{"title":"Nucleic Acid Computing and its Potential to Transform Silicon-Based Technology","authors":"Seth G. Abels, Emil F Khisamutdinov","doi":"10.1515/rnan-2015-0003","DOIUrl":"https://doi.org/10.1515/rnan-2015-0003","url":null,"abstract":"Abstract Molecular computers have existed on our planet for more than 3.5 billion years. Molecular computing devices, composed of biological substances such as nucleic acids, are responsible for the logical processing of a variety of inputs, creating viable outputs that are key components of the cellular machinery of all living organisms. We have begun to adopt some of the structural and functional knowledge of the cellular apparatus in order to fabricate nucleic-acid-based molecular computers in vitro and in vivo. Nucleic acid computing is directly dependent on advances in DNA and RNA nanotechnology. The field is still emerging and a number of challenges persist. Perhaps the most salient among these is how to translate a variety of nucleic-acid-based logic gates, developed by numerous research laboratories, into the realm of silicon-based computing. This mini-review provides some basic information on the advances in nucleic-acid-based computing and its potential to serve as an alternative that can revolutionize silicon-based technology.","PeriodicalId":93282,"journal":{"name":"DNA and RNA nanotechnology","volume":"2 1","pages":"13 - 22"},"PeriodicalIF":0.0,"publicationDate":"2015-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1515/rnan-2015-0003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66982654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structural identification of the novel 3 way-junction motif","authors":"D. Jedrzejczyk, A. Chworos","doi":"10.1515/rnan-2015-0004","DOIUrl":"https://doi.org/10.1515/rnan-2015-0004","url":null,"abstract":"Abstract A novel RNA motif was identified based on its sequence by computational structure modeling. The RNA molecule was reported to be a substrate for the structurally specific endoribonuclease, Dicer, which cleaves doublestranded RNA and cuts out 20−25 nucleotide fragments. This enzymatic property was essential for the potential utilization of the motif in the nanoparticle design of further biological experiments. Herein, the protocol for the prediction of the structure of this motif in-silico is presented, starting from its primary sequence and proceeding through secondary and tertiary structure predictions. Applying RNA architectonics, this novel structural motif, 3wj-nRA, was used for rational RNA nanoparticle design. The molecules, which are based on this three-way junction fold, may assemble into more complex, triangular shaped nano-objects. This trimeric nanoparticle containing 3wj-nRA motif can be further utilized for functionalization and application.","PeriodicalId":93282,"journal":{"name":"DNA and RNA nanotechnology","volume":"2 1","pages":"36 - 41"},"PeriodicalIF":0.0,"publicationDate":"2015-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1515/rnan-2015-0004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66982318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bich Ngoc Dao, Mathias Viard, Angelica N Martins, Wojciech K Kasprzak, Bruce A Shapiro, Kirill A Afonin
{"title":"Triggering RNAi with multifunctional RNA nanoparticles and their delivery.","authors":"Bich Ngoc Dao, Mathias Viard, Angelica N Martins, Wojciech K Kasprzak, Bruce A Shapiro, Kirill A Afonin","doi":"10.1515/rnan-2015-0001","DOIUrl":"10.1515/rnan-2015-0001","url":null,"abstract":"<p><p>Proteins are considered to be the key players in structure, function, and metabolic regulation of our bodies. The mechanisms used in conventional therapies often rely on inhibition of proteins with small molecules, but another promising method to treat disease is by targeting the corresponding mRNAs. In 1998, Craig Mellow and Andrew Fire discovered dsRNA-mediated gene silencing <i>via</i> RNA interference or RNAi. This discovery introduced almost unlimited possibilities for new gene silencing methods, thus opening new doors to clinical medicine. RNAi is a biological process that inhibits gene expression by targeting the mRNA. RNAi-based therapeutics have several potential advantages (i) <i>a priori</i> ability to target any gene, (ii) relatively simple design process, (iii) site-specificity, (iv) potency, and (v) a potentially safe and selective knockdown of the targeted cells. However, the problem lies within the formulation and delivery of RNAi therapeutics including rapid excretion, instability in the bloodstream, poor cellular uptake, and inefficient intracellular release. In an attempt to solve these issues, different types of RNAi therapeutic delivery strategies including multifunctional RNA nanoparticles are being developed. In this mini-review, we will briefly describe some of the current approaches.</p>","PeriodicalId":93282,"journal":{"name":"DNA and RNA nanotechnology","volume":"2 1","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6b/b8/nihms-1723228.PMC8315566.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39254691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Engineered RNA Nanodesigns for Applications in RNA Nanotechnology.","authors":"Kirill A Afonin, Brian Lindsay, Bruce A Shapiro","doi":"10.2478/rnan-2013-0001","DOIUrl":"10.2478/rnan-2013-0001","url":null,"abstract":"<p><p>Nucleic acids have emerged as an extremely promising platform for nanotechnological applications because of their unique biochemical properties and functions. RNA, in particular, is characterized by relatively high thermal stability, diverse structural flexibility, and its capacity to perform a variety of functions in nature. These properties make RNA a valuable platform for bio-nanotechnology, specifically RNA Nanotechnology, that can create <b><i>de novo</i></b> nanostructures with unique functionalities through the design, integration, and re-engineering of powerful mechanisms based on a variety of existing RNA structures and their fundamental biochemical properties. This review highlights the principles that underlie the rational design of RNA nanostructures, describes the main strategies used to construct self-assembling nanoparticles, and discusses the challenges and possibilities facing the application of RNA Nanotechnology in the future.</p>","PeriodicalId":93282,"journal":{"name":"DNA and RNA nanotechnology","volume":"1 1","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8315564/pdf/nihms-1723729.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39254690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Vehicles for Small Interfering RNA transfection: Exosomes versus Synthetic Nanocarriers","authors":"M. Duechler","doi":"10.2478/rnan-2013-0002","DOIUrl":"https://doi.org/10.2478/rnan-2013-0002","url":null,"abstract":"Abstract Therapies based on RNA interference (RNAi) hold a great potential for targeted interference of the expression of specific genes. Small-interfering RNAs (siRNA) and micro-RNAs interrupt protein synthesis by inducing the degradation of messenger RNAs or by blocking their translation. RNAibased therapies can modulate the expression of otherwise undruggable target proteins. Full exploitation of RNAi for medical purposes depends on efficient and safe methods for delivery of small RNAs to the target cells. Tremendous effort has gone into the development of synthetic carriers to meet all requirements for efficient delivery of nucleic acids into particular tissues. Recently, exosomes unveiled their function as a natural communication system which can be utilized for the transport of small RNAs into target cells. In this review, the capabilities of exosomes as delivery vehicles for small RNAs are compared to synthetic carrier systems. The step by step requirements for efficient transfection are considered: production of the vehicle, RNA loading, protection against degradation, lack of immunogenicity, targeting possibilities, cellular uptake, cytotoxicity, RNA release into the cytoplasm and gene silencing efficiency. An exosomebased siRNA delivery system shows many advantages over conventional transfection agents, however, some crucial issues need further optimization before broad clinical application can be realized.","PeriodicalId":93282,"journal":{"name":"DNA and RNA nanotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2478/rnan-2013-0002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68797237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"DNA Nanotechnology: From Structure to Function","authors":"Chunhai Fan","doi":"10.1007/978-3-642-36077-0","DOIUrl":"https://doi.org/10.1007/978-3-642-36077-0","url":null,"abstract":"","PeriodicalId":93282,"journal":{"name":"DNA and RNA nanotechnology","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85359283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}