DNA and RNA nanotechnology最新文献

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Nucleic Acid Computing and its Potential to Transform Silicon-Based Technology 核酸计算及其改变硅基技术的潜力

DNA and RNA nanotechnology

Pub Date : 2015-12-17 DOI: 10.1515/rnan-2015-0003

Seth G. Abels, Emil F Khisamutdinov

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.

分子计算机已经在地球上存在了超过35亿年。由核酸等生物物质组成的分子计算设备负责对各种输入进行逻辑处理，产生可行的输出，这些输出是所有生物体细胞机器的关键组成部分。我们已经开始采用一些细胞装置的结构和功能知识，以便在体外和体内制造基于核酸的分子计算机。核酸计算直接依赖于DNA和RNA纳米技术的进步。该领域仍处于新兴阶段，许多挑战依然存在。也许其中最突出的是如何将众多研究实验室开发的各种基于核酸的逻辑门转化为基于硅的计算领域。这篇小型综述提供了一些关于基于核酸的计算进展的基本信息，以及它作为一种可能彻底改变基于硅的技术的替代方案的潜力。

引用次数: 5

Structural identification of the novel 3 way-junction motif 新型三路结基序的结构鉴定

DNA and RNA nanotechnology

Pub Date : 2015-01-18 DOI: 10.1515/rnan-2015-0004

D. Jedrzejczyk, A. Chworos

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.

摘要采用计算结构建模的方法，根据RNA基序序列鉴定出一个新的RNA基序。据报道，RNA分子是结构特异性核糖核酸内切酶Dicer的底物，该酶可切割双链RNA并切割20 - 25个核苷酸片段。这种酶的性质对于该基序在进一步生物实验的纳米颗粒设计中的潜在利用是必不可少的。本文提出了该基序的结构预测方案，从其一级序列开始，通过二级和三级结构预测。应用RNA结构学原理，利用这种新型结构基序3wj-nRA进行合理的RNA纳米颗粒设计。基于这种三向结折叠的分子可以组装成更复杂的三角形纳米物体。这种含有3wj-nRA基序的三聚体纳米颗粒可以进一步用于功能化和应用。

引用次数: 3

Triggering RNAi with multifunctional RNA nanoparticles and their delivery. 利用多功能 RNA 纳米粒子及其传输技术触发 RNAi。

DNA and RNA nanotechnology

Pub Date : 2015-01-01 Epub Date: 2015-07-27 DOI: 10.1515/rnan-2015-0001

Bich Ngoc Dao, Mathias Viard, Angelica N Martins, Wojciech K Kasprzak, Bruce A Shapiro, Kirill A Afonin

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 via 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) a priori 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.

蛋白质被认为是人体结构、功能和代谢调节的关键因素。传统疗法中使用的机制通常依赖于用小分子抑制蛋白质，但另一种有希望治疗疾病的方法是靶向相应的 mRNA。1998 年，克雷格-梅洛（Craig Mellow）和安德鲁-费尔（Andrew Fire）发现了通过 RNA 干扰或 RNAi 来介导的 dsRNA 基因沉默。这一发现为新的基因沉默方法带来了几乎无限的可能性，从而为临床医学打开了新的大门。RNAi 是一种通过靶向 mRNA 抑制基因表达的生物过程。基于 RNAi 的疗法有几个潜在的优势：(i) 可以先验地靶向任何基因；(ii) 设计过程相对简单；(iii) 位点特异性；(iv) 效力；(v) 可以安全、选择性地敲除靶细胞。然而，RNAi 疗法的配方和给药存在问题，包括排泄快、在血液中不稳定、细胞吸收差以及细胞内释放效率低。为了解决这些问题，人们正在开发不同类型的 RNAi 治疗递送策略，包括多功能 RNA 纳米颗粒。在这篇小型综述中，我们将简要介绍目前的一些方法。

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引用次数: 0

Engineered RNA Nanodesigns for Applications in RNA Nanotechnology. 用于 RNA 纳米技术应用的工程 RNA 纳米设计。

DNA and RNA nanotechnology

Pub Date : 2015-01-01 Epub Date: 2013-05-31 DOI: 10.2478/rnan-2013-0001

Kirill A Afonin, Brian Lindsay, Bruce A Shapiro

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 de novo 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.

核酸因其独特的生化特性和功能，已成为纳米技术应用中极具前景的平台。尤其是 RNA，其特点是热稳定性相对较高，结构灵活多样，并能在自然界中发挥各种功能。这些特性使 RNA 成为生物纳米技术（特别是 RNA 纳米技术）的重要平台，通过设计、整合和再造基于各种现有 RNA 结构及其基本生化特性的强大机制，可以创造出具有独特功能的全新纳米结构。本综述强调了合理设计 RNA 纳米结构的基本原理，介绍了用于构建自组装纳米粒子的主要策略，并讨论了 RNA 纳米技术未来应用所面临的挑战和可能性。

引用次数: 0

Vehicles for Small Interfering RNA transfection: Exosomes versus Synthetic Nanocarriers 小干扰RNA转染载体:外泌体与合成纳米载体

DNA and RNA nanotechnology

Pub Date : 2013-05-31 DOI: 10.2478/rnan-2013-0002

M. Duechler

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.

基于RNA干扰(RNAi)的治疗方法在靶向干扰特定基因的表达方面具有很大的潜力。小干扰rna (siRNA)和微rna通过诱导信使rna降解或阻断其翻译来中断蛋白质合成。基于rnai的治疗方法可以调节其他不可药物的靶蛋白的表达。充分利用RNAi用于医疗目的取决于有效和安全的方法将小rna递送到靶细胞。合成载体的开发已经付出了巨大的努力，以满足将核酸有效输送到特定组织的所有要求。最近，外泌体揭示了它们作为一种天然通讯系统的功能，可用于将小rna运输到靶细胞中。在这篇综述中，外泌体作为小rna的运载工具的能力与合成载体系统进行了比较。考虑了高效转染的一步一步要求:载体的生产，RNA装载，防止降解，缺乏免疫原性，靶向可能性，细胞摄取，细胞毒性，RNA释放到细胞质和基因沉默效率。基于外泌体的siRNA传递系统显示出许多优于传统转染试剂的优点，然而，在实现广泛的临床应用之前，一些关键问题需要进一步优化。

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引用次数: 10

DNA Nanotechnology: From Structure to Function DNA纳米技术:从结构到功能

DNA and RNA nanotechnology

Pub Date : 2013-01-01 DOI: 10.1007/978-3-642-36077-0

Chunhai Fan

引用次数: 9

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