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Journal articles on the topic 'DNA self-assembling'

Author: Grafiati
Published: 14 March 2023

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1

Sa-Ardyen, Phiset, Natašsa Jonoska, and Nadrian C. Seeman. "Self-assembling DNA graphs." Natural Computing 2, no. 4 (2003): 427–38. http://dx.doi.org/10.1023/b:naco.0000006771.95566.34.

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2

Li, Sinan, Pingang He, Jianhua Dong, Zhixin Guo, and Liming Dai. "DNA-Directed Self-Assembling of Carbon Nanotubes." Journal of the American Chemical Society 127, no. 1 (January 2005): 14–15. http://dx.doi.org/10.1021/ja0446045.

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3

Largo, Julio, Francis W. Starr, and Francesco Sciortino. "Self-Assembling DNA Dendrimers: A Numerical Study." Langmuir 23, no. 11 (May 2007): 5896–905. http://dx.doi.org/10.1021/la063036z.

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4

Carbone, A., and N. C. Seeman. "Circuits and programmable self-assembling DNA structures." Proceedings of the National Academy of Sciences 99, no. 20 (September 13, 2002): 12577–82. http://dx.doi.org/10.1073/pnas.202418299.

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5

Vecchioni, S., M. C. Capece, E. Toomey, L. J. Rothschild, and S. J. Wind. "Toward electronically-functional, self-assembling DNA nanostructures." Journal of Self-Assembly and Molecular Electronics 6, no. 1 (2018): 1. http://dx.doi.org/10.13052/jsame2245-4551.2018008.

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6

Grome, Michael W., Zhao Zhang, Frédéric Pincet, and Chenxiang Lin. "Vesicle Tubulation with Self-Assembling DNA Nanosprings." Angewandte Chemie 130, no. 19 (April 14, 2018): 5428–32. http://dx.doi.org/10.1002/ange.201800141.

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7

Grome, Michael W., Zhao Zhang, Frédéric Pincet, and Chenxiang Lin. "Vesicle Tubulation with Self-Assembling DNA Nanosprings." Angewandte Chemie International Edition 57, no. 19 (April 14, 2018): 5330–34. http://dx.doi.org/10.1002/anie.201800141.

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8

Mohammed, Abdul M., Petr Šulc, John Zenk, and Rebecca Schulman. "Self-assembling DNA nanotubes to connect molecular landmarks." Nature Nanotechnology 12, no. 4 (December 19, 2016): 312–16. http://dx.doi.org/10.1038/nnano.2016.277.

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9

Samano, Enrique C., Mauricio Pilo-Pais, Sarah Goldberg, Briana N. Vogen, Gleb Finkelstein, and Thomas H. LaBean. "Self-assembling DNA templates for programmed artificial biomineralization." Soft Matter 7, no. 7 (2011): 3240. http://dx.doi.org/10.1039/c0sm01318h.

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10

Fahlman, Richard P., and Dipankar Sen. "“Synapsable” DNA Double Helices: Self-Selective Modules for Assembling DNA Superstructures." Journal of the American Chemical Society 121, no. 48 (December 1999): 11079–85. http://dx.doi.org/10.1021/ja992574d.

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11

Chandran, Harish, Abhijit Rangnekar, Geetha Shetty, Erik A. Schultes, John H. Reif, and Thomas H. LaBean. "An autonomously self-assembling dendritic DNA nanostructure for target DNA detection." Biotechnology Journal 8, no. 2 (October 10, 2012): 221–27. http://dx.doi.org/10.1002/biot.201100499.

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12

Jorge, Andreia, and Ramon Eritja. "Overview of DNA Self-Assembling: Progresses in Biomedical Applications." Pharmaceutics 10, no. 4 (December 11, 2018): 268. http://dx.doi.org/10.3390/pharmaceutics10040268.

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Molecular self-assembling is ubiquitous in nature providing structural and functional machinery for the cells. In recent decades, material science has been inspired by the nature’s assembly principles to create artificially higher-order structures customized with therapeutic and targeting molecules, organic and inorganic fluorescent probes that have opened new perspectives for biomedical applications. Among these novel man-made materials, DNA nanostructures hold great promise for the modular assembly of biocompatible molecules at the nanoscale of multiple shapes and sizes, designed via molecular programming languages. Herein, we summarize the recent advances made in the designing of DNA nanostructures with special emphasis on their application in biomedical research as imaging and diagnostic platforms, drug, gene, and protein vehicles, as well as theranostic agents that are meant to operate in-cell and in-vivo.
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13

Cai, Jianfeng, Erik M. Shapiro, and Andrew D. Hamilton. "Self-Assembling DNA Quadruplex Conjugated to MRI Contrast Agents." Bioconjugate Chemistry 20, no. 2 (February 18, 2009): 205–8. http://dx.doi.org/10.1021/bc8004182.

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14

Sugawara-Narutaki, Ayae, and Yukiko Kamiya. "Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids." International Journal of Molecular Sciences 21, no. 9 (May 6, 2020): 3276. http://dx.doi.org/10.3390/ijms21093276.

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15

Saoji, Maithili, and Paul J. Paukstelis. "Sequence-dependent structural changes in a self-assembling DNA oligonucleotide." Acta Crystallographica Section D Biological Crystallography 71, no. 12 (November 26, 2015): 2471–78. http://dx.doi.org/10.1107/s1399004715019598.

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DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson–Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg2+through a combination of Watson–Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson–Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A–G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G–A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson–Crick duplex region. These results provide important new insights into the sequence–structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson–Crick and noncanonical base pairs that is responsible for crystallization fate.
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16

He, Pingang, Sinan Li, and Liming Dai. "DNA-modified Carbon Nanotubes for Self-assembling and Biosensing Applications." Synthetic Metals 154, no. 1-3 (September 2005): 17–20. http://dx.doi.org/10.1016/j.synthmet.2005.07.007.

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17

Marullo, Rachel, and Matthew Tirrell. "Self-Assembling Peptide Amphiphiles for DNA Binding and Nuclear Targeting." Biophysical Journal 98, no. 3 (January 2010): 662a. http://dx.doi.org/10.1016/j.bpj.2009.12.3633.

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18

Campbell, Eleanor A., Evan Peterson, and Dmitry M. Kolpashchikov. "Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles." ChemPhysChem 18, no. 13 (March 24, 2017): 1730–34. http://dx.doi.org/10.1002/cphc.201700109.

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19

Jiménez Blanco, J. L., F. Ortega-Caballero, L. Blanco-Fernández, T. Carmona, G. Marcelo, M. Martínez-Negro, E. Aicart, et al. "Trehalose-based Janus cyclooligosaccharides: the “Click” synthesis and DNA-directed assembly into pH-sensitive transfectious nanoparticles." Chemical Communications 52, no. 66 (2016): 10117–20. http://dx.doi.org/10.1039/c6cc04791b.

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20

Angioletti-Uberti, Stefano, Bortolo M. Mognetti, and Daan Frenkel. "Theory and simulation of DNA-coated colloids: a guide for rational design." Physical Chemistry Chemical Physics 18, no. 9 (2016): 6373–93. http://dx.doi.org/10.1039/c5cp06981e.

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21

Mohri, Kohta, Eri Kusuki, Shozo Ohtsuki, Natsuki Takahashi, Masayuki Endo, Kumi Hidaka, Hiroshi Sugiyama, Yuki Takahashi, Yoshinobu Takakura, and Makiya Nishikawa. "Self-Assembling DNA Dendrimer for Effective Delivery of Immunostimulatory CpG DNA to Immune Cells." Biomacromolecules 16, no. 4 (March 27, 2015): 1095–101. http://dx.doi.org/10.1021/bm501731f.

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22

Warner, Christian N., Zachary D. Hunter, Destiny D. Carte, Tyler J. Skidmore, Erik S. Vint, and B. Scott Day. "Structure and Function Analysis of DNA Monolayers Created from Self-Assembling DNA–Dendron Conjugates." Langmuir 36, no. 19 (April 27, 2020): 5428–34. http://dx.doi.org/10.1021/acs.langmuir.0c00340.

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23

Nguyen, Dan T., and Omar A. Saleh. "Tuning phase and aging of DNA hydrogels through molecular design." Soft Matter 13, no. 32 (2017): 5421–27. http://dx.doi.org/10.1039/c7sm00557a.

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Using self-assembling, multi-valent DNA nanostars, we show that DNA hydrogel phase and structure can be controlled by tuning hydrogel aging kinetics through the rational design of gel-forming elements and solvent conditions.
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24

WETTIG, Shawn D., Chen-Zhong LI, Yi-Tao LONG, Heinz-Bernhard KRAATZ, and Jeremy S. LEE. "M-DNA: A Self-Assembling Molecular Wire for Nanoelectronics and Biosensing." Analytical Sciences 19, no. 1 (2003): 23–26. http://dx.doi.org/10.2116/analsci.19.23.

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25

Ciasca, G., L. Businaro, M. Papi, A. Notargiacomo, M. Chiarpotto, A. De Ninno, V. Palmieri, et al. "Self-assembling of large ordered DNA arrays using superhydrophobic patterned surfaces." Nanotechnology 24, no. 49 (November 14, 2013): 495302. http://dx.doi.org/10.1088/0957-4484/24/49/495302.

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26

Dwyer, C., V. Johri, M. Cheung, J. Patwardhan, A. Lebeck, and D. Sorin. "Design tools for a DNA-guided self-assembling carbon nanotube technology." Nanotechnology 15, no. 9 (July 24, 2004): 1240–45. http://dx.doi.org/10.1088/0957-4484/15/9/022.

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27

Simmons, Chad R., Fei Zhang, Tara MacCulloch, Nour Eddine Fahmi, Nicholas Stephanopoulos, Yan Liu, and Hao Yan. "Enantiomeric structures of a self-assembling three-dimensional DNA crystal scaffold." Acta Crystallographica Section A Foundations and Advances 73, a1 (May 26, 2017): a53. http://dx.doi.org/10.1107/s0108767317099470.

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28

Svahn, Mathias G., Maroof Hasan, Valeria Sigot, Juan José Valle-Delgado, Mark W. Rutland, Karin E. Lundin, and C. I. Edvard Smith. "Self-Assembling Supramolecular Complexes by Single-Stranded Extension from Plasmid DNA." Oligonucleotides 17, no. 1 (March 2007): 80–94. http://dx.doi.org/10.1089/oli.2006.0045.

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29

Xu, Yang, Shuoxing Jiang, Chad R. Simmons, Raghu Pradeep Narayanan, Fei Zhang, Ann-Marie Aziz, Hao Yan, and Nicholas Stephanopoulos. "Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks." ACS Nano 13, no. 3 (March 5, 2019): 3545–54. http://dx.doi.org/10.1021/acsnano.8b09798.

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30

Rattanakiat, Sakulrat, Makiya Nishikawa, and Yoshinobu Takakura. "Self-assembling CpG DNA nanoparticles for efficient antigen delivery and immunostimulation." European Journal of Pharmaceutical Sciences 47, no. 2 (September 2012): 352–58. http://dx.doi.org/10.1016/j.ejps.2012.06.015.

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31

Bartke, Marianne, Bernhard Eickenberg, Frank Wittbracht, and Andreas Hütten. "DNA-Mediated Stabilization of Self-Assembling Bead Monolayers for Microfluidic Applications." Particle & Particle Systems Characterization 32, no. 5 (January 12, 2015): 583–87. http://dx.doi.org/10.1002/ppsc.201400093.

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32

Mizuta, R., J. M. Devos, J. Webster, W. L. Ling, T. Narayanan, A. Round, D. Munnur, et al. "Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide." Nanoscale 10, no. 12 (2018): 5550–58. http://dx.doi.org/10.1039/c7nr03875e.

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33

Liu, Shiyun, Satoshi Murata, and Ibuki Kawamata. "DNA Ring Motif with Flexible Joints." Micromachines 11, no. 11 (October 31, 2020): 987. http://dx.doi.org/10.3390/mi11110987.

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The invention of DNA origami has expanded the geometric complexity and functionality of DNA nanostructures. Using DNA origami technology, we develop a flexible multi-joint ring motif as a novel self-assembling module. The motif can connect with each other through self-complementary sequences on its segments. The flexible joints can be fixed in a straightened position as desired, thereby allowing the motif to take various shapes. We can adjust the number of flexible joints and the number of connectable segments, thereby enabling programmable self-assembly of the motif. We successfully produced the motif and evaluated several self-assembly patterns. The proposed multi-joint ring motif can provide a novel method for creating functional molecular devices.
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34

Budharaju, Harshavardhan, Allen Zennifer, Swaminathan Sethuraman, Arghya Paul, and Dhakshinamoorthy Sundaramurthi. "Designer DNA biomolecules as a defined biomaterial for 3D bioprinting applications." Materials Horizons 9, no. 4 (2022): 1141–66. http://dx.doi.org/10.1039/d1mh01632f.

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DNA can be rationally designed, synthesized, and modified/functionalized to enable pH, light, or ion-responsive self-assembling mechanism. These DNA bioinks can be used for the bioprinting of biological constructs by utilizing specific triggers.
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35

Wang, Maonan, Yun Chen, Weijuan Cai, Huan Feng, Tianyu Du, Weiwei Liu, Hui Jiang, Alberto Pasquarelli, Yossi Weizmann, and Xuemei Wang. "In situ self-assembling Au-DNA complexes for targeted cancer bioimaging and inhibition." Proceedings of the National Academy of Sciences 117, no. 1 (December 16, 2019): 308–16. http://dx.doi.org/10.1073/pnas.1915512116.

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Cancer remains one of the most challenging diseases to treat. For accurate cancer diagnosis and targeted therapy, it is important to assess the localization of the affected area of cancers. The general approaches for cancer diagnostics include pathological assessments and imaging. However, these methods only generally assess the tumor area. In this study, by taking advantage of the unique microenvironment of cancers, we effectively utilize in situ self-assembled biosynthetic fluorescent gold nanocluster-DNA (GNC-DNA) complexes to facilitate safe and targeted cancer theranostics. In in vitro and in vivo tumor models, our self-assembling biosynthetic approach allowed for precise bioimaging and inhibited cancer growth after one injection of DNA and gold precursors. These results demonstrate that in situ bioresponsive self-assembling GNC-PTEN (phosphatase and tensin homolog) complexes could be an effective noninvasive technique for accurate cancer bioimaging and treatment, thus providing a safe and promising cancer theranostics platform for cancer therapy.
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36

Sakamoto, Takashi, Daisaku Hasegawa, and Kenzo Fujimoto. "Disassembly-driven signal turn-on probes for bimodal detection of DNA with 19F NMR and fluorescence." Organic & Biomolecular Chemistry 16, no. 39 (2018): 7157–62. http://dx.doi.org/10.1039/c8ob02218f.

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37

Tarvirdipour, Shabnam, Cora-Ann Schoenenberger, Yaakov Benenson, and Cornelia G. Palivan. "A self-assembling amphiphilic peptide nanoparticle for the efficient entrapment of DNA cargoes up to 100 nucleotides in length." Soft Matter 16, no. 6 (2020): 1678–91. http://dx.doi.org/10.1039/c9sm01990a.

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To overcome the low efficiency and cytotoxicity associated with most non-viral DNA delivery systems we developed a purely peptidic self-assembling system that is able to entrap single- and double-stranded DNA of up to 100 nucleotides in length.
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38

Song, Huan, Yangzi Zhang, Ping Cheng, Xu Chen, Yunbo Luo, and Wentao Xu. "A rapidly self-assembling soft-brush DNA hydrogel based on RCA products." Chemical Communications 55, no. 37 (2019): 5375–78. http://dx.doi.org/10.1039/c9cc01022j.

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39

Cai, Jianfeng, Dariusz M. Niedzwiedzki, Harry A. Frank, and Andrew D. Hamilton. "Ultrafast energy transfer within pyropheophorbide-a tethered to self-assembling DNA quadruplex." Chem. Commun. 46, no. 4 (2010): 544–46. http://dx.doi.org/10.1039/b908435e.

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40

Drmanac, R., A. B. Sparks, M. J. Callow, A. L. Halpern, N. L. Burns, B. G. Kermani, P. Carnevali, et al. "Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays." Science 327, no. 5961 (November 5, 2009): 78–81. http://dx.doi.org/10.1126/science.1181498.

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41

Simmons, Chad R., Fei Zhang, Tara MacCulloch, Noureddine Fahmi, Nicholas Stephanopoulos, Yan Liu, Nadrian C. Seeman, and Hao Yan. "Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals." Journal of the American Chemical Society 139, no. 32 (August 2, 2017): 11254–60. http://dx.doi.org/10.1021/jacs.7b06485.

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42

Medintz, Igor L., Lorenzo Berti, Thomas Pons, Amy F. Grimes, Douglas S. English, Andrea Alessandrini, Paolo Facci, and Hedi Mattoussi. "A Reactive Peptidic Linker for Self-Assembling Hybrid Quantum Dot−DNA Bioconjugates." Nano Letters 7, no. 6 (June 2007): 1741–48. http://dx.doi.org/10.1021/nl070782v.

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43

Liebendorfer, Adam. "Lattice models provide fast and accurate way to simulate DNA self-assembling." Scilight 2018, no. 51 (December 17, 2018): 510011. http://dx.doi.org/10.1063/1.5085723.

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44

Pitard, B. "Negatively charged self-assembling DNA/poloxamine nanospheres for in vivo gene transfer." Nucleic Acids Research 32, no. 20 (November 16, 2004): e159-e159. http://dx.doi.org/10.1093/nar/gnh153.

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45

Griesser, Helmut, Alexander Schwenger, and Clemens Richert. "Encapsulating Active Pharmaceutical Ingredients in Self-Assembling Adamantanes with Short DNA Zippers." ChemMedChem 12, no. 21 (October 9, 2017): 1759–67. http://dx.doi.org/10.1002/cmdc.201700466.

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46

Irrera, Simona, Sergio E. Ruiz-Hernandez, Melania Reggente, Daniele Passeri, Marco Natali, Fabrizio Gala, Giuseppe Zollo, Marco Rossi, and Gustavo Portalone. "Self-assembling of calcium salt of the new DNA base 5-carboxylcytosine." Applied Surface Science 407 (June 2017): 297–306. http://dx.doi.org/10.1016/j.apsusc.2017.02.171.

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47

Chen, Chen, Xiufang Ding, Nimrah Akram, Song Xue, and Shi-Zhong Luo. "Fused in Sarcoma: Properties, Self-Assembly and Correlation with Neurodegenerative Diseases." Molecules 24, no. 8 (April 24, 2019): 1622. http://dx.doi.org/10.3390/molecules24081622.

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Fused in sarcoma (FUS) is a DNA/RNA binding protein that is involved in RNA metabolism and DNA repair. Numerous reports have demonstrated by pathological and genetic analysis that FUS is associated with a variety of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), and polyglutamine diseases. Traditionally, the fibrillar aggregation of FUS was considered to be the cause of those diseases, especially via its prion-like domains (PrLDs), which are rich in glutamine and asparagine residues. Lately, a nonfibrillar self-assembling phenomenon, liquid–liquid phase separation (LLPS), was observed in FUS, and studies of its functions, mechanism, and mutual transformation with pathogenic amyloid have been emerging. This review summarizes recent studies on FUS self-assembling, including both aggregation and LLPS as well as their relationship with the pathology of ALS, FTLD, and other neurodegenerative diseases.
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48

Pflueger, Iris, Coralie Charrat, Carmen Ortiz Mellet, José M. García Fernández, Christophe Di Giorgio, and Juan M. Benito. "Cyclodextrin-based facial amphiphiles: assessing the impact of the hydrophilic–lipophilic balance in the self-assembly, DNA complexation and gene delivery capabilities." Organic & Biomolecular Chemistry 14, no. 42 (2016): 10037–49. http://dx.doi.org/10.1039/c6ob01882c.

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49

Stepanova, Veronika, Vladimir Smolko, Vladimir Gorbatchuk, Ivan Stoikov, Gennady Evtugyn, and Tibor Hianik. "DNA-Polylactide Modified Biosensor for Electrochemical Determination of the DNA-Drugs and Aptamer-Aflatoxin M1 Interactions." Sensors 19, no. 22 (November 14, 2019): 4962. http://dx.doi.org/10.3390/s19224962.

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DNA sensors were assembled by consecutive deposition of thiacalix[4]arenes bearing oligolactic fragments, poly(ethylene imine), and DNA onto the glassy carbon electrode. The assembling of the layers was monitored with scanning electron microscopy, cyclic voltammetry and electrochemical impedance spectroscopy. The configuration of the thiacalix[4]arene core determined self-assembling of the polymeric species to the nano/micro particles with a size of 70–350 nm. Depending on the granulation, the coatings show the accumulation of a variety of DNA quantities, charges, and internal pore volumes. These parameters were used to optimize the DNA sensors based on these coatings. Thus, doxorubicin was determined to have limits of detection of 0.01 nM (cone configuration), 0.05 nM (partial cone configuration), and 0.10 nM (1,3-alternate configuration of the macrocycle core). Substitution of native DNA with aptamer specific to aflatoxin M1 resulted in the detection of the toxin in the range of 20 to 200 ng/L (limit of detection 5 ng/L). The aptasensor was tested in spiked milk samples and showed a recovery of 80 and 85% for 20 and 50 ng/L of the aflatoxin M1, respectively.
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50

Xu, Yang, Shuoxing Jiang, Chad R. Simmons, Raghu Pradeep Narayanan, Fei Zhang, Ann-Marie Aziz, Hao Yan, and Nicholas Stephanopoulos. "Correction to Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks." ACS Nano 14, no. 6 (May 18, 2020): 7673. http://dx.doi.org/10.1021/acsnano.0c02484.

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