, by Yeast and Human DNA Polymerase η

2002 ◽  
Vol 278 (2) ◽  
pp. 784-790 ◽  
Author(s):  
Irina G. Minko ◽  
M. Todd Washington ◽  
Manorama Kanuri ◽  
Louise Prakash ◽  
Satya Prakash ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Translesion Synthesis ◽  
Dna Adduct ◽  
Human Dna

scholarly journals Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion

2020 ◽  
Vol 477 (5) ◽  
pp. 937-951
Author(s):  
Hala Ouzon-Shubeita ◽  
Caroline K. Vilas ◽  
Seongmin Lee
Keyword(s):  
Dna Polymerase ◽  
Active Site ◽  
Cisplatin Resistance ◽  
Structural Basis ◽  
Abasic Site ◽  
Dna Polymerase Β ◽  
Dna Lesion ◽  
Human Dna ◽  
Optimal Conformation ◽  
Structural Insights

The cisplatin-1,2-d(GpG) (Pt-GG) intrastrand cross-link is the predominant DNA lesion generated by cisplatin. Cisplatin has been shown to predominantly induce G to T mutations and Pt-GG permits significant misincorporation of dATP by human DNA polymerase β (polβ). In agreement, polβ overexpression, which is frequently observed in cancer cells, is linked to cisplatin resistance and a mutator phenotype. However, the structural basis for the misincorporation of dATP opposite Pt-GG is unknown. Here, we report the first structures of a DNA polymerase inaccurately bypassing Pt-GG. We solved two structures of polβ misincorporating dATP opposite the 5′-dG of Pt-GG in the presence of Mg2+ or Mn2+. The Mg2+-bound structure exhibits a sub-optimal conformation for catalysis, while the Mn2+-bound structure is in a catalytically more favorable semi-closed conformation. In both structures, dATP does not form a coplanar base pairing with Pt-GG. In the polβ active site, the syn-dATP opposite Pt-GG appears to be stabilized by protein templating and pi stacking interactions, which resembles the polβ-mediated dATP incorporation opposite an abasic site. Overall, our results suggest that the templating Pt-GG in the polβ active site behaves like an abasic site, promoting the insertion of dATP in a non-instructional manner.

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