Special Issue "DNA Damage Response"
A special issue of Biomolecules (ISSN 2218-273X).
Deadline for manuscript submissions: closed (30 September 2012)
Prof. Dr. Wolf-Dietrich Heyer
Department of Microbiology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
Phone: +1 530 752 3001
Fax: +1 530 752 3011
Interests: regulation and mechanisms of homologous recombination; genome stability; DNA damage response
Prof. Dr. Thomas Helleday
1 Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford OX3 7DQ, UK
2 Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
Phone: +44 1865 617337
Fax: +44 1865 617334
Interests: DNA damage signalling; homologous recombination at replication forks in mammalian cells
Prof. Dr. Fumio Hanaoka
Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
Phone: +81 3 3986 0221 ext. 6457
Fax: +81 3 5992 1029
Interests: molecular mechanisms of translesion synthesis and nucleotide excision repair; understanding the cellular responses to DNA damages; interactions between cell cycle control and DNA repair
In two ground breaking publications in Science in 1988/1989, Ted Weinert and Lee Hartwell conceptualized many previous observations on how cells react to genotoxic stress by developing the checkpoint model. They validated the concept by isolating the first DNA damage checkpoint mutant in the budding yeast Saccharomyces cerevisiae and showing that RAD9 controlled transient cell cycle arrest after ionizing radiation exposure. These seminal discoveries propelled an entire field that is still thriving. We realize over 20 years later that the cell cycle response is only one, albeit critical aspect, of a much broader cellular answer to genotoxic stress that is now called the DNA Damage Response. This issue intends to showcase up to date reviews about emerging concepts from future leaders in this exciting area of research.
We thus invite submission review manuscripts (although original research manuscripts are welcome as well) that cover any aspect of the DNA damage response, a complex web of interconnected pathways that control many cellular processes including DNA replication, DNA repair, the mitotic and meiotic cell cycle, and nuclear architecture. The DNA damage response is intricately linked to cancer. Defects in the DNA damage response predispose humans to cancer, and many forms of anti-cancer treatment involve inducing localized or systemic DNA damage. Thus insights into the fundamental mechanisms of the DNA damage response are poised for translation into clinical practice.
We look forward to reading your contributions.
Prof. Dr. Wolf-Dietrich Heyer
Prof. Dr. Thomas Helleday
Prof. Dr. Fumio Hanaoka
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed Open Access quarterly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.
- DNA damage
- DNA checkpoints
- DNA repair
- DNA replication
- genome instability
- cell cycle control
Biomolecules 2012, 2(3), 376-388; doi:10.3390/biom2030376
Received: 1 August 2012; in revised form: 23 August 2012 / Accepted: 24 August 2012 / Published: 4 September 2012| Download PDF Full-text (680 KB) | Download XML Full-text
Biomolecules 2012, 2(4), 483-504; doi:10.3390/biom2040483
Received: 10 August 2012; in revised form: 5 October 2012 / Accepted: 8 October 2012 / Published: 16 October 2012| Download PDF Full-text (642 KB) | Download XML Full-text
Review: Preserving Yeast Genetic Heritage through DNA Damage Checkpoint Regulation and Telomere Maintenance
Biomolecules 2012, 2(4), 505-523; doi:10.3390/biom2040505
Received: 10 September 2012; in revised form: 10 October 2012 / Accepted: 22 October 2012 / Published: 30 October 2012| Download PDF Full-text (538 KB) | Download XML Full-text
Biomolecules 2012, 2(4), 524-548; doi:10.3390/biom2040524
Received: 18 September 2012; in revised form: 24 October 2012 / Accepted: 31 October 2012 / Published: 12 November 2012| Download PDF Full-text (594 KB) | Download XML Full-text
Article: Human DNA Glycosylase NEIL1’s Interactions with Downstream Repair Proteins Is Critical for Efficient Repair of Oxidized DNA Base Damage and Enhanced Cell Survival
Biomolecules 2012, 2(4), 564-578; doi:10.3390/biom2040564
Received: 15 October 2012; in revised form: 7 November 2012 / Accepted: 9 November 2012 / Published: 15 November 2012| Download PDF Full-text (833 KB) | Download XML Full-text
Biomolecules 2012, 2(4), 579-607; doi:10.3390/biom2040579
Received: 17 October 2012; in revised form: 17 November 2012 / Accepted: 23 November 2012 / Published: 30 November 2012| Download PDF Full-text (517 KB) | Download XML Full-text |
Article: Decorin Content and Near Infrared Spectroscopy Analysis of Dried Collagenous Biomaterial Samples
Biomolecules 2012, 2(4), 622-634; doi:10.3390/biom2040622
Received: 10 October 2012; in revised form: 30 November 2012 / Accepted: 3 December 2012 / Published: 14 December 2012| Download PDF Full-text (358 KB) | Download XML Full-text
Review: Strategies for the Use of Poly(adenosine diphosphate ribose) Polymerase (PARP) Inhibitors in Cancer Therapy
Biomolecules 2012, 2(4), 635-649; doi:10.3390/biom2040635
Received: 12 October 2012; in revised form: 29 November 2012 / Accepted: 9 December 2012 / Published: 14 December 2012| Download PDF Full-text (455 KB) | Download XML Full-text
Biomolecules 2013, 3(1), 1-17; doi:10.3390/biom3010001
Received: 24 October 2012; in revised form: 1 December 2012 / Accepted: 17 December 2012 / Published: 21 December 2012| Download PDF Full-text (414 KB) | Download XML Full-text
Biomolecules 2013, 3(1), 39-71; doi:10.3390/biom3010039
Received: 30 October 2012; in revised form: 11 December 2012 / Accepted: 11 December 2012 / Published: 27 December 2012| Download PDF Full-text (829 KB) | Download XML Full-text
Biomolecules 2013, 3(1), 75-84; doi:10.3390/biom3010075
Received: 3 December 2012; in revised form: 9 January 2013 / Accepted: 10 January 2013 / Published: 16 January 2013| Download PDF Full-text (397 KB) | Download XML Full-text
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Title: Homologous Recombination as a Replication Fork Escort: Fork-protection and Recovery
Authors: Audrey Costes 1,2 and Sarah Lambert 1,2
Affiliations: 1 Institut Curie, Centre de Recherche, France
2 CNRS, UMR3348, Centre Universitaire, Bat110, 91405, Orsay, France; E-Mail: firstname.lastname@example.org (S.L.)
Abstract: Homologous recombination is a universal mechanism that promotes DNA repair and supports DNA replication. The basic function of homologous recombination is to promote a strand exchange reaction that ultimately results in a genetic exchange. Thus, homologous recombination is a fundamental process promoting genetic diversity both during conjugation in prokaryotes and during meiosis in eukaryotes. Whereas the role of homologous recombination during the repair of double strand break has been extensively studies and it is now well characterized, the function of homologous recombination as a support for DNA replication remains poorly understood in eukaryotes. Nonetheless, studies in bacteria have enlightened multiple roles for homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving homologous recombination to support faithful DNA replication. Beyond its role in fork-repair and in rebuilding a functional replication fork apparatus, homologous recombination might also acts as a fork-protection mechanism. We speculate that this last function might be independent of the ability of homologous recombination to perform a strand exchange reaction and we refer to this mechanism as a Strand Exchange Free event (SEX-free recombination).
Type of Paper: Article
Title: Human DNA Glycosylase NEIL1’s Interactions with Downstream Repair Proteins Is Critical for Efficient Repair of Oxidized Genome Damage and Cell Survival
Authors: Muralidhar L. Hegde1,2, Pavana M. Hegde1, Arijit Dutta1 and Sankar Mitra1,3,*
Affiliations: 1 Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB) at Galveston, Texas 77555, USA
2 Departments of Neurology, University of Texas Medical Branch (UTMB) at Galveston, Texas 77555, USA
3 Departments of Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB) at Galveston, Texas 77555, USA; E-Mails: email@example.com (M.L.H.); firstname.lastname@example.org (P.M.H.); email@example.com (A.D.); firstname.lastname@example.org (S.M.)
Abstract: NEIL1 is unique among the oxidative base damage repair-initiating DNA glycosylases in the human genome for its S phase specific activation and ability to excise substrate base lesions from single-stranded DNA. We recently characterized NEIL1’s specific binding to several downstream conventional repair and non-canonical accessory proteins, all of which involves NEIL1’s disordered, C-terminal segment as the common interaction domain (CID). This domain is dispensable for NEIL1’s lesion excision and abasic (AP) lyase activities but is required for their enhancement via interactions with downstream partner proteins. Here, we show that truncated NEIL1 lacking the CID is markedly deficient in initiating in vitro repair of 5-hydroxyuracil (oxidative deamination product of C) present in a plasmid, compared to the wild type NEIL1, suggesting the critical role of CID in coordination of overall repair. Furthermore, while NEIL1 downregulation significantly sensitized human embryonic kidney (HEK) 293 cells to reactive oxygen species (ROS), as expected, ectopic wild type NEIL1, but not the truncated mutant, complemented ROS sensitivity. These results demonstrate that NEIL-dependent repair of oxidative DNA base damage and cell survival requires interaction among repair proteins which could be exploited as a therapeutic target in cancer for increasing the efficiency of chemo/radiation treatment.
Keywords: NEIL1; DNA glycosylase; base excision repair; protein-protein interaction; reactive oxygen species; common interaction domain; disordered structure
Last update: 25 September 2012