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Browsing MIT Open Access Articles by Title

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  • Nakagawa, So; Gisselbrecht, Stephen S.; Rogers, Julia M.; Hartl, Daniel L.; Bulyk, Martha L. (National Academy of Sciences (U.S.), 2013-07)
    The evolution of transcriptional regulatory networks entails the expansion and diversification of transcription factor (TF) families. The forkhead family of TFs, defined by a highly conserved winged helix DNA-binding domain ...
  • Weizmann, Yossi; Chenoweth, David M.; Swager, Timothy Manning (American Chemical Society (ACS), 2011-02)
    The ability to detect biological analytes in a rapid, sensitive, operationally simple, and cost-effective manner will impact human health and safety. Hybrid biocatalyzed-carbon nanotube (CNT) nanowire-based detection methods ...
  • Nordman, Jared T.; Kozhevnikova, Elena N.; Verrijzer, C. Peter; Pindyurin, Alexey V.; Andreyeva, Evgeniya N.; Shloma, Victor V.; Zhimulev, Igor F.; Orr-Weaver, Terry L.; Orr-Weaver, Terry L.; Nordman, Jared T. (Elsevier, 2014-10)
    Proper control of DNA replication is essential to ensure faithful transmission of genetic material and prevent chromosomal aberrations that can drive cancer progression and developmental disorders. DNA replication is ...
  • Reinhardt, H. Christian; Hasskamp, Pia; Schmedding, Ingolf; Morandell, Sandra; van Vugt, Marcel A.T.M.; Wang, XiaoZhe; Linding, Rune; Ong, Shao-En; Weaver, David; Carr, Steven A.; Yaffe, Michael B. (Elsevier B.V., 2010-10)
    Following genotoxic stress, cells activate a complex kinase-based signaling network to arrest the cell cycle and initiate DNA repair. p53-defective tumor cells rewire their checkpoint response and become dependent on the ...
  • Yanch, Jacquelyn C.; Engelward, Bevin P. (National Institute of Environmental Health Sciences, 2012-10)
    We thank Beyea for his comments and would like to respond, in particular, regarding the works he cites in his letter. First, the results of our study are, in fact, consistent with the findings of many human epidemiologic ...
  • Modell, Joshua Wexler; Hopkins, Alexander C.; Laub, Michael T. (Cold Spring Harbor Laboratory, 2011-05)
    Following DNA damage, cells typically delay cell cycle progression and inhibit cell division until their chromosomes have been repaired. The bacterial checkpoint systems responsible for these DNA damage responses are ...
  • Modell, Joshua W.; Kambara, Tracy K.; Laub, Michael T.; Perchuk, Barrett (Public Library of Science, 2014-10)
    Cells must coordinate DNA replication with cell division, especially during episodes of DNA damage. The paradigm for cell division control following DNA damage in bacteria involves the SOS response where cleavage of the ...
  • Gilbert, Luke A.; Hemann, Michael (Elsevier B.V., 2010-10)
    While numerous cell-intrinsic processes are known to play decisive roles in chemotherapeutic response, relatively little is known about the impact of the tumor microenvironment on therapeutic outcome. Here, we use a ...
  • 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 ...
  • Smith, Zachary D.; Chan, Michelle M.; 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, 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 ...
  • Calvo, Jennifer; 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, G. E.; Olivas, A.; Park, T.; Churchwell, M.; Doerge, D.; 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 ...
  • 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.; Bulyk, Martha L. (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 ...
  • 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 ...
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