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Journal articles on the topic 'Nucleic acid nanostructures'

Author: Grafiati

Published: 6 September 2023

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1

Cutler, Joshua I., Ke Zhang, Dan Zheng, Evelyn Auyeung, Andrew E. Prigodich, and Chad A. Mirkin. "Polyvalent Nucleic Acid Nanostructures." Journal of the American Chemical Society 133, no. 24 (June 22, 2011): 9254–57. http://dx.doi.org/10.1021/ja203375n.

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2

Zhang, Ke, Xiao Zhu, Fei Jia, Evelyn Auyeung, and Chad A. Mirkin. "Temperature-Activated Nucleic Acid Nanostructures." Journal of the American Chemical Society 135, no. 38 (September 16, 2013): 14102–5. http://dx.doi.org/10.1021/ja408465t.

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3

Seeman, Nadrian C. "Nucleic Acid Nanostructures and Topology." Angewandte Chemie International Edition 37, no. 23 (December 17, 1998): 3220–38. http://dx.doi.org/10.1002/(sici)1521-3773(19981217)37:23<3220::aid-anie3220>3.0.co;2-c.

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4

Li, Hanying, Thomas H. LaBean, and Kam W. Leong. "Nucleic acid-based nanoengineering: novel structures for biomedical applications." Interface Focus 1, no. 5 (June 28, 2011): 702–24. http://dx.doi.org/10.1098/rsfs.2011.0040.

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Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

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5

Han, Lin, Yuang Wang, Wantao Tang, Jianbing Liu, and Baoquan Ding. "Bioimaging Based on Nucleic Acid Nanostructures." Chemical Research in Chinese Universities 37, no. 4 (April 8, 2021): 823–28. http://dx.doi.org/10.1007/s40242-021-1055-0.

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6

Smith, David, Verena Schüller, Christian Engst, Joachim Rädler, and Tim Liedl. "Nucleic acid nanostructures for biomedical applications." Nanomedicine 8, no. 1 (January 2013): 105–21. http://dx.doi.org/10.2217/nnm.12.184.

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7

Bechinger, Burkhard. "Peptide-nucleic acid nanostructures for transfection." BioMolecular Concepts 3, no. 3 (June 1, 2012): 283–93. http://dx.doi.org/10.1515/bmc-2011-0067.

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AbstractTo use nucleic acids in biomedical research and medical applications, these highly hydrophilic macromolecules have to be transported through the organism, targeted to specific cell surfaces, and have to cross cellular barriers. To this end, nanosized transfection complexes have been designed and several of them have been successfully tested. Here, the different steps of the transfection process and the particular optimization protocols are reviewed, including the physicochemical properties of such vectors (size, charge, composition), protection in serum, cellular uptake, endosomal escape, and intracellular targeting. The transfection process has been subdivided into separate steps and here special emphasis is given to peptides that have been designed to optimize these steps individually. Finally, complex devices encompassing a multitude of beneficial functionalities for transfection have been developed.

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8

Bellassai, Noemi, Roberta D’Agata, and Giuseppe Spoto. "Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications." Analytical and Bioanalytical Chemistry 413, no. 24 (April 6, 2021): 6063–77. http://dx.doi.org/10.1007/s00216-021-03309-4.

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AbstractNucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

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9

Richard Chandrasekaran, Arun. "Enhancing the biostability of nucleic acid nanostructures." Biophysical Journal 121, no. 3 (February 2022): 422a. http://dx.doi.org/10.1016/j.bpj.2021.11.667.

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10

Teller, Carsten, and Itamar Willner. "Functional nucleic acid nanostructures and DNA machines." Current Opinion in Biotechnology 21, no. 4 (August 2010): 376–91. http://dx.doi.org/10.1016/j.copbio.2010.06.001.

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11

Liu, Jianbing, Zhengang Wang, Shuai Zhao, and Baoquan Ding. "Multifunctional nucleic acid nanostructures for gene therapies." Nano Research 11, no. 10 (May 23, 2018): 5017–27. http://dx.doi.org/10.1007/s12274-018-2093-x.

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12

Wang, Xudong, Min Xu, Kaixun Huang, Xiaoding Lou, and Fan Xia. "AIEgens/Nucleic Acid Nanostructures for Bioanalytical Applications." Chemistry – An Asian Journal 14, no. 6 (January 7, 2019): 689–99. http://dx.doi.org/10.1002/asia.201801595.

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13

Wang, Pengfei, Cheng Tian, Xiang Li, and Chengde Mao. "Assembly of Barcode-like Nucleic Acid Nanostructures." Small 10, no. 19 (June 30, 2014): 3923–26. http://dx.doi.org/10.1002/smll.201400942.

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14

Seeman, Nadrian C. "ChemInform Abstract: Nucleic Acid Nanostructures and Topology." ChemInform 30, no. 17 (June 16, 2010): no. http://dx.doi.org/10.1002/chin.199917346.

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15

Fu, Jinglin, Sung Won Oh, Kristin Monckton, Georgia Arbuckle‐Keil, Yonggang Ke, and Ting Zhang. "Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures." Small 15, no. 26 (March 18, 2019): 1900256. http://dx.doi.org/10.1002/smll.201900256.

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16

Pan, Keyao, Etienne Boulais, Lun Yang, and Mark Bathe. "Structure-based model for light-harvesting properties of nucleic acid nanostructures." Nucleic Acids Research 42, no. 4 (December 5, 2013): 2159–70. http://dx.doi.org/10.1093/nar/gkt1269.

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Abstract Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.

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17

Hashemzadeh, Mohammad S. "Peptide nucleic acid (PNA) as a novel tool in the detection and treatment of biological threatening diseases." Romanian Journal of Military Medicine 124, no. 1 (January 2, 2021): 54–60. http://dx.doi.org/10.55453/rjmm.2021.124.1.7.

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"Abstract: Peptide Nucleic Acids (PNAs) are nanostructures similar to nucleic acid molecules (synthetic DNA/RNA analogs) wherein the negatively charged backbone (sugar-phosphate) present in DNA/RNA molecules is replaced by a backbone without polyamide or peptide charge. Later, it was found that PNAs containing both purine and pyrimidine bases form highly stable duplexes with DNA and RNA. Although it is not as stable as 2PNA/DNA triplexes containing a homopyrimidine strand, it is still more stable than DNA/DNA and/or DNA/RNA duplexes. The unique characteristics of PNAs add new aspects to these nanostructures relative to conventional analogs to make them appropriate for molecular biology studies. The most important applications include the use of these nanostructures in the detection and treatment of diseases caused by threatening biological agents using the antisense/antigen technology and as genetic regulator drugs. Keywords: Peptide Nucleic Acids (PNAs), synthetic DNA analog, genetic regulator drugs, antisense-antigen technology"

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18

Kim, Haejoo, and Minseok Kwak. "Structures and Applications of Nucleic Acid-Based Micelles for Cancer Therapy." International Journal of Molecular Sciences 24, no. 2 (January 13, 2023): 1592. http://dx.doi.org/10.3390/ijms24021592.

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Nucleic acids have become important building blocks in nanotechnology over the last 30 years. DNA and RNA can sequentially build specific nanostructures, resulting in versatile drug delivery systems. Self-assembling amphiphilic nucleic acids, composed of hydrophilic and hydrophobic segments to form micelle structures, have the potential for cancer therapeutics due to their ability to encapsulate hydrophobic agents into their core and position functional groups on the surface. Moreover, DNA or RNA within bio-compatible micelles can function as drugs by themselves. This review introduces and discusses nucleic acid-based spherical micelles from diverse amphiphilic nucleic acids and their applications in cancer therapy.

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19

Zhang, Zhikun, Xiaojie Ye, Qingqing Liu, Cuixia Hu, Jimmy Yun, Runjing Liu, and Yumin Liu. "Colorimetric Nucleic Acid Detection Based on Gold Nanoparticles with Branched DNA." Nano 15, no. 08 (August 2020): 2050110. http://dx.doi.org/10.1142/s1793292020501106.

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Nucleic acid detection is becoming increasingly important in the diagnostics of genetic diseases for biological analysis. We herein propose gold nanoparticles as probe for colorimetric detection of nucleic acids with branched DNA nanostructures, which enables a novel and simple colorimetric biosensor. In our system, the target DNA specifically triggered two short-chain ssDNA probes to generate branched DNA nanostructures (Y-shape DNA), which prevent AuNPs from aggregation in aqueous NaCl solution. On the contrary, when the target DNA did not exist, gold nanoparticles were unstable and aggregated easily because there is no anti-aggregation function from Y-shape DNA. Sensor response was found to be proportional to the target DNA concentration from 5 to 100[Formula: see text]nM, with detection limits determined as 5[Formula: see text]nM. The developed platform is for colorimetric nucleic acid detection without enzymes, label and modification holds great promise for practical applications.

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20

Subjakova, Veronika, Veronika Oravczova, and Tibor Hianik. "Polymer Nanoparticles and Nanomotors Modified by DNA/RNA Aptamers and Antibodies in Targeted Therapy of Cancer." Polymers 13, no. 3 (January 21, 2021): 341. http://dx.doi.org/10.3390/polym13030341.

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Polymer nanoparticles and nano/micromotors are novel nanostructures that are of increased interest especially in the diagnosis and therapy of cancer. These structures are modified by antibodies or nucleic acid aptamers and can recognize the cancer markers at the membrane of the cancer cells or in the intracellular side. They can serve as a cargo for targeted transport of drugs or nucleic acids in chemo- immuno- or gene therapy. The various mechanisms, such as enzyme, ultrasound, magnetic, electrical, or light, served as a driving force for nano/micromotors, allowing their transport into the cells. This review is focused on the recent achievements in the development of polymer nanoparticles and nano/micromotors modified by antibodies and nucleic acid aptamers. The methods of preparation of polymer nanoparticles, their structure and properties are provided together with those for synthesis and the application of nano/micromotors. The various mechanisms of the driving of nano/micromotors such as chemical, light, ultrasound, electric and magnetic fields are explained. The targeting drug delivery is based on the modification of nanostructures by receptors such as nucleic acid aptamers and antibodies. Special focus is therefore on the method of selection aptamers for recognition cancer markers as well as on the comparison of the properties of nucleic acid aptamers and antibodies. The methods of immobilization of aptamers at the nanoparticles and nano/micromotors are provided. Examples of applications of polymer nanoparticles and nano/micromotors in targeted delivery and in controlled drug release are presented. The future perspectives of biomimetic nanostructures in personalized nanomedicine are also discussed.

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21

Tan, Xuyu, Ben B. Li, Xueguang Lu, Fei Jia, Clarissa Santori, Priyanka Menon, Hui Li, Bohan Zhang, Jean J. Zhao, and Ke Zhang. "Light-Triggered, Self-Immolative Nucleic Acid-Drug Nanostructures." Journal of the American Chemical Society 137, no. 19 (May 7, 2015): 6112–15. http://dx.doi.org/10.1021/jacs.5b00795.

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22

McCluskey, Joshua B., Douglas S. Clark, and Dominic J. Glover. "Functional Applications of Nucleic Acid–Protein Hybrid Nanostructures." Trends in Biotechnology 38, no. 9 (September 2020): 976–89. http://dx.doi.org/10.1016/j.tibtech.2020.02.007.

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23

de Vries, Jan Willem, Feng Zhang, and Andreas Herrmann. "Drug delivery systems based on nucleic acid nanostructures." Journal of Controlled Release 172, no. 2 (December 2013): 467–83. http://dx.doi.org/10.1016/j.jconrel.2013.05.022.

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24

Kwak, Minseok, and Andreas Herrmann. "Nucleic acid amphiphiles: synthesis and self-assembled nanostructures." Chemical Society Reviews 40, no. 12 (2011): 5745. http://dx.doi.org/10.1039/c1cs15138j.

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25

Chandrasekaran, Arun Richard, Heitham Wady, and Hari K. K. Subramanian. "Nucleic Acid Nanostructures for Chemical and Biological Sensing." Small 12, no. 20 (April 4, 2016): 2689–700. http://dx.doi.org/10.1002/smll.201503854.

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26

Poppleton, Erik, Aatmik Mallya, Swarup Dey, Joel Joseph, and Petr Šulc. "Nanobase.org: a repository for DNA and RNA nanostructures." Nucleic Acids Research 50, no. D1 (November 8, 2021): D246—D252. http://dx.doi.org/10.1093/nar/gkab1000.

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Abstract We introduce a new online database of nucleic acid nanostructures for the field of DNA and RNA nanotechnology. The database implements an upload interface, searching and database browsing. Each deposited nanostructures includes an image of the nanostructure, design file, an optional 3D view, and additional metadata such as experimental data, protocol or literature reference. The database accepts nanostructures in any preferred format used by the uploader for the nanostructure design. We further provide a set of conversion tools that encourage design file conversion into common formats (oxDNA and PDB) that can be used for setting up simulations, interactive editing or 3D visualization. The aim of the repository is to provide to the DNA/RNA nanotechnology community a resource for sharing their designs for further reuse in other systems and also to function as an archive of the designs that have been achieved in the field so far. Nanobase.org is available at https://nanobase.org/.

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27

Valsangkar, Vibhav A., Arun Richard Chandrasekaran, Lifeng Zhuo, Song Mao, Goh Woon Lee, Megan Kizer, Xing Wang, Ken Halvorsen, and Jia Sheng. "Click and photo-release dual-functional nucleic acid nanostructures." Chemical Communications 55, no. 65 (2019): 9709–12. http://dx.doi.org/10.1039/c9cc03806j.

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28

Yamankurt, Gokay, Robert J. Stawicki, Diana M. Posadas, Joseph Q. Nguyen, Richard W. Carthew, and Chad A. Mirkin. "The effector mechanism of siRNA spherical nucleic acids." Proceedings of the National Academy of Sciences 117, no. 3 (January 3, 2020): 1312–20. http://dx.doi.org/10.1073/pnas.1915907117.

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Spherical nucleic acids (SNAs) are nanostructures formed by chemically conjugating short linear strands of oligonucleotides to a nanoparticle template. When made with modified small interfering RNA (siRNA) duplexes, SNAs act as single-entity transfection and gene silencing agents and have been used as lead therapeutic constructs in several disease models. However, the manner in which modified siRNA duplex strands that comprise the SNA lead to gene silencing is not understood. Herein, a systematic analysis of siRNA biochemistry involving SNAs shows that Dicer cleaves the modified siRNA duplex from the surface of the nanoparticle, and the liberated siRNA subsequently functions in a way that is dependent on the canonical RNA interference mechanism. By leveraging this understanding, a class of SNAs was chemically designed which increases the siRNA content by an order of magnitude through covalent attachment of each strand of the duplex. As a consequence of increased nucleic acid content, this nanostructure architecture exhibits less cell cytotoxicity than conventional SNAs without a decrease in siRNA activity.

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29

Thompson, Avery. "Building and evaluating nucleic acid nanostructures for in vivo applications." Scilight 2023, no. 3 (January 20, 2023): 031105. http://dx.doi.org/10.1063/10.0017093.

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30

Valsangkar, Vibhav A., Arun Richard Chandrasekaran, Lifeng Zhou, Song Mao, Goh Woon Lee, Megan Kizer, Xing Wang, Ken Halvorsen, and Jia Sheng. "Correction: Click and photo-release dual-functional nucleic acid nanostructures." Chemical Communications 55, no. 69 (2019): 10320. http://dx.doi.org/10.1039/c9cc90365h.

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31

Sun, Yue, Lingxian Meng, Yuxin Zhang, Dan Zhao, and Yunfeng Lin. "The Application of Nucleic Acids and Nucleic Acid Materials in Antimicrobial Research." Current Stem Cell Research & Therapy 16, no. 1 (December 1, 2021): 66–73. http://dx.doi.org/10.2174/1574888x15666200521084417.

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Due to the misuse of antibiotics, multiple drug-resistant pathogenic bacteria have increasingly emerged. This has increased the difficulty of treatment as these bacteria directly affect public health by diminishing the potency of existing antibiotics. Developing alternative therapeutic strategies is the urgent need to reduce the mortality and morbidity related to drug-resistant bacterial infections. In the past 10 to 20 years, nanomedicines have been widely studied and applied as an antibacterial agent. They have become a novel tool for fighting resistant bacteria. The most common innovative substances, metal and metal oxide nanoparticles (NPs), have been widely reported. Until recently, DNA nanostructures were used alone or functionalized with specific DNA sequences by many scholars for antimicrobial purposes which were alternatively selected as therapy for severe bacterial infections. These are a potential candidate for treatments and have a considerable role in killing antibiotic-resistant bacteria. This review involves the dimensions of multidrug resistance and the mechanism of bacteria developing drug resistance. The importance of this article is that we summarized the current study of nano-materials based on nucleic acids in antimicrobial use. Meanwhile, the current progress and the present obstacles for their antibacterial and therapeutic use and special function of stem cells in this field are also discussed.

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32

Prajapati, Rama, and Álvaro Somoza. "Albumin Nanostructures for Nucleic Acid Delivery in Cancer: Current Trend, Emerging Issues, and Possible Solutions." Cancers 13, no. 14 (July 9, 2021): 3454. http://dx.doi.org/10.3390/cancers13143454.

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Cancer is one of the major health problems worldwide, and hence, suitable therapies with enhanced efficacy and reduced side effects are desired. Gene therapy, involving plasmids, small interfering RNAs, and antisense oligonucleotides have been showing promising potential in cancer therapy. In recent years, the preparation of various carriers for nucleic acid delivery to the tumor sites is gaining attention since intracellular and extracellular barriers impart major challenges in the delivery of naked nucleic acids. Albumin is a versatile protein being used widely for developing carriers for nucleic acids. It provides biocompatibility, tumor specificity, the possibility for surface modification, and reduces toxicity. In this review, the advantages of using nucleic acids in cancer therapy and the challenges associated with their delivery are presented. The focus of this article is on the different types of albumin nanocarriers, such as nanoparticles, polyplexes, and nanoconjugates, employed to overcome the limitations of the direct use of nucleic acids in vivo. This review also highlights various approaches for the modification of the surface of albumin to enhance its transfection efficiency and targeted delivery in the tumor sites.

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33

Fu, Jinglin, Gabriele Stankeviciute, Sung Won Oh, John Collins, Yinghui Zhong, and Ting Zhang. "Self-assembled Nucleic Acid Nanostructures for Cancer Theranostic Medicines." Current Topics in Medicinal Chemistry 17, no. 16 (April 28, 2017): 1815–28. http://dx.doi.org/10.2174/1568026617666161122115722.

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34

Buchberger, Alex, Chad R. Simmons, Nour Eddine Fahmi, Ronit Freeman, and Nicholas Stephanopoulos. "Hierarchical Assembly of Nucleic Acid/Coiled-Coil Peptide Nanostructures." Journal of the American Chemical Society 142, no. 3 (December 10, 2019): 1406–16. http://dx.doi.org/10.1021/jacs.9b11158.

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35

Fu, Jinglin, Minghui Liu, Yan Liu, and Hao Yan. "Spatially-Interactive Biomolecular Networks Organized by Nucleic Acid Nanostructures." Accounts of Chemical Research 45, no. 8 (May 29, 2012): 1215–26. http://dx.doi.org/10.1021/ar200295q.

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36

Gudipati, Saketh, Ke Zhang, and Jessica L. Rouge. "Towards Self-Transfecting Nucleic Acid Nanostructures for Gene Regulation." Trends in Biotechnology 37, no. 9 (September 2019): 983–94. http://dx.doi.org/10.1016/j.tibtech.2019.01.008.

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37

Chandler, Morgan, Martin Panigaj, Lewis A. Rolband, and Kirill A. Afonin. "Challenges in optimizing RNA nanostructures for large-scale production and controlled therapeutic properties." Nanomedicine 15, no. 13 (June 2020): 1331–40. http://dx.doi.org/10.2217/nnm-2020-0034.

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Nucleic acids have been utilized to construct an expansive collection of nanoarchitectures varying in design, physicochemical properties, cellular processing and biomedical applications. However, the broader therapeutic adaptation of nucleic acid nanoassemblies in general, and RNA-based nanoparticles in particular, have faced several challenges in moving towards (pre)clinical settings. For one, the large-batch synthesis of nucleic acids is still under development, with multi-stranded and chemically modified assemblies requiring greater production capacity while maintaining consistent medical-grade outputs. Furthermore, the unknown immunostimulation by these nanomaterials poses additional challenges, necessary to be overcome for optimizing future development of clinically approved RNA nanoparticles.

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38

Dabkowska, Aleksandra P., Agnes Michanek, Luc Jaeger, Michael Rabe, Arkadiusz Chworos, Fredrik Höök, Tommy Nylander, and Emma Sparr. "Assembly of RNA nanostructures on supported lipid bilayers." Nanoscale 7, no. 2 (2015): 583–96. http://dx.doi.org/10.1039/c4nr05968a.

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39

Higashi, Sayuri L., Normazida Rozi, Sharina Abu Hanifah, and Masato Ikeda. "Supramolecular Architectures of Nucleic Acid/Peptide Hybrids." International Journal of Molecular Sciences 21, no. 24 (December 12, 2020): 9458. http://dx.doi.org/10.3390/ijms21249458.

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Supramolecular architectures that are built artificially from biomolecules, such as nucleic acids or peptides, with structural hierarchical orders ranging from the molecular to nano-scales have attracted increased attention in molecular science research fields. The engineering of nanostructures with such biomolecule-based supramolecular architectures could offer an opportunity for the development of biocompatible supramolecular (nano)materials. In this review, we highlighted a variety of supramolecular architectures that were assembled from both nucleic acids and peptides through the non-covalent interactions between them or the covalently conjugated molecular hybrids between them.

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40

Wang, Fei, Pan Li, Hoi Ching Chu, and Pik Kwan Lo. "Nucleic Acids and Their Analogues for Biomedical Applications." Biosensors 12, no. 2 (February 4, 2022): 93. http://dx.doi.org/10.3390/bios12020093.

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Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.

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41

Dantsu, Yuliya, Ying Zhang, and Wen Zhang. "Advances in Therapeutic L-Nucleosides and L-Nucleic Acids with Unusual Handedness." Genes 13, no. 1 (December 24, 2021): 46. http://dx.doi.org/10.3390/genes13010046.

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Nucleic-acid-based small molecule and oligonucleotide therapies are attractive topics due to their potential for effective target of disease-related modules and specific control of disease gene expression. As the non-naturally occurring biomolecules, modified DNA/RNA nucleoside and oligonucleotide analogues composed of L-(deoxy)riboses, have been designed and applied as innovative therapeutics with superior plasma stability, weakened cytotoxicity, and inexistent immunogenicity. Although all the chiral centers in the backbone are mirror converted from the natural D-nucleic acids, L-nucleic acids are equipped with the same nucleobases (A, G, C and U or T), which are critical to maintain the programmability and form adaptable tertiary structures for target binding. The types of L-nucleic acid drugs are increasingly varied, from chemically modified nucleoside analogues that interact with pathogenic polymerases to nanoparticles containing hundreds of repeating L-nucleotides that circulate durably in vivo. This article mainly reviews three different aspects of L-nucleic acid therapies, including pharmacological L-nucleosides, Spiegelmers as specific target-binding aptamers, and L-nanostructures as effective drug-delivery devices.

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42

Xia, Jiarui, Wenwen Li, Mengtao Sun, and Huiting Wang. "Application of SERS in the Detection of Fungi, Bacteria and Viruses." Nanomaterials 12, no. 20 (October 12, 2022): 3572. http://dx.doi.org/10.3390/nano12203572.

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In this review, we report the recent advances of SERS in fungi, bacteria, and viruses. Firstly, we briefly introduce the advantage of SERS over fluorescence on virus identification and detection. Secondly, we review the feasibility analysis of Raman/SERS spectrum analysis, identification, and fungal detection on SERS substrates of various nanostructures with a signal amplification mechanism. Thirdly, we focus on SERS spectra for nucleic acid, pathogens for the detection of viruses and bacteria, and furthermore introduce SERS-based microdevices, including SERS-based microfluidic devices, and three-dimensional nanostructured plasmonic substrates.

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43

Poppleton, Erik, Joakim Bohlin, Michael Matthies, Shuchi Sharma, Fei Zhang, and Petr Šulc. "Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation." Nucleic Acids Research 48, no. 12 (May 25, 2020): e72-e72. http://dx.doi.org/10.1093/nar/gkaa417.

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Abstract This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures.

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IWAURA, Rika. "Diverse Nanostructures Formed from Nucleic Acid−Appended Amphiphilic Lipid Molecules." Oleoscience 14, no. 7 (2014): 275–82. http://dx.doi.org/10.5650/oleoscience.14.275.

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Kwak, Minseok, and Andreas Herrmann. "ChemInform Abstract: Nucleic Acid Amphiphiles: Synthesis and Self-Assembled Nanostructures." ChemInform 43, no. 12 (February 23, 2012): no. http://dx.doi.org/10.1002/chin.201212239.

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Ghosal, Souvik, Sagar Bag, and Sudipta Bhowmik. "Unravelling the Drug Encapsulation Ability of Functional DNA Origami Nanostructures: Current Understanding and Future Prospects on Targeted Drug Delivery." Polymers 15, no. 8 (April 12, 2023): 1850. http://dx.doi.org/10.3390/polym15081850.

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Rapid breakthroughs in nucleic acid nanotechnology have always driven the creation of nano-assemblies with programmable design, potent functionality, good biocompatibility, and remarkable biosafety during the last few decades. Researchers are constantly looking for more powerful techniques that provide enhanced accuracy with greater resolution. The self-assembly of rationally designed nanostructures is now possible because of bottom-up structural nucleic acid (DNA and RNA) nanotechnology, notably DNA origami. Because DNA origami nanostructures can be organized precisely with nanoscale accuracy, they serve as a solid foundation for the exact arrangement of other functional materials for use in a number of applications in structural biology, biophysics, renewable energy, photonics, electronics, medicine, etc. DNA origami facilitates the creation of next-generation drug vectors to help in the solving of the rising demand on disease detection and therapy, as well as other biomedicine-related strategies in the real world. These DNA nanostructures, generated using Watson–Crick base pairing, exhibit a wide variety of properties, including great adaptability, precise programmability, and exceptionally low cytotoxicity in vitro and in vivo. This paper summarizes the synthesis of DNA origami and the drug encapsulation ability of functionalized DNA origami nanostructures. Finally, the remaining obstacles and prospects for DNA origami nanostructures in biomedical sciences are also highlighted.

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Chandrasekaran, Arun Richard, Johnsi Mathivanan, Parisa Ebrahimi, Javier Vilcapoma, Alan A. Chen, Ken Halvorsen, and Jia Sheng. "Hybrid DNA/RNA nanostructures with 2′-5′ linkages." Nanoscale 12, no. 42 (2020): 21583–90. http://dx.doi.org/10.1039/d0nr05846g.

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We report here the first instance of nucleic acid nanostructures that contain 2′-5′ linkages and characterize structures of different complexities: a simple duplex to a 4-arm junction, a double crossover (DX) motif and a tensegrity triangle motif.

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Li, Yueran, Xifeng Chen, Bidou Wang, Guangxing Liu, Yuguo Tang, and Peng Miao. "DNA tetrahedron and star trigon nanostructures for target recycling detection of nucleic acid." Analyst 141, no. 11 (2016): 3239–41. http://dx.doi.org/10.1039/c6an00762g.

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Wang, Shuya, Lei Qin, Gokay Yamankurt, Kacper Skakuj, Ziyin Huang, Peng-Cheng Chen, Donye Dominguez, Andrew Lee, Bin Zhang, and Chad A. Mirkin. "Rational vaccinology with spherical nucleic acids." Proceedings of the National Academy of Sciences 116, no. 21 (May 8, 2019): 10473–81. http://dx.doi.org/10.1073/pnas.1902805116.

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In the case of cancer immunotherapy, nanostructures are attractive because they can carry all of the necessary components of a vaccine, including both antigen and adjuvant. Herein, we explore how spherical nucleic acids (SNAs), an emerging class of nanotherapeutic materials, can be used to deliver peptide antigens and nucleic acid adjuvants to raise immune responses that kill cancer cells, reduce (or eliminate) tumor growth, and extend life in three established mouse tumor models. Three SNA structures that are compositionally nearly identical but structurally different markedly vary in their abilities to cross-prime antigen-specific CD8+ T cells and raise subsequent antitumor immune responses. Importantly, the most effective structure is the one that exhibits synchronization of maximum antigen presentation and costimulatory marker expression. In the human papillomavirus-associated TC-1 model, vaccination with this structure improved overall survival, induced the complete elimination of tumors from 30% of the mice, and conferred curative protection from tumor rechallenges, consistent with immunological memory not otherwise achievable. The antitumor effect of SNA vaccination is dependent on the method of antigen incorporation within the SNA structure, underscoring the modularity of this class of nanostructures and the potential for the deliberate design of new vaccines, thereby defining a type of rational cancer vaccinology.

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Wang, Jing, Dong-Xia Wang, Jia-Yi Ma, Ya-Xin Wang, and De-Ming Kong. "Three-dimensional DNA nanostructures to improve the hyperbranched hybridization chain reaction." Chemical Science 10, no. 42 (2019): 9758–67. http://dx.doi.org/10.1039/c9sc02281c.

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