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DNA-based molecular architecture with spatially localized components

Richard A. Muscat, Karin Strauss, Luis Ceze, Georg Seelig
2013 Proceedings of the 40th Annual International Symposium on Computer Architecture - ISCA '13  
This paper proposes practical spatial isolation of components, leading to more easily designed DNA-based circuits.  ...  DNA nanotechnology is currently at a turning point, with many proposed applications being realized [20, 9] .  ...  [6] have proposed a design for strand displacement-based Boolean logic circuits with spatially localized components.  ... 
doi:10.1145/2485922.2485938 dblp:conf/isca/MuscatSCS13 fatcat:kg3iqjd5znh43hb55geyj3dvhi

DNA-based molecular architecture with spatially localized components

Richard A. Muscat, Karin Strauss, Luis Ceze, Georg Seelig
2013 SIGARCH Computer Architecture News  
This paper proposes practical spatial isolation of components, leading to more easily designed DNA-based circuits.  ...  DNA nanotechnology is currently at a turning point, with many proposed applications being realized [20, 9] .  ...  [6] have proposed a design for strand displacement-based Boolean logic circuits with spatially localized components.  ... 
doi:10.1145/2508148.2485938 fatcat:cxibidg7jfffzcqsrq4orrvv6e

DNA-based assembly lines and nanofactories

Friedrich C Simmel
2012 Current Opinion in Biotechnology  
One exciting prospect is the realization of dynamic systems based on DNA, in which chemical reactions are precisely controlled by the spatial arrangement of components, ultimately resulting in nanoscale  ...  This review will discuss recent progress toward this goal, ranging from DNA-templated synthesis over artificial DNA-based enzyme cascades to first examples of 'molecular robots'. Address  ...  Conclusions In the past years, DNA has been proven to be an extraordinary material for the assembly of complex molecular architectures.  ... 
doi:10.1016/j.copbio.2011.12.024 pmid:22237015 fatcat:gze6lvwtmne27mddg4wakmgcvi

Chromosome architecture is a key element of bacterial cellular organization

Jerod L. Ptacin, Lucy Shapiro
2012 Cellular Microbiology  
Recent studies have begun to identify and characterize novel systems that utilize the three dimensional spatial information encoded by chromosomal architecture to coordinate and direct fundamental cellular  ...  In addition, it is becoming increasingly clear that yet another level of information is encoded by the bacterial chromosome-the three-dimensional packaging of the chromosomal DNA molecule itself and its  ...  (right) A 3D model of the Caulobacter swarmer cell chromosome generated by molecular dynamics simulations based on locus-specific DNA interaction sites, showing chromosomal arms twisted upon one another  ... 
doi:10.1111/cmi.12049 pmid:23078580 pmcid:PMC3660146 fatcat:fxzi5v2pqfbb7lcnnz5zs3o75a

A Spatially Localized Architecture for Fast and Modular Computation at the Molecular Scale [article]

Gourab Chatterjee, Neil Dalchau, Richard A. Muscat, Andrew Phillips, Georg Seelig
2017 bioRxiv   pre-print
Co-localization of circuit elements decreases computation time from hours to minutes compared to circuits with diffusible components. Detailed computational models enable predictive circuit design.  ...  We create logic gates and signal transmission lines by spatially arranging reactive DNA hairpins on a DNA origami.  ...  Dna-based molecular architecture with 268 spatially localized components. SIGARCH Comput. Archit. News 41, 177-188 (2013). 26 . 26 Chandran, H., Gopalkrishnan, N., Phillips, A. & Reif, J. H.  ... 
doi:10.1101/110965 fatcat:uyyswiv3mve3rntdgogafj2pyu

Genomics tools for unraveling chromosome architecture

Bas van Steensel, Job Dekker
2010 Nature Biotechnology  
As a consequence, DNA that is in molecular contact with the nuclear lamina in vivo is methylated by the tethered Dam.  ...  Recent genome-wide mapping techniques have begun to provide more global insights into the molecular interactions of chromosomes with components of the nuclear envelope.  ...  Recent genome-wide mapping techniques have begun to provide more global insights into the molecular interactions of chromosomes with components of the nuclear envelope.  ... 
doi:10.1038/nbt.1680 pmid:20944601 pmcid:PMC3023824 fatcat:p2m5dnf6wzfxfjfqjpk3bll6nm

A New Approach to Design an Interactive System for Molecular Analysis [chapter]

Mouna Essabbah, Samir Otmane, Joan Hérisson, Malik Mallem
2009 Lecture Notes in Computer Science  
The rapid evolution of molecule's imaging and observation's techniques has caused a growing interest in studying molecular structures.  ...  On the other hand, DNA spatial visualization provides an opportunity to study its interaction with other molecules, especially proteins.  ...  Hardware Architecture The hardware architecture of our molecular modeling environment is based on a semi-immersive VR/AR multimodal platform called EVR@ 1 (see Fig. 9 ).  ... 
doi:10.1007/978-3-642-02583-9_77 fatcat:3clir2h3q5epbdrlpopnclsniu

In vivo formaldehyde cross-linking: it is time for black box analysis

Alexey Gavrilov, Sergey V. Razin, Giacomo Cavalli
2014 Briefings in Functional Genomics  
Formaldehyde cross-linking is an important component of many technologies, including chromatin immunoprecipitation and chromosome conformation capture.  ...  His research focuses on the relationship between nuclear architecture, genome spatial organization and gene expression.  ...  His team uses 3C-based approaches to study how genomes are organized in intact cells and how the spatial organization of genomes contributes to their function.  ... 
doi:10.1093/bfgp/elu037 pmid:25241225 pmcid:PMC6090872 fatcat:27hbaokpffaarjqwohucwfsbq4

Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy

Jianquan Xu, Yang Liu
2021 Frontiers in Cell and Developmental Biology  
Biochemical assays coupled with the state-of-the-art genomic technologies have been traditionally used to probe chromatin architecture.  ...  Recent advances in single molecule localization microscopy (SMLM) open up new opportunities to directly visualize higher-order chromatin architecture, its compaction status and its functional states at  ...  an essential component.  ... 
doi:10.3389/fcell.2021.653077 pmid:34178982 pmcid:PMC8222792 fatcat:fffhkvvwqfbotltzk62ktfnvsq

Tracking Chromosome Conformation in Live Cells with CRISPR Imaging

Juan Guan, Jeffrey Hu, Baohui Chen, Sakaya Sekine, Sanjeev Balakrishnan, Bo Huang
2015 Biophysical Journal  
Chromatin serves as substrate to a number of biological processes, e.g. gene expression and DNA replication, which require it to become locally restructured.  ...  High-resolution crystal structures of nucleosome core particles are fitted to the electron density maps and the intervening segments of linker DNA are modeled based on a sampling protocol that utilizes  ...  A nucleosome, 146 or 147 base-pair DNA wrapped around a histone octamer composed of two copies of each H3, H4, H2A, and H2B histone proteins, is a compact unit structure to store eukaryotic DNA into the  ... 
doi:10.1016/j.bpj.2014.11.2963 fatcat:5ydi2iqauzct3atiuwx3n62viq

Unique Mechanical Properties of Cell Nuclei Regulated by Chromatin

Chii J. Chan, Wenhong Li, Jana Scholze, Mirjam Schürmann, Jochen Guck
2015 Biophysical Journal  
Chromatin serves as substrate to a number of biological processes, e.g. gene expression and DNA replication, which require it to become locally restructured.  ...  High-resolution crystal structures of nucleosome core particles are fitted to the electron density maps and the intervening segments of linker DNA are modeled based on a sampling protocol that utilizes  ...  A nucleosome, 146 or 147 base-pair DNA wrapped around a histone octamer composed of two copies of each H3, H4, H2A, and H2B histone proteins, is a compact unit structure to store eukaryotic DNA into the  ... 
doi:10.1016/j.bpj.2014.11.2962 fatcat:gir3txv4pngahfucrtw3t2pzqm

Functional compartmentalization of the nucleus

J Strouboulis, A P Wolffe
1996 Journal of Cell Science  
morphologically distinct nuclear organelles with defined functional properties.  ...  We discuss the possible existence of novel regulatory functions inherent to nuclear architecture itself.  ...  This implies that DNA moves through a fixed architecture containing the molecular machines directing replication.  ... 
pmid:8856494 fatcat:mq3lcv7dlfaw3idmh5p74wbbyi

Mechanism and Function of Chromatin Positional Fluctuations in Interphase

Alexandra Zidovska
2015 Biophysical Journal  
Chromatin serves as substrate to a number of biological processes, e.g. gene expression and DNA replication, which require it to become locally restructured.  ...  High-resolution crystal structures of nucleosome core particles are fitted to the electron density maps and the intervening segments of linker DNA are modeled based on a sampling protocol that utilizes  ...  A nucleosome, 146 or 147 base-pair DNA wrapped around a histone octamer composed of two copies of each H3, H4, H2A, and H2B histone proteins, is a compact unit structure to store eukaryotic DNA into the  ... 
doi:10.1016/j.bpj.2014.11.2961 fatcat:jantdmouc5ff3ivgztkkqhy7ry

Matrix Constraints Regulate Transcription Dependent 3D Organization of Chromosomes

Yejun wang, Mallika Nagarajan, G.V. Shivashankar
2015 Biophysical Journal  
Chromatin serves as substrate to a number of biological processes, e.g. gene expression and DNA replication, which require it to become locally restructured.  ...  High-resolution crystal structures of nucleosome core particles are fitted to the electron density maps and the intervening segments of linker DNA are modeled based on a sampling protocol that utilizes  ...  A nucleosome, 146 or 147 base-pair DNA wrapped around a histone octamer composed of two copies of each H3, H4, H2A, and H2B histone proteins, is a compact unit structure to store eukaryotic DNA into the  ... 
doi:10.1016/j.bpj.2014.11.2960 fatcat:n4huhftd6fhhzomad2f2jgqbwy

A fractal model for nuclear organization: current evidence and biological implications

A. Bancaud, C. Lavelle, S. Huet, J. Ellenberg
2012 Nucleic Acids Research  
Recent studies indicate that a fractal model of chromatin architecture is consistent with both the reaction-diffusion properties of chromatin interacting proteins and with structural data on chromatin  ...  To fully understand any of these processes at the molecular level under physiological conditions, a clear picture of the polymorphic and dynamic organization of chromatin in the eukaryotic nucleus is required  ...  They also thank Raphae¨l Voituriez and Jean-Marc Victor for critical comments on the manuscript, Nathalie Daigle for proofreading, and the Nuclear Architecture and Dynamics research network (CNRS GDR 3536  ... 
doi:10.1093/nar/gks586 pmid:22790985 pmcid:PMC3467038 fatcat:2owrnohfl5by3ktom2lckwlzom
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