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Homing endonucleases: DNA scissors on a mission

Mohamed Hafez, Georg Hausner, L. Bonen
2012 Genome  
Homing endonucleases have been applied in promoting DNA modification or genome editing such as gene repair or "gene knockouts".  ...  Bioprospecting for native HEGs and the possibility of using these HEs as scaffolds for engineering a variety of HEs with new sequence specificities will make this group of rare-cutting molecular scissors  ...  of a bacterial DNA defense strategy against foreign DNAs.  ... 
doi:10.1139/g2012-049 pmid:22891613 fatcat:qahpxpfiqbabba2i3by5sxvxge

DNA Scissors Device Used to Measure MutS Binding to DNA Mis-pairs

Hongzhou Gu, Wei Yang, Nadrian C. Seeman
2010 Journal of the American Chemical Society  
MutS is a DNA repair protein that recognizes unpaired and bulged bases. When it binds to DNA it bends the double helix.  ...  We have developed a novel DNA-based nanomechanical device that measures the amount of work that a DNA-bending protein can do when it binds to the double helix.  ...  Figure 1 . 1 The Scissors-Based Device to Measure the Work Done by DNA Bending Proteins Double helical DNA is shown as rectangular boxes.  ... 
doi:10.1021/ja910188p pmid:20205420 pmcid:PMC2848700 fatcat:4mtlpic3t5e43jlmwy56b52mbq

Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors

Tatsuya Nishino, Kosuke Morikawa
2002 Oncogene  
DNA nucleases catalyze the cleavage of phosphodiester bonds.  ...  These enzymes play crucial roles in various DNA repair processes, which involve DNA replication, base excision repair, nucleotide excision repair, mismatch repair, and double strand break repair.  ...  Nucleases can be regarded as molecular scissors, which cleave phosphodiester bonds between the sugars and the phosphate moieties of DNA.  ... 
doi:10.1038/sj.onc.1206135 pmid:12483517 fatcat:ziorgt6ra5bxvfzxttg256gqpy

TALENs: Customizable Molecular DNA Scissors for Genome Engineering of Plants

Kunling Chen, Caixia Gao
2013 Journal of Genetics and Genomics  
Because of the simplicity of the DNA recognition code and their modular assembly, TALENs can act as customizable molecular DNA scissors inducing double-strand breaks (DSBs) at given genomic location.  ...  Transcription activator-like effector nucleases (TALENs), consisting of an engineered specific (TALE) DNA binding domain and a Fok I cleavage domain, are newly developed versatile reagents for genome engineering  ...  Thus TALENs, act as customizable molecular DNA scissors, and open the way to the next generation of genome engineering in plants.  ... 
doi:10.1016/j.jgg.2013.03.009 pmid:23790626 fatcat:wj42f5oozvdk7koohbfcsoyeqm

A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors

Teresa Lauria, Creina Slator, Vickie McKee, Markus Müller, Samuele Stazzoni, Antony L. Crisp, Thomas Carell, Andrew Kellett
2020 Chemistry - A European Journal  
Therefore, the TFO and 'clicked' ligands work synergistically to provide sequence-selectivity to the copper cutting unit which, in turn, confers high stabilisation to the DNA triplex.  ...  Several of the hybrids provide significant stabilisation toward melting in parallel triplexes (>20 °C) and DNA damage can be triggered upon copper binding in the presence of added reductant.  ...  Another tertiary structure is triplex DNA which is formed by the sequence-specific binding of a triplex forming oligonucleotide (TFO) in the major groove of duplex DNA.  ... 
doi:10.1002/chem.202002860 pmid:32706904 fatcat:szsp3xkqijgglapdozx5kbz74e

Spatially sculpted laser scissors for study of DNA damage and repair

Jared Stephens, Samarendra K. Mohanty, Suzanne Genc, Xiangduo Kong, Kyoko Yokomori, Michael W. Berns
2009 Journal of Biomedical Optics  
Localized immunostaining by the DNA double strand break ͑DSB͒ markers phosphorylated H2AX ͑␥H2AX͒ and Nbs1 in the nuclei of HeLa cells exposed to the "line scissors" was shown via confocal imaging.  ...  The line scissors method proved more efficient than the scanning mirror and scanning stage methods at induction of DNA DSB damage with the added benefit of having a greater potential for high throughput  ...  Color online only.͒ scissors is a comparatively simple tool for inducing DNA damage.  ... 
doi:10.1117/1.3213601 pmid:19895106 pmcid:PMC2774973 fatcat:vg7vb4rfqrbk5dr2pzeaio6yni

Atomic Scissors: A New Method of Tracking the 5-Bromo-2′-Deoxyuridine-Labeled DNA In Situ

Anna Ligasová, Dmytro Strunin, Radek Liboska, Ivan Rosenberg, Karel Koberna, Johannes N. Spelbrink
2012 PLoS ONE  
The alternative presently-used methods result in protein denaturation and/or extensive DNA cleavage followed by the DNA-bound proteins peeling off.  ...  A new method of the light microscopy detection of BrdU-labeled DNA in situ is described.  ...  in DNA cleavage.  ... 
doi:10.1371/journal.pone.0052584 pmid:23300711 pmcid:PMC3530445 fatcat:t53jokomp5hvjo6p6byzmto774

Evolving cheating DNA networks: a Case Study with the Rock–Paper–Scissors Game

Nathanael Aubert, Quang Dinh, Masami Hagiya, Teruo Fujii, Hitoshi Iba, Nicolas Bredeche, Yannick Rondelez
2013 Advances in Artificial Life, ECAL 2013  
More specifically, those individuals were represented as biochemical systems built on the DNA toolbox, a paradigm that allows both easy in-vitro implementation and predictive in-silico simulation.  ...  In the game of rock-paper-scissors, the simple monitoring of the opponent's move before it was played is a sufficient condition to trigger an arms race of detection and misinformation among evolved individuals  ...  Each possible move (rock, paper or scissors) is mapped to a specific chemical species (DNA sequences, more specifically signal sequences from the DNA toolbox).  ... 
doi:10.7551/978-0-262-31709-2-ch174 dblp:conf/ecal/AubertDHIFBR13 fatcat:zg44s5egejewpffdj2qblhg36q

Restriction enzyme scissor cut

Jonathan B Weitzman
2001 Genome Biology  
It seems, from the freeenzyme structure, that an unusual scissor-like motion allows the entry of DNA.  ...  The individual monomers swing out by as much as 50°, like scissor blades, producing significant effects on the tertiary and quaternary structure.  ... 
doi:10.1186/gb-spotlight-20010219-02 fatcat:zddvcqldyvhive3pmst35x5zzu

BMI1 Is Recruited to DNA Breaks and Contributes to DNA Damage-Induced H2A Ubiquitination and Repair

V. Ginjala, K. Nacerddine, A. Kulkarni, J. Oza, S. J. Hill, M. Yao, E. Citterio, M. van Lohuizen, S. Ganesan
2011 Molecular and Cellular Biology  
DNA damage activates signaling pathways that lead to modification of local chromatin and recruitment of DNA repair proteins.  ...  This DNA damage-induced histone ubiquitination is thought to play a critical role in mediating the DNA damage response.  ...  UVA laser scissors.  ... 
doi:10.1128/mcb.00981-10 pmid:21383063 pmcid:PMC3133356 fatcat:w2x3m4ftxnbubdetfsoyhix67u

Editorial: Optical Trapping (Laser Tweezers) and Nanosurgery (Laser Scissors)

Michael W. Berns, Halina Rubinsztein-Dunlop, Daryl Preece, Monika Ritsch-Marte
2021 Frontiers in Physics  
In addition to the studies on DNA repair using laser scissors, a study by Mo et al. is included, which uses laser tweezers that is applied directly on the DNA molecule in order to study DNA molecule elasticity  ...  Related to manipulation of genetic material inside of living cells is a brief review paper (perspective) by Kong et al. that reviews the use of laser scissors (nanosurgery) for production of DNA damage  ... 
doi:10.3389/fphy.2021.789600 fatcat:jmaow4rugjddlbkmavj6x42wx4

Tripartite Motif-containing 33 (TRIM33) Protein Functions in the Poly(ADP-ribose) Polymerase (PARP)-dependent DNA Damage Response through Interaction with Amplified in Liver Cancer 1 (ALC1) Protein

Atul Kulkarni, Jay Oza, Ming Yao, Honeah Sohail, Vasudeva Ginjala, Antonia Tomas-Loba, Zuzana Horejsi, Antoinette R. Tan, Simon J. Boulton, Shridar Ganesan
2013 Journal of Biological Chemistry  
Results: TRIM33 associates with ALC1 after DNA damage and regulates its retention at DNA breaks. Conclusion: TRIM33 has a role in the PARP-dependent DNA damage response pathway.  ...  PARP activation at sites of DNA breaks leads to recruitment of chromatin remodeling enzymes such as ALC1.  ...  TRIM33 Localizes to DNA Breaks-Given that TRIM33 interacts with ALC1 in response to DNA damage, we next sought to determine whether TRIM33 is also recruited to DNA damage acutely induced by UV laser scissors  ... 
doi:10.1074/jbc.m113.459164 pmid:23926104 pmcid:PMC3820871 fatcat:faqqvynijnezfkwiuuinxkg5ye

The mammalian INO80 complex is recruited to DNA damage sites in an ARP8 dependent manner

Shu-ichiro Kashiwaba, Kazuyuki Kitahashi, Takumi Watanabe, Fumitoshi Onoda, Masaya Ohtsu, Yasufumi Murakami
2010 Biochemical and Biophysical Research Communications - BBRC  
Dynamic changes in chromatin structure are essential for efficient DNA processing such as transcription, replication, and DNA repair.  ...  However, the function of the mammalian INO80 complex in DNA repair is mostly unknown.  ...  Next, we introduce DNA damages using laser scissors, and we then detected mammalian INO80 at the laser-induced DNA damage sites.  ... 
doi:10.1016/j.bbrc.2010.10.066 pmid:20971067 fatcat:lzkd6csqyvgt7ktdddkjxev6d4

Preparation of single rice chromosome for construction of a DNA library using a laser microbeam trap

2004 Journal of Biotechnology  
The cell wall of metaphase rice cell was cut by optical scissors. The released single chromosome was captured by an optical trap and transported to an area without cell debris.  ...  Optical scissors and optical trap are two kinds of laser micromanipulators.  ...  A metaphase cell with clear shaped chromosomes was cut by optical scissors.  ... 
doi:10.1016/s0168-1656(04)00014-8 fatcat:xl6ojybesze5bmxsvkxungndj4

Repeat Sequence Mapping Shows Different W Chromosome Evolutionary Pathways in Two Caprimulgiformes Families

Marcelo Santos de Souza, Rafael Kretschmer, Suziane Alves Barcellos, Alice Lemos Costa, Marcelo de Bello Cioffi, Edivaldo Herculano Corrêa de Oliveira, Analía Del Valle Garnero, Ricardo José Gunski
2020 Birds  
, by applying C-banding, G-banding and mapping of repetitive DNAs (microsatellite repeats and 18S rDNA).  ...  However, 9 out of 11 microsatellite sequences hybridized in the large W chromosome in the Common Potoo, while none of them hybridized in the W chromosome of the Scissor-tailed Nightjar.  ...  highly condensed DNA regions, which corresponds to constitutive heterochromatin.  ... 
doi:10.3390/birds1010004 fatcat:aupf2b64gbcrfj2odtiobqi2ai
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