TY  - JOUR
A1  - Petruseva, Irina
A1  - Naumenko, Natalia
A1  - Kuper, Jochen
A1  - Anarbaev, Rashid
A1  - Kappenberger, Jeannette
A1  - Kisker, Caroline
A1  - Lavrik, Olga
T1  - The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage
JF  - Frontiers in Cell and Developmental Biology
N2  - The successful elimination of bulky DNA damages via the nucleotide excision repair (NER) system is largely determined by the damage recognition step. This step consists of primary recognition and verification of the damage. The TFIIH helicase XPD plays a key role in the verification step during NER. To date, the mechanism of damage verification is not sufficiently understood and requires further detailed research. This study is a systematic investigation of the interaction of ctXPD (Chaetomium thermophilum) as well as ctXPD-ctp44 with model DNAs, which contain structurally different bulky lesions with previously estimated NER repair efficiencies. We have used ATPase and DNA binding studies to assess the interaction of ctXPD with damaged DNA. The result of the analysis of ctXPD-ctp44 binding to DNA containing fluorescent and photoactivatable lesions demonstrates the relationship between the affinity of XPD for DNAs containing bulky damages and the ability of the NER system to eliminate the damage. Photo-cross-linking of ctXPD with DNA probes containing repairable and unrepairable photoactivatable damages reveals differences in the DNA interaction efficiency in the presence and absence of ctp44. In general, the results obtained indicate the ability of ctXPD-ctp44 to interact with a damage and suggest a significant role for ctp44 subunit in the verification process.
KW  - nucleotide excision repair
KW  - XPD helicase
KW  - DNA damage
KW  - protein-DNA interaction
KW  - bulky damages recognition
KW  - photo-cross-linking
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-231806
SN  - 2296-634X
VL  - 9
ER  - 
TY  - INPR
A1  - Neitz, Hermann
A1  - Bessi, Irene
A1  - Kuper, Jochen
A1  - Kisker, Caroline
A1  - Höbartner, Claudia
T1  - Programmable DNA interstrand crosslinking by alkene-alkyne [2+2] photocycloaddition
T2  - Journal of the American Chemical Society
N2  - Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2’-deoxyuridine (\(^{Phe}\)dU). The crosslinking ability of \(^{Phe}\)dU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2+2] cycloaddition within the DNA duplex, resulting in efficient formation of a \(^{Phe}\)dU-dimer after short irradiation times of a few seconds. A \(^{Phe}\)dU dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.
KW  - light-induced interstrand DNA crosslinking
KW  - alkene-alkyne [2+2] photocycloaddition
KW  - DNA-based nanostructures
KW  - DNA-processing enzymes
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-311822
N1  - This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Journal of the American Chemical Society, copyright © 2023 The Authors. Published by American Chemical Society. after peer review. To access the final edited and published work see https://doi.org/10.1021/jacs.3c01611.
ET  - submitted version
ER  -