Mispair-Aligned N3T-alkyl-N3T Interstrand Cross-Linked DNA:  Synthesis and Characterization of Duplexes with Interstrand Cross-Links of Variable Lengths

2004 ◽  
Vol 126 (30) ◽  
pp. 9257-9265 ◽  
Author(s):  
Christopher J. Wilds ◽  
Anne M. Noronha ◽  
Sebastien Robidoux ◽  
Paul S. Miller
Keyword(s):  
Dna Synthesis ◽  
Synthesis And Characterization ◽  
Interstrand Cross Links ◽  
Cross Links

N4C−Ethyl−N4C Cross-Linked DNA:  Synthesis and Characterization of Duplexes with Interstrand Cross-Links of Different Orientations†

Biochemistry ◽  
2002 ◽  
Vol 41 (3) ◽  
pp. 760-771 ◽  
Author(s):  
Anne M. Noronha ◽  
David M. Noll ◽  
Christopher J. Wilds ◽  
Paul S. Miller
Keyword(s):  
Dna Synthesis ◽  
Synthesis And Characterization ◽  
Interstrand Cross Links ◽  
Cross Links

scholarly journals Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA

2015 ◽  
Vol 43 (7) ◽  
pp. 3434-3441 ◽  
Author(s):  
Nathan E. Price ◽  
Michael J. Catalano ◽  
Shuo Liu ◽  
Yinsheng Wang ◽  
Kent S. Gates
Keyword(s):  
Structural Characterization ◽  
Duplex Dna ◽  
Abasic Sites ◽  
Interstrand Cross Links ◽  
Cross Links

scholarly journals Structural insight into FANCI–FANCD2 monoubiquitination

2020 ◽  
Vol 64 (5) ◽  
pp. 807-817 ◽  
Author(s):  
Landing Li ◽  
Winnie Tan ◽  
Andrew J. Deans
Keyword(s):  
Dna Repair ◽  
Bone Marrow Failure ◽  
Core Complex ◽  
Bone Marrow Failure Syndrome ◽  
Cryo Electron Microscopy ◽  
Ubiquitin Ligase Complex ◽  
Interstrand Cross Links ◽  
Cross Links ◽  
Made In

Abstract The Fanconi anemia (FA) pathway coordinates a faithful repair mechanism for DNA damage that blocks DNA replication, such as interstrand cross-links. A key step in the FA pathway is the conjugation of ubiquitin on to FANCD2 and FANCI, which is facilitated by a large E3 ubiquitin ligase complex called the FA core complex. Mutations in FANCD2, FANCI or FA core complex components cause the FA bone marrow failure syndrome. Despite the importance of these proteins to DNA repair and human disease, our molecular understanding of the FA pathway has been limited due to a deficit in structural studies. With the recent development in cryo-electron microscopy (EM), significant advances have been made in structural characterization of these proteins in the last 6 months. These structures, combined with new biochemical studies, now provide a more detailed understanding of how FANCD2 and FANCI are monoubiquitinated and how DNA repair may occur. In this review, we summarize these recent advances in the structural and molecular understanding of these key components in the FA pathway, compare the activation steps of FANCD2 and FANCI monoubiquitination and suggest molecular steps that are likely to be involved in regulating its activity.

scholarly journals Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1

Science ◽  
2014 ◽  
Vol 346 (6213) ◽  
pp. 1127-1130 ◽  
Author(s):  
Renjing Wang ◽  
Nicole S. Persky ◽  
Barney Yoo ◽  
Ouathek Ouerfelli ◽  
Agata Smogorzewska ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Crystal Structures ◽  
Dna Adducts ◽  
Fanconi Anemia ◽  
Biochemical Data ◽  
Degenerative Diseases ◽  
Cross Link ◽  
Interstrand Cross Links ◽  
Cross Links

DNA interstrand cross-links (ICLs) are highly toxic lesions associated with cancer and degenerative diseases. ICLs can be repaired by the Fanconi anemia (FA) pathway and through FA-independent processes involving the FAN1 nuclease. In this work, FAN1-DNA crystal structures and biochemical data reveal that human FAN1 cleaves DNA successively at every third nucleotide. In vitro, this exonuclease mechanism allows FAN1 to excise an ICL from one strand through flanking incisions. DNA access requires a 5′-terminal phosphate anchor at a nick or a 1- or 2-nucleotide flap and is augmented by a 3′ flap, suggesting that FAN1 action is coupled to DNA synthesis or recombination. FAN1’s mechanism of ICL excision is well suited for processing other localized DNA adducts as well.

scholarly journals DNA Interstrand Cross-Links Induce Futile Repair Synthesis in Mammalian Cell Extracts

2000 ◽  
Vol 20 (7) ◽  
pp. 2446-2454 ◽  
Author(s):  
David Mu ◽  
Tadayoshi Bessho ◽  
Lubomir V. Nechev ◽  
David J. Chen ◽  
Thomas M. Harris ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Excision Repair ◽  
Mutant Cell ◽  
Complex Structure ◽  
Cross Link ◽  
Repair Synthesis ◽  
Cell Extracts ◽  
Interstrand Cross Links ◽  
Cross Links ◽  
The Cross

ABSTRACT DNA interstrand cross-links are induced by many carcinogens and anticancer drugs. It was previously shown that mammalian DNA excision repair nuclease makes dual incisions 5′ to the cross-linked base of a psoralen cross-link, generating a gap of 22 to 28 nucleotides adjacent to the cross-link. We wished to find the fates of the gap and the cross-link in this complex structure under conditions conducive to repair synthesis, using cell extracts from wild-type and cross-linker-sensitive mutant cell lines. We found that the extracts from both types of strains filled in the gap but were severely defective in ligating the resulting nick and incapable of removing the cross-link. The net result was a futile damage-induced DNA synthesis which converted a gap into a nick without removing the damage. In addition, in this study, we showed that the structure-specific endonuclease, the XPF-ERCC1 heterodimer, acted as a 3′-to-5′ exonuclease on cross-linked DNA in the presence of RPA. Collectively, these observations shed some light on the cellular processing of DNA cross-links and reveal that cross-links induce a futile DNA synthesis cycle that may constitute a signal for specific cellular responses to cross-linked DNA.

scholarly journals Interstrand Cross-Links Induce DNA Synthesis in Damaged and Undamaged Plasmids in Mammalian Cell Extracts

1999 ◽  
Vol 19 (8) ◽  
pp. 5619-5630 ◽  
Author(s):  
Lei Li ◽  
Carolyn A. Peterson ◽  
Xiaoyan Lu ◽  
Ping Wei ◽  
Randy J. Legerski
Keyword(s):  
Dna Synthesis ◽  
Mammalian Cell ◽  
Functional Characterization ◽  
Complementation Group ◽  
Cross Link ◽  
Repair Synthesis ◽  
Cell Extracts ◽  
Interstrand Cross Links ◽  
Cross Links ◽  
Dna Repair Synthesis

ABSTRACT Mammalian cell extracts have been shown to carry out damage-specific DNA repair synthesis induced by a variety of lesions, including those created by UV and cisplatin. Here, we show that a single psoralen interstrand cross-link induces DNA synthesis in both the damaged plasmid and a second homologous unmodified plasmid coincubated in the extract. The presence of the second plasmid strongly stimulates repair synthesis in the cross-linked plasmid. Heterologous DNAs also stimulate repair synthesis to variable extents. Psoralen monoadducts and double-strand breaks do not induce repair synthesis in the unmodified plasmid, indicating that such incorporation is specific to interstrand cross-links. This induced repair synthesis is consistent with previous evidence indicating a recombinational mode of repair for interstrand cross-links. DNA synthesis is compromised in extracts from mutants (deficient in ERCC1, XPF, XRCC2, and XRCC3) which are all sensitive to DNA cross-linking agents but is normal in extracts from mutants (XP-A, XP-C, and XP-G) which are much less sensitive. Extracts from Fanconi anemia cells exhibit an intermediate to wild-type level of activity dependent upon the complementation group. The DNA synthesis deficit in ERCC1- and XPF-deficient extracts is restored by addition of purified ERCC1-XPF heterodimer. This system provides a biochemical assay for investigating mechanisms of interstrand cross-link repair and should also facilitate the identification and functional characterization of cellular proteins involved in repair of these lesions.

Photo-cleavable nucleotides for primer free enzyme mediated DNA synthesis

2016 ◽  
Vol 14 (35) ◽  
pp. 8278-8288 ◽  
Author(s):  
Anu Stella Mathews ◽  
Haikang Yang ◽  
Carlo Montemagno
Keyword(s):  
Dna Synthesis ◽  
Free Enzyme ◽  
Synthesis And Characterization

The synthesis and characterization of eight 3′-O modified 2′-deoxyribonucleoside triphosphates for template-less enzyme mediated photo-triggered “stop–start” DNA synthesis is presented.

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