1. A role for DNA primase in coupling DNA replication to DNA damage response
Federica Marini, Achille Pellicioli, Vera Paciotti, Giovanna Lucchini, Paolo Plevani, David F. Stern, Marco Foiani
SUMMARY: The temperature-sensitive yeast DNA primase mutant pri1-M4 fails to execute an early step of DNA replication and exhibits a dominant, allele-specific sensitivity to DNA-damaging
CONTEXT: Introduction Eukaryotic cells have developed a network of highly conserved surveillance mechanisms (checkpoints), ensuring that damaged chromosomes are repaired before being replicated or segregated. These mechanisms are essential for...
The EMBO Journal 16, 639 - 650 (01 Feb 1997), doi: 10.1093/emboj/16.3.639, Article
2. Ku protein stimulates DNA end joining by mammalian DNA ligases: a direct role for Ku in repair of DNA double-strand breaks
Dale A. Ramsden, Martin Gellert
SUMMARY: Ku protein binds to DNA ends and is a cofactor for the DNA-dependent protein kinase. Both of these components are involved in DNA double-strand
CONTEXT: Introduction DNA double-strand breaks (DSBs) result from a variety of exogenous DNA-damaging agents, such as ionizing radiation. They are repaired either by using an intact copy of the broken region as a template (homologous...
The EMBO Journal 17, 609 - 614 (15 Jan 1998), doi: 10.1093/emboj/17.2.609, Article
3. Replication-mediated DNA damage by camptothecin induces phosphorylation of RPA by DNA-dependent protein kinase and dissociates RPA:DNA-PK complexes
Rong-Guang Shao, Chun-Xia Cao, Hongliang Zhang, Kurt W. Kohn, Marc S. Wold, Yves Pommier
SUMMARY: Replication protein A (RPA) is a DNA single-strand binding protein essential for DNA replication, recombination and repair. In human cells treated with the topoisomerase
CONTEXT: Introduction Replication protein A (RPA) is an ubiquitous eukaryotic single-stranded DNA (ssDNA)-binding protein complex, which was originally identified as an essential factor for simian virus 40 (SV40) DNA replication in vitro (Wobbe...
The EMBO Journal 18, 1397 - 1406 (01 Mar 1999), doi: 10.1093/emboj/18.5.1397, Article
4. Human DNA polymerase β initiates DNA synthesis during long-patch repair of reduced AP sites in DNA
Andrej Ja. Podlutsky, Irina I. Dianova, Vladimir N. Podust, Vilhelm A. Bohr, Grigory L. Dianov
SUMMARY: Simple base damages are repaired through a short-patch base excision pathway where a single damaged nucleotide is removed and replaced. DNA polymerase β (Pol
CONTEXT: Introduction Abasic (apurinic/apyrimidinic, AP) sites can arise in DNA as a result of spontaneous hydrolysis of the N-glycosylic bond or the removal of altered bases by DNA glycosylases (Lindahl, 1993). It has been estimated that 10 000...
The EMBO Journal 20, 1477 - 1482 (15 Mar 2001), doi: 10.1093/emboj/20.6.1477, Article
5. MOT1-catalyzed TBP–DNA disruption: uncoupling DNA conformational change and role of upstream DNA
Russell P. Darst, Dongyan Wang, David T. Auble
SUMMARY: SNF2/SWI2-related ATPases employ ATP hydrolysis to disrupt protein–DNA interactions, but how ATP hydrolysis is coupled to disruption is not understood. Here we examine the
CONTEXT: Introduction The ATPase activities of SNF2/SWI2-related proteins are of at least two types (Pazin and Kadonaga, 1997; Vignali et al., 2000). Many proteins in this family possess DNA-stimulated ATPase activity. ATPases with DNA-stimulated...
The EMBO Journal 20, 2028 - 2040 (17 Apr 2001), doi: 10.1093/emboj/20.8.2028, Article
6. Crystal structure of the CENP-B protein–DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA
Yoshinori Tanaka, Osamu Nureki, Hitoshi Kurumizaka, Shuya Fukai, Shinichi Kawaguchi, Mari Ikuta, Junji Iwahara, Tsuneko Okazaki, Shigeyuki Yokoyama
SUMMARY: The human centromere protein B (CENP-B), one of the centromere components, specifically binds a 17 bp sequence (the CENP-B box), which appears in every
CONTEXT: Introduction The centromere is a region of the chromosome essential for its segregation during cell division, and has a special chromatin structure involving -satellite DNA repeats and their associated proteins. In the human, the...
The EMBO Journal 20, 6612 - 6618 (03 Dec 2001), doi: 10.1093/emboj/20.23.6612, Article
7. Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs
Jasminka Boskovic, Angel Rivera-Calzada, Joseph D. Maman, Pablo Chacón, Keith R. Willison, Laurence H. Pearl, Oscar Llorca
SUMMARY: The catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) is essential for the repair of double-stranded DNA breaks (DSBs) in non- homologous end joining
CONTEXT: Introduction DNA is constantly being exposed to insults that compromise its integrity and its information content. Ionizing radiation and some chemotherapeutic drugs generate double-stranded DNA breaks (DSBs) that must be repaired to...
The EMBO Journal 22, 5875 - 5882 (03 Nov 2003), doi: 10.1093/emboj/cdg555, Article
8. Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV
Christine Anne Koch, Roger Agyei, Sarah Galicia, Pavel Metalnikov, Paul O'Donnell, Andrei Starostine, Michael Weinfeld, Daniel Durocher
SUMMARY: Nonhomologous end joining (NHEJ) is the major DNA double-strand break (DSB) repair pathway in mammalian cells. A critical step in this process is DNA
CONTEXT: Introduction DNA double-strand breaks (DSBs) pose a major threat to cell survival and genome stability. If left unrepaired, DSBs can result in the loss of genetic material or cell death. Moreover, mutations or gross genetic aberrations...
The EMBO Journal 23, 3874 - 3885 (29 Sep 2004), doi: 10.1038/sj.emboj.7600375, Article
9. DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC–DNA binding
Dirk Remus, Eileen L Beall, Michael R Botchan
SUMMARY: Drosophila origin recognition complex (ORC) localizes to defined positions on chromosomes, and in follicle cells the chorion gene amplification loci are well-studied examples. However,
CONTEXT: Introduction In a eukaryotic cell committed to duplication, chromosomal DNA replication initiates at many sites called origins of DNA replication. The process that determines origin selection is understood in some depth for fungal...
The EMBO Journal 23, 897 - 907 (25 Feb 2004), doi: 10.1038/sj.emboj.7600077, Article
10. p53 is involved in regulation of the DNA repair gene O6-methylguanine-DNA methyltransferase (MGMT) by DNA damaging agents
Thomas Grombacher, Uta Eichhorn, Bernd Kaina
SUMMARY: The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) is inducible by genotoxic stress. MGMT induction results from transcriptional activation of the MGMT gene which is
CONTEXT: C:\WINDOWS>echo off
Oncogene 17, 845 - 851 (18 Aug 1998), doi: 10.1038/sj.onc.1202000, Original Article
11. Structure of the Elk-1–DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA
SUMMARY: SAP-1 and Elk-1 are members of a large group of eukaryotic transcription factors that contain a conserved ETS DNA binding domain and that cooperate
CONTEXT: The ETS (E26 transformation specific or E twenty-six) domain transcription factors form a family of eukaryotic proteins with highly conserved DNA binding domains and as such are used as a paradigm for studying DNA binding specificity....
Nature Structural Biology 7, 292 - 297 (01 Apr 2000), doi: 10.1038/74055, Letters
12. A DNA-dependent DNA Polymerase and a DNA Endonuclease in Virions of Rous Sarcoma Virus
SATOSHI MIZUTANI, DAVID BOETTIGER, HOWARD M. TEMIN
SUMMARY: The virion contains a DNA-dependent DNA polymerase which replicates duplex DNA and an endonuclease which attacks it. A ligase system may also be present.
CONTEXT: The virion contains a DNA-dependent DNA polymerase which replicates duplex DNA and an endonuclease which attacks it. A ligase system may also be present. THE replication of RNA tumour viruses seems to involve a DNA intermediate-the DNA...
Nature 228, 424 - 427 (31 Oct 1970), doi: 10.1038/228424a0, Article
13. DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination
Clifford D. Mol, Tadahide Izumi, Sankar Mitra, John A. Tainer
SUMMARY: Non-coding apurinic/apyrimidinic (AP) sites in DNA are continually created in cells both spontaneously and by damage-specific DNA glycosylases. The biologically critical human base excision repa
CONTEXT: Non-coding apurinic/apyrimidinic (AP) sites in DNA are continually created in cells both spontaneously and by damage-specific DNA glycosylases. The biologically critical human base excision repair enzyme APE1 cleaves the DNA...
Nature 403, 451 - 456 (27 Jan 2000), doi: 10.1038/35000249, Letter
14. Apoptotic DNA fragmentation is detected by a semi-quantitative ligation-mediated PCR of blunt DNA ends
Kristina Staley, Anne J Blaschke, Jerold Chun
SUMMARY: Apoptosis is a form of programmed cell death (PCD) characterized by morphological changes and stereotypical DNA degradation described as a nucleosomal `ladder'. However, nucleosomal
CONTEXT: C:\WINDOWS>echo off
Cell Death and Differentiation 4, 66 - 75 (04 Dec 1996), doi: 10.1038/sj.cdd.4400207, Original Article
15. Genetic interaction between DNA polymerase β and DNA-PKcs in embryogenesis and neurogenesis
N Niimi,
SUMMARY: DNA polymerase β (Polβ) has been implicated in base excision repair. Polβ knockout mice exhibit apoptosis in postmitotic neuronal cells and die at birth.
CONTEXT: Introduction The genome is continuously damaged by a variety of endogenous and exogenous agents. Repair of such damage is a crucial mechanism for maintaining genomic integrity. A failure in faithful repair causes mutations with an...
Cell Death and Differentiation 12, 184 - 191 (01 Feb 2005), doi: 10.1038/sj.cdd.4401543, Original Paper
16. Retroviral DNA integration and the DNA damage response
A M Skalka, R A Katz
SUMMARY: Retroviral DNA integration creates a discontinuity in the host cell chromatin and repair of this damage is required to complete the integration process. As
CONTEXT: Introduction Viruses are obligate parasites that require host cell functions for their survival and propagation. Successful viruses have evolved mechanisms to exploit and/or counteract host defense systems, and modify or redirect normal...
Cell Death and Differentiation 12, 971 - 978 (01 Aug 2005), doi: 10.1038/sj.cdd.4401573, Reviews
17. DNA vaccination with AFP-encoding plasmid DNA prevents growth of subcutaneous AFP-expressing tumors and does not interfere with liver regeneration in mice
SUMMARY: The oncofetal alpha-fetoprotein (AFP) is reexpressed in the majority of hepatocellular carcinomas and may be used as a target molecule for an immunotherapy or
CONTEXT: Hepatocellular carcinoma (HCC) is a common malignancy with a very poor prognosis. Only a minority of patients are eligible for surgical therapies due to advanced tumors or extrahepatic disease at primary diagnosis.1,2 Therefore, novel...
Cancer Gene Therapy 9, 346 - 355 (03 Apr 2002), doi: 10.1038/sj.cgt.7700445, Original Article
18. A novel protein-DNA interaction involved with the CpG dinucleotide at -30 upstream is linked to the DNA methylation mediated transcription silencing of the MAGE-A1 gene
Jie ZHANG, Jian YU, Jun GU, Bao Mei GAO, Ying Jun ZHAO, Peng WANG, Hong Yu ZHANG, Jing De ZHU
SUMMARY: ABSTRACT To understand the DNA-methylation mediated gene silencing mechanisms, we analyzed in cell culture of the promoter function of the MAGE-A1 gene, which is frequently
CONTEXT: INTRODUCTION Addition of a methyl group at the fifth carbon of the cytosine in the CpG dinucleotide is the sole covalent modification of DNA in vertebrate genome and recognized as an important epigenetic signature 1. The vital importance...
Cell Research 14, 283 - 294 (00 Aug 2004), doi: 10.1038/sj.cr.7290229, Article
19. LDFF, the large molecular weight DNA fragmentation factor, is responsible for the large molecular weight DNA degradation during apoptosis in Xenopus egg extracts
Zhi Gang LU, Chuan Mao ZHANG, Zhong He ZHAI
SUMMARY: ABSTRACT DNA degradation is a biochemical hallmark in apoptosis. It has been demonstrated in many cell types that there are two stages of DNA fragmentation
CONTEXT: INTRODUCTION Apoptosis, a morphologically distinct form of programmed cell death, has attracted considerable attention for its implicated roles in embryonic development, tissue homeostasis and protection against diseases. A cell in...
Cell Research 14, 134 - 140 (00 Apr 2004), doi: 10.1038/sj.cr.7290212, Article
20. Homologous recombination in DNA repair and DNA damage tolerance
Xuan Li, Wolf-Dietrich Heyer
SUMMARY: Homologous recombination (HR) comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks (DSBs) and interstrand crosslinks (ICLs). In addition, recombi
CONTEXT: Introduction DNA damage is a fact of life as a consequence of endogenous sources and processes as well as exogenous sources 1. Homologous recombination (HR) is a DNA metabolic process found in all forms of life that provides...
Cell Research 18, 99 - 113 (07 Jan 2008), doi: 10.1038/cr.2008.1, Review
21. XRCC1 and DNA polymerase [beta] in cellular protection against cytotoxic DNA single-strand breaks
Julie K Horton, Mary Watson, Donna F Stefanick, Daniel T Shaughnessy, Jack A Taylor, Samuel H Wilson
SUMMARY: Single-strand breaks (SSBs) can occur in cells either directly, or indirectly following initiation of base excision repair (BER). SSBs generally have blocked termini lacking the conventional 5|[
CONTEXT: Introduction Cells have evolved intricate DNA repair mechanisms to circumvent genomic instability. Thousands of spontaneous single-strand breaks (SSBs) occur in cellular DNA each day 1 and, if they persist, can convert to potentially...
Cell Research 18, 48 - 63 (07 Jan 2008), doi: 10.1038/cr.2008.7, Review
22. Cell polarity protein Par3 complexes with DNA-PK via Ku70 and regulates DNA double-strand break repair
Longhou Fang, YiGuo Wang, Dan Du, Guang Yang, Tim Tak Kwok, Siu Kai Kong, Benjamin Chen, David J Chen, Zhengjun Chen
SUMMARY: The partitioning-defective 3 (Par3), a key component in the conserved Par3/Par6/aPKC complex, plays fundamental roles in cell polarity. Herein we report the identification of
CONTEXT: Introduction Cell polarity is vital for the development of multicellular organisms and for the proper functions of epithelial cells in different organs. Polarity in epithelial cells is characterized by different lipid and protein...
Cell Research 17, 100 - 116 (01 Feb 2007), doi: 10.1038/sj.cr.7310145, Original Article
23. Sensitivity of markers of DNA stability and DNA repair activity to folate supplementation in healthy volunteers
G P Basten, S J Duthie, L Pirie,
SUMMARY: We have previously reported that supplementation with folic acid (1.2 mg day-1 for 12 week) elicited a significant improvement in the folate status of 61 healthy
CONTEXT: Epidemiological studies have consistently revealed an association between the consumption of fruit and vegetables and reduced incidence of cancers at various sites. Although the active dietary components have not been identified, folate...
British Journal of Cancer 94, 1942 - 1947 (19 Jun 2006), doi: 10.1038/sj.bjc.6603197, Genetics And Genomics
24. Brostallicin (PNU-166196) – a new DNA minor groove binder that retains sensitivity in DNA mismatch repair-deficient tumour cells
A Fedier, C Fowst, J Tursi, C Geroni, U Haller,
SUMMARY: Defects in DNA mismatch repair (MMR) are associated with a predisposition to tumorigenesis and with drug resistance owing to high mutation rates and failure
CONTEXT: Minor groove binders (MGBs) represent an interesting class of anticancer agents, which have been shown to be highly effective in in vitro and in vivo preclinical tumour models unresponsive to other antineoplastic agents (Martin et al,...
British Journal of Cancer 89, 1559 - 1565 (20 Oct 2003), doi: 10.1038/sj.bjc.6601316, Experimental Therapeutics
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