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Browsing MIT Open Access Articles by Title

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  • Gehring, Mary; Reik, Wolf; Henikoff, Steven (Elsevier Science Publishers, 2009-02)
    Active DNA demethylation underlies key facets of reproduction in flowering plants and mammals and serves a general genome housekeeping function in plants. A family of 5-methylcytosine DNA glycosylases catalyzes plant ...
  • Hemann, Michael; Liu, Chuan; Ding, Hongyu; Li, Xiaoxi; Pallasch, Christian; Hong, Liya; Guo, Dianwu; Chen, Yi; Wang, Difei; Wang, Wei; Wang, Yajie; Jiang, Hai (Wiley Blackwell, 2015-03)
    Genotoxic drugs constitute a major treatment modality for human cancers; however, cancer cells' intrinsic DNA repair capability often increases the threshold of lethality and renders these drugs ineffective. The emerging ...
  • Smith, Zachary D.; Chan, Michelle Mei Wah; Humm, Kathryn C.; Karnik, Rahul; Mekhoubad, Shila; Regev, Aviv; Eggan, Kevin; Meissner, Alexander (Nature Publishing Group, 2014-07)
    In mammals, cytosine methylation is predominantly restricted to CpG dinucleotides and stably distributed across the genome, with local, cell-type-specific regulation directed by DNA binding factors. This comparatively ...
  • Shell, Scarlet S.; Baek, Seung-Hun; Shah, Rupal R.; Sassetti, Christopher M.; Dedon, Peter C.; Fortune, Sarah M.; Prestwich, Erin (Public Library of Science, 2013-07)
    DNA methylation regulates gene expression in many organisms. In eukaryotes, DNA methylation is associated with gene repression, while it exerts both activating and repressive effects in the Proteobacteria through largely ...
  • Kim, A Ra; Moon, James J.; Irvine, Darrell J.; Sunghwan Jung, Darrell J.; Um, Soong Ho (Institute of Electrical and Electronics Engineers (IEEE), 2010-08)
    DNA has been used as a new generic material due to its selectivity and intrinsic biocompatibility, to construct a variety of nano-architectures such as cubic, tetrahedral, and even complicated origami. Recently, a 3-D ...
  • Dupradeau, François-Yves; Case, David A.; Chen, Jingyang; Turner, Christopher John; Stubbe, JoAnne (Oxford University Press (OUP), 2007-11)
    Abasic sites are common DNA lesions resulting from spontaneous depurination and excision of damaged nucleobases by DNA repair enzymes. However, the influence of the local sequence context on the structure of the abasic ...
  • Wang, Lianrong; Chen, Shi; Vergin, Kevin L.; Giovannoni, Stephen J.; Chan, Simon W.; DeMott, Michael S.; Taghizadeh, Koli; Cordero Sanchez, Otto Xavier; Cutler, Michael Barry; Timberlake, Sonia; Alm, Eric J.; Polz, Martin F.; Pinhassi, Jarone; Deng, Zixin; Dedon, Peter C.; Chan, Simon W. (National Academy of Sciences, 2011-02)
    Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the ...
  • Braithwaite, Elena K.; Kedar, Padmini S.; Stumpo, Deborah J.; Bertocci, Barbara; Freedman, Jonathan H.; Wilson, Samuel H.; Samson, Leona D. (Public Library of Science, 2010-08)
    Base excision repair (BER) is a DNA repair pathway designed to correct small base lesions in genomic DNA. While DNA polymerase beta (pol β) is known to be the main polymerase in the BER pathway, various studies have ...
  • Kitange, Gaspar J.; Gupta, Shiv K.; Sarkaria, Jann N.; Nagel, Zachary D.; Joughin, Brian Alan; Chaim, Isaac Alexander; Mazzucato, Patrizia; Lauffenburger, Douglas A; Samson, Leona D (American Association for Cancer Research (AACR), 2016-10)
    Cancer cells can resist the effects of DNA-damaging therapeutic agents via utilization of DNA repair pathways, suggesting that DNA repair capacity (DRC) measurements in cancer cells could be used to identify patients most ...
  • Calvo, Jennifer A.; Meira, Lisiane B.; Lee, Chun-Yue I.; Moroski-Erkul, Catherine A.; Abolhassani, Nona; Taghizadeh, Koli; Eichinger, Lindsey Wood; Muthupalani, Sureshkumar; Nordstrand, Line M.; Klungland, Arne; Samson, Leona D. (American Society for Clinical Investigation, 2012-06)
    More than 15% of cancer deaths worldwide are associated with underlying infections or inflammatory conditions, therefore understanding how inflammation contributes to cancer etiology is important for both cancer prevention ...
  • Samson, Leona D.; Kisby, Glen E.; Olivas, A.; Park, T.; Churchwell, Mona; Doerge, Daniel R.; Gerson, S. L.; Turker, M. S. (Elsevier Pub. Co., 2009-01)
    Neurons of the developing brain are especially vulnerable to environmental agents that damage DNA (i.e., genotoxicants), but the mechanism is poorly understood. The focus of the present study is to demonstrate that DNA ...
  • Lan, Yuk Yuen; Bouley, Richard; Rooney, Michael S.; Hacohen, Nir; Londono, Diana; Rooney, Michael S. (Elsevier, 2014-10)
    Deficiencies in DNA-degrading nucleases lead to accumulation of self DNA and induction of autoimmunity in mice and in monogenic and polygenic human diseases. However, the sources of DNA and the mechanisms that trigger ...
  • Xiao, Zeyu; Ji, Changwei; Shi, Jinjun; Frieder, Jillian; Wu, Jun; Farokhzad, Omid C.; Pridgen, Eric Michael; Shi, JinJun (Wiley Blackwell, 2012-10)
    Targeted cancer therapy: Inspired by the ability of DNA hybridization, a targeted near-infrared (NIR) light-responsive delivery system has been developed through simple DNA self-assembly (see picture; PEG=polyethylene ...
  • Charoensawan, Varodom; Janga, Sarath Chandra; Bulyk, Martha L.; Babu, M. Madan; Teichmann, Sarah A. (Elsevier, 2012-07)
    Transcription factors (TFs) and histone octamers are two abundant classes of DNA binding proteins that coordinate the transcriptional program in cells. Detailed studies of individual TFs have shown that TFs bind to ...
  • Hsu, Patrick; Scott, David Arthur; Weinstein, Joshua; Ran, F. Ann; Konermann, Silvana M.; Agarwala, Vineeta; Li, Yinqing; Fine, Eli J.; Wu, Xavier; Shalem, Ophir; Cradick, Thomas J.; Marraffini, Luciano A.; Bao, Gang; Zhang, Feng (Nature Publishing Group, 2013-09)
    The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of single-guide RNAs (sgRNAs) to enable genome editing1, 2, 3, 4, 5, 6, 7, 8, 9, 10. Here, we characterize SpCas9 ...
  • Li, Cheri Yingjie; Wood, David K.; Hsu, Caroline M.; Bhatia, Sangeeta N. (Royal Society of Chemistry, The, 2011-07)
    Patterning multiple cell types is a critical step for engineering functional tissues, but few methods provide three-dimensional positioning at the cellular length scale. Here, we present a “bottom-up” approach for fabricating ...
  • Patel, Suraj J.; Yarmush, Martin; King, Kevin R.; Casali, Monica (United States National Academy of Sciences, 2009-05)
    Cells respond to infection by sensing pathogens and communicating danger signals to noninfected neighbors; however, little is known about this complex spatiotemporal process. Here we show that activation of the innate ...
  • Bajaj, Vikram S.; Mak-Jurkauskas, Melody L.; Belenky, Marina; Herzfeld, Judith; Griffin, Robert Guy (Elsevier, 2009-09)
    We describe a new approach to multiple [superscript 13]C–[superscript 15]N distance measurements in uniformly labeled solids, frequency-selective (FS) TEDOR. The method shares features with FS-REDOR and ZF- and BASE-TEDOR, ...
  • Ravera, Enrico; Corzilius, Bjorn; Michaelis, Vladimir K.; Luchinat, Claudio; Griffin, Robert Guy; Bertini, Ivano (American Chemical Society (ACS), 2014-03)
    Protein sedimentation sans cryoprotection is a new approach to magic angle spinning (MAS) and dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) spectroscopy of proteins. It increases the sensitivity of ...
  • Maier, Pauline (Omohundro Institute of Early American History and Culture, 2011-01)
    Start with the almost 250-page cumulative index in Volume XXIII of The Documentary History of the Ratification of the Constitution, or DHRC, the last of five volumes on ratification in New York. Predictably, it includes ...
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