Journal articles: 'DNA origami'

1

HALFORD, BETHANY. "DNA ORIGAMI." Chemical & Engineering News 84, no. 12 (March 20, 2006): 10. http://dx.doi.org/10.1021/cen-v084n012.p010.

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Laurel Oldach. "DNA origami inspired by paper origami." C&EN Global Enterprise 101, no. 23 (July 17, 2023): 5. http://dx.doi.org/10.1021/cen-10123-scicon4.

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Endo, Masayuki, and Hiroshi Sugiyama. "DNA Origami Nanomachines." Molecules 23, no. 7 (July 18, 2018): 1766. http://dx.doi.org/10.3390/molecules23071766.

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DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

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Ribeiro, Yasmin de Araújo, Vitor Nolasco de Moraes, Danyel Fernandes Contiliani, and Tiago Campos Pereira. "Origami de DNA." Genética na Escola 15, no. 2 (May 24, 2020): 98–107. http://dx.doi.org/10.55838/1980-3540.ge.2020.349.

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O material genético carrega informações fundamentais para o desenvolvimento de todos os organismos, dos mais simples aos mais complexos. Durante muito tempo, o DNA foi visto apenas como o elemento detentor de informações essenciais para a célula. Contudo, recentemente, pesquisas inovadoras têm usado o DNA como uma molécula estrutural, como um tijolo molecular muito versátil. Nesse sentido, a tradicional e secular arte japonesa de dobrar o papel, o origami, inspirou uma nova nanotecnologia denominada origami de DNA. Nesta abordagem, os cientistas propõem dobraduras de DNA, formando diversas estruturas moleculares e abrindo portas para aplicações terapêuticas, na indústria de nanomateriais, no desenvolvimento da ciência básica e em muitas outras áreas.

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Andersen, Ebbe Sloth. "DNA origami rewired." Nature Nanotechnology 10, no. 9 (September 2015): 733–34. http://dx.doi.org/10.1038/nnano.2015.204.

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Choi, Charles Q. "Origami from DNA." Scientific American 294, no. 5 (May 2006): 28. http://dx.doi.org/10.1038/scientificamerican0506-28d.

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Bell, Nicholas, Silvia Hernandez-Ainsa, Christian Engst, Tim Liedl, and Ulrich Keyser. "DNA Origami Nanopores." Biophysical Journal 104, no. 2 (January 2013): 517a. http://dx.doi.org/10.1016/j.bpj.2012.11.2859.

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Bell, Nicholas A. W., Christian R. Engst, Marc Ablay, Giorgio Divitini, Caterina Ducati, Tim Liedl, and Ulrich F. Keyser. "DNA Origami Nanopores." Nano Letters 12, no. 1 (December 29, 2011): 512–17. http://dx.doi.org/10.1021/nl204098n.

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9

Zhang, Yiyang, Chao Wang, Yuanchen Dong, Dianming Wang, Tianyang Cao, Shuo Wang, and Dongsheng Liu. "Fold 2D Woven DNA Origami to Origami + Structures." Advanced Functional Materials 29, no. 22 (April 3, 2019): 1809097. http://dx.doi.org/10.1002/adfm.201809097.

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10

Wang, Shih-Ting, Melissa A. Gray, Sunting Xuan, Yiyang Lin, James Byrnes, Andy I. Nguyen, Nevena Todorova, et al. "DNA origami protection and molecular interfacing through engineered sequence-defined peptoids." Proceedings of the National Academy of Sciences 117, no. 12 (March 12, 2020): 6339–48. http://dx.doi.org/10.1073/pnas.1919749117.

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DNA nanotechnology has established approaches for designing programmable and precisely controlled nanoscale architectures through specific Watson−Crick base-pairing, molecular plasticity, and intermolecular connectivity. In particular, superior control over DNA origami structures could be beneficial for biomedical applications, including biosensing, in vivo imaging, and drug and gene delivery. However, protecting DNA origami structures in complex biological fluids while preserving their structural characteristics remains a major challenge for enabling these applications. Here, we developed a class of structurally well-defined peptoids to protect DNA origamis in ionic and bioactive conditions and systematically explored the effects of peptoid architecture and sequence dependency on DNA origami stability. The applicability of this approach for drug delivery, bioimaging, and cell targeting was also demonstrated. A series of peptoids (PE1–9) with two types of architectures, termed as “brush” and “block,” were built from positively charged monomers and neutral oligo-ethyleneoxy monomers, where certain designs were found to greatly enhance the stability of DNA origami. Through experimental and molecular dynamics studies, we demonstrated the role of sequence-dependent electrostatic interactions of peptoids with the DNA backbone. We showed that octahedral DNA origamis coated with peptoid (PE2) can be used as carriers for anticancer drug and protein, where the peptoid modulated the rate of drug release and prolonged protein stability against proteolytic hydrolysis. Finally, we synthesized two alkyne-modified peptoids (PE8 and PE9), conjugated with fluorophore and antibody, to make stable DNA origamis with imaging and cell-targeting capabilities. Our results demonstrate an approach toward functional and physiologically stable DNA origami for biomedical applications.

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Wang, Yanfeng, Wenwen Zhang, Xing Li, and Guangzhao Cui. "Localized DNA Circuits on DNA Origami." Journal of Computational and Theoretical Nanoscience 13, no. 6 (June 1, 2016): 3942–47. http://dx.doi.org/10.1166/jctn.2016.5230.

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12

Wang, Shuang, Zhaoyu Zhou, Ningning Ma, Sichang Yang, Kai Li, Chao Teng, Yonggang Ke, and Ye Tian. "DNA Origami-Enabled Biosensors." Sensors 20, no. 23 (December 3, 2020): 6899. http://dx.doi.org/10.3390/s20236899.

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Biosensors are small but smart devices responding to the external stimulus, widely used in many fields including clinical diagnosis, healthcare and environment monitoring, etc. Moreover, there is still a pressing need to fabricate sensitive, stable, reliable sensors at present. DNA origami technology is able to not only construct arbitrary shapes in two/three dimension but also control the arrangement of molecules with different functionalities precisely. The functionalization of DNA origami nanostructure endows the sensing system potential of filling in weak spots in traditional DNA-based biosensor. Herein, we mainly review the construction and sensing mechanisms of sensing platforms based on DNA origami nanostructure according to different signal output strategies. It will offer guidance for the application of DNA origami structures functionalized by other materials. We also point out some promising directions for improving performance of biosensors.

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13

Tikhomirov, Grigory, Philip Petersen, and Lulu Qian. "Triangular DNA Origami Tilings." Journal of the American Chemical Society 140, no. 50 (December 4, 2018): 17361–64. http://dx.doi.org/10.1021/jacs.8b10609.

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14

Doerr, Allison. "DNA origami in 3D." Nature Methods 8, no. 6 (May 27, 2011): 454. http://dx.doi.org/10.1038/nmeth0611-454.

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15

Szuromi, P. "Simplifying DNA origami design." Science 352, no. 6293 (June 23, 2016): 1530–32. http://dx.doi.org/10.1126/science.352.6293.1530-l.

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16

Strano, M. S. "Functional DNA Origami Devices." Science 338, no. 6109 (November 15, 2012): 890–91. http://dx.doi.org/10.1126/science.1231024.

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17

Marchi, Alexandria N., Ishtiaq Saaem, Briana N. Vogen, Stanley Brown, and Thomas H. LaBean. "Toward Larger DNA Origami." Nano Letters 14, no. 10 (September 8, 2014): 5740–47. http://dx.doi.org/10.1021/nl502626s.

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18

Bradley, David. "Printing up DNA origami." Materials Today 17, no. 9 (November 2014): 422. http://dx.doi.org/10.1016/j.mattod.2014.10.013.

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19

Sameiyan, Elham, Elnaz Bagheri, Mohammad Ramezani, Mona Alibolandi, Khalil Abnous, and Seyed Mohammad Taghdisi. "DNA origami-based aptasensors." Biosensors and Bioelectronics 143 (October 2019): 111662. http://dx.doi.org/10.1016/j.bios.2019.111662.

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20

Gerling, Thomas, and Hendrik Dietz. "Faltkunst mit DNA-Origami." BIOspektrum 18, no. 3 (May 2012): 271–74. http://dx.doi.org/10.1007/s12268-012-0176-x.

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21

Nickels, Philipp C., Phil Holzmeister, Bettina Wünsch, Dina Grohmann, Philipp Tinnefeld, and Tim Liedl. "DNA Origami Force Balance." Biophysical Journal 110, no. 3 (February 2016): 563a. http://dx.doi.org/10.1016/j.bpj.2015.11.3012.

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22

Somoza, Álvaro. "Evolution of DNA Origami." Angewandte Chemie International Edition 48, no. 50 (November 17, 2009): 9406–8. http://dx.doi.org/10.1002/anie.200904802.

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23

Zhang, Tao, Caroline Hartl, Kilian Frank, Amelie Heuer-Jungemann, Stefan Fischer, Philipp C. Nickels, Bert Nickel, and Tim Liedl. "3D DNA Origami Crystals." Advanced Materials 30, no. 28 (May 18, 2018): 1800273. http://dx.doi.org/10.1002/adma.201800273.

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24

Hegde, Shreya, Oliver Polachini, Alejandra Velasquez, Moumita Dasgupta, and Ashley Carter. "Protamine revives DNA origami." Biophysical Journal 123, no. 3 (February 2024): 461a. http://dx.doi.org/10.1016/j.bpj.2023.11.2795.

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25

Watanabe, Taiki, Yusuke Sato, Hayato Otaka, Ibuki Kawamata, Satoshi Murata, and Shin-Ichiro M. Nomura. "DNA Origami “Quick” Refolding inside of a Micron-Sized Compartment." Molecules 25, no. 1 (December 18, 2019): 8. http://dx.doi.org/10.3390/molecules25010008.

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Investigations into the refolding of DNA origami leads to the creation of reconstructable nanostructures and deepens our understanding of the sustainability of life. Here, we report the refolding of the DNA origami structure inside a micron-sized compartment. In our experiments, conventional DNA origami and truss-type DNA origami were annealed and purified to remove the excess staples in a test tube. The DNA origami was then encapsulated inside of a micron-sized compartment of water-in-oil droplets, composed of neutral surfactants. The re-annealing process was then performed to initiate refolding in the compartment. The resulting 100-nm-sized DNA nanostructures were observed using atomic force microscopy (AFM), and the qualities of their structures were evaluated based on their shape. We found that the refolding of the DNA origami structure was favored inside the droplets compared with refolding in bulk solution. The refolded structures were able to fold even under “quick” one-minute annealing conditions. In addition, the smaller droplets (average diameter: 1.2 µm) appeared to be more advantageous for the refolding of the origamis than larger droplets. These results are expected to contribute to understanding the principles of life phenomena based on multimolecular polymer self-assembly in a micron-sized compartment, and for the production and maintenance of artificially designed molecules.

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26

Sakai, Yusuke, Md Sirajul Islam, Martyna Adamiak, Simon Chi-Chin Shiu, Julian Alexander Tanner, and Jonathan Gardiner Heddle. "DNA Aptamers for the Functionalisation of DNA Origami Nanostructures." Genes 9, no. 12 (November 23, 2018): 571. http://dx.doi.org/10.3390/genes9120571.

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DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures that are intended to carry out useful biomedical tasks in vivo, is to endow them with the ability to detect and respond to molecules of interest. Target molecules may be disease indicators or cell surface receptors, and the responses may include conformational changes leading to the release of therapeutically relevant cargo. Nucleic acid aptamers are ideally suited to this task and are beginning to be used in DNA origami designs. In this review, we consider examples of uses of DNA aptamers in DNA origami structures and summarise what is currently understood regarding aptamer-origami integration. We review three major roles for aptamers in such applications: protein immobilisation, triggering of structural transformation, and cell targeting. Finally, we consider future perspectives for DNA aptamer integration with DNA origami.

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27

Peil, Andreas, Pengfei Zhan, and Na Liu. "DNA Origami Catenanes: DNA Origami Catenanes Templated by Gold Nanoparticles (Small 6/2020)." Small 16, no. 6 (February 2020): 2070029. http://dx.doi.org/10.1002/smll.202070029.

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28

Engelen, Wouter, and Hendrik Dietz. "Advancing Biophysics Using DNA Origami." Annual Review of Biophysics 50, no. 1 (May 6, 2021): 469–92. http://dx.doi.org/10.1146/annurev-biophys-110520-125739.

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DNA origami enables the bottom-up construction of chemically addressable, nanoscale objects with user-defined shapes and tailored functionalities. As such, not only can DNA origami objects be used to improve existing experimental methods in biophysics, but they also open up completely new avenues of exploration. In this review, we discuss basic biophysical concepts that are relevant for prospective DNA origami users. We summarize biochemical strategies for interfacing DNA origami with biomolecules of interest. We describe various applications of DNA origami, emphasizing the added value or new biophysical insights that can be generated: rulers and positioning devices, force measurement and force application devices, alignment supports for structural analysis for biomolecules in cryogenic electron microscopy and nuclear magnetic resonance, probes for manipulating and interacting with lipid membranes, and programmable nanopores. We conclude with some thoughts on so-far little explored opportunities for using DNA origami in more complex environments such as the cell or even organisms.

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29

Hernández-Ainsa, Silvia, Nicholas A. W. Bell, Vivek V. Thacker, Kerstin Göpfrich, Karolis Misiunas, Maria Eugenia Fuentes-Perez, Fernando Moreno-Herrero, and Ulrich F. Keyser. "DNA Origami Nanopores for Controlling DNA Translocation." ACS Nano 7, no. 7 (June 7, 2013): 6024–30. http://dx.doi.org/10.1021/nn401759r.

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30

Saccà, Barbara, and Christof M. Niemeyer. "DNA Origami: The Art of Folding DNA." Angewandte Chemie International Edition 51, no. 1 (December 7, 2011): 58–66. http://dx.doi.org/10.1002/anie.201105846.

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31

Saccà, Barbara, and Christof M. Niemeyer. "DNA-Origami: die Kunst, DNA zu falten." Angewandte Chemie 124, no. 1 (December 7, 2011): 60–69. http://dx.doi.org/10.1002/ange.201105846.

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32

Gao, Rui, Zhuang Cai, Jianbang Wang, and Huajie Liu. "Condensed DNA Nanosphere for DNA Origami Cryptography." Chemistry 5, no. 4 (November 8, 2023): 2406–17. http://dx.doi.org/10.3390/chemistry5040159.

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Maintaining the confidentiality and integrity of the messages during a transmission is one of the most important aims of encrypted communication systems. Many achievements were made using biomolecules to improve the quality of the messages in communication. At the same time, it is still a challenge to construct cooperative communications based on the interactions between biomolecules to achieve the confidentiality and integrity of the transmitted messages. DNA-based encrypted communications have been developed, and in particular, DNA-origami-based message encryption can combine steganography and pattern encryption and exhibits extremely high confidentiality. Nevertheless, limited by biological characteristics, encrypted messages based on DNA require a strict storage environment in the process of transmission. The integrity of the message encoded in the DNA may be damaged when the DNA is in an unfriendly and hard environment. Therefore, it is particularly significant to improve the stability of DNA when it is exposed to a harsh environment during transmission. Here, we encoded the information into the DNA strands that were condensed for encryption to form a nanosphere covered with a shell of SiO2, which brings high-density messages and exhibits higher stability than separated DNA. The solid shell of SiO2 could prevent DNA from contacting the harsh environment, thereby protecting the DNA structure and maintaining the integrity of the information. At the same time, DNA nanospheres can achieve high throughput input and higher storage density per unit volume, which contribute to confusing the message strand (M-strand) with the interference strand in the stored information. Condensing DNA into the nanosphere that is used for DNA origami cryptography has the potential to be used in harsh conditions with higher confidentiality and integrity for the transmitted messages.

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33

Dass, Mihir, Fatih N. Gür, Karol Kołątaj, Maximilian J. Urban, and Tim Liedl. "DNA Origami-Enabled Plasmonic Sensing." Journal of Physical Chemistry C 125, no. 11 (February 25, 2021): 5969–81. http://dx.doi.org/10.1021/acs.jpcc.0c11238.

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34

Balakrishnan, Dhanasekaran, Gerrit D. Wilkens, and Jonathan G. Heddle. "Delivering DNA origami to cells." Nanomedicine 14, no. 7 (April 2019): 911–25. http://dx.doi.org/10.2217/nnm-2018-0440.

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35

Shani, Lior, Philip Tinnefeld, Yafit Fleger, Amos Sharoni, Boris Ya Shapiro, Avner Shaulov, Oleg Gang, and Yosef Yeshurun. "DNA origami based superconducting nanowires." AIP Advances 11, no. 1 (January 1, 2021): 015130. http://dx.doi.org/10.1063/5.0029781.

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36

Sepel, Lenira M. N., and Elgion L. S. Loreto. "Estrutura do DNA em origami." Genética na Escola 2, no. 1 (March 15, 2007): 3–5. http://dx.doi.org/10.55838/1980-3540.ge.2007.32.

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Apresentamos sugestões para o emprego didático de modelos tridimensionais da molécula de DNA feitos pela técnica do origami. O grande potencial didático desses modelos reside no fato de apresentar uma atividade desafiadora e envolvente, requerendo materiais muito baratos. Por meio do modelo os alunos podem visualizar e discutir as principais características da estrutura secundária da molécula de DNA como, por exemplo, a dupla hélice, o anti-paralelismo das fitas, o emparelhamento das bases, a cadeia açúcar-fosfato hidrofílica localizada na fase externa da molécula, a posição interna das bases, entre outras.

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37

Sakai, Yusuke, Gerrit D. Wilkens, Karol Wolski, Szczepan Zapotoczny, and Jonathan G. Heddle. "Topogami: Topologically Linked DNA Origami." ACS Nanoscience Au 2, no. 1 (November 12, 2021): 57–63. http://dx.doi.org/10.1021/acsnanoscienceau.1c00027.

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38

Kaganman, Irene. "An origami chip of DNA." Nature Methods 5, no. 3 (March 2008): 222. http://dx.doi.org/10.1038/nmeth0308-222.

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39

Zhang, Tao. "DNA origami-based microtubule analogue." Nanotechnology 31, no. 50 (October 9, 2020): 50LT01. http://dx.doi.org/10.1088/1361-6528/abb395.

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40

Linko, Veikko, and Mauri A. Kostiainen. "Automated design of DNA origami." Nature Biotechnology 34, no. 8 (August 2016): 826–27. http://dx.doi.org/10.1038/nbt.3647.

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41

Szuromi, Phil. "Patterning nanoparticles with DNA origami." Science 368, no. 6496 (June 11, 2020): 1202.4–1203. http://dx.doi.org/10.1126/science.368.6496.1202-d.

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42

Klein, William P., Charles N. Schmidt, Blake Rapp, Sadao Takabayashi, William B. Knowlton, Jeunghoon Lee, Bernard Yurke, William L. Hughes, Elton Graugnard, and Wan Kuang. "Multiscaffold DNA Origami Nanoparticle Waveguides." Nano Letters 13, no. 8 (July 10, 2013): 3850–56. http://dx.doi.org/10.1021/nl401879r.

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43

Burns, Jonathan R., Baptiste Lamarre, Alice L. B. Pyne, James E. Noble, and Maxim G. Ryadnov. "DNA Origami Inside-Out Viruses." ACS Synthetic Biology 7, no. 3 (February 7, 2018): 767–73. http://dx.doi.org/10.1021/acssynbio.7b00278.

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44

Kuzyk, Anton, Ralf Jungmann, Guillermo P. Acuna, and Na Liu. "DNA Origami Route for Nanophotonics." ACS Photonics 5, no. 4 (February 12, 2018): 1151–63. http://dx.doi.org/10.1021/acsphotonics.7b01580.

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45

Chandrasekaran, Arun Richard, Muthuirulan Pushpanathan, and Ken Halvorsen. "Evolution of DNA origami scaffolds." Materials Letters 170 (May 2016): 221–24. http://dx.doi.org/10.1016/j.matlet.2016.01.161.

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46

Wood, Jonathan. "The art of DNA origami." Materials Today 9, no. 5 (May 2006): 9. http://dx.doi.org/10.1016/s1369-7021(06)71472-9.

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47

Bradley, David. "Nanodevices hinge on DNA origami." Materials Today 18, no. 3 (April 2015): 126–27. http://dx.doi.org/10.1016/j.mattod.2015.02.006.

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48

Thomas, Guillaume, Cheikh Tidiane Diagne, Xavier Baillin, Thierry Chevolleau, Thomas Charvolin, and Raluca Tiron. "DNA Origami for Silicon Patterning." ACS Applied Materials & Interfaces 12, no. 32 (July 17, 2020): 36799–809. http://dx.doi.org/10.1021/acsami.0c10211.

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49

SHI, DangWei, BaoQuan DING, ZhenGang WANG, and JingKun XU. "Recent progress in DNA origami." Chinese Science Bulletin 58, no. 24 (August 1, 2013): 2367–76. http://dx.doi.org/10.1360/972012-1626.

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Kuzuya, Akinori, Ryosuke Watanabe, Yusei Yamanaka, Takuya Tamaki, Masafumi Kaino, and Yuichi Ohya. "Nanomechanical DNA Origami pH Sensors." Sensors 14, no. 10 (October 16, 2014): 19329–35. http://dx.doi.org/10.3390/s141019329.

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Journal articles on the topic 'DNA origami'

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