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序列定义的DNA聚合物:用于DNA纳米技术和核酸治疗的新工具。

Sequence-Defined DNA Polymers: New Tools for DNA Nanotechnology and Nucleic Acid Therapy.

作者信息

Rafique Muhammad Ghufran, Laurent Quentin, Dore Michael D, Fakih Hassan H, Trinh Tuan, Rizzuto Felix J, Sleiman Hanadi F

机构信息

Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.

University Grenoble Alpes, CNRS, DCM UMR 5250, 38058 Grenoble Cedex 9, France.

出版信息

Acc Chem Res. 2025 Jan 21;58(2):177-188. doi: 10.1021/acs.accounts.4c00580. Epub 2025 Jan 8.


DOI:10.1021/acs.accounts.4c00580
PMID:39772484
Abstract

Structural DNA nanotechnology offers a unique self-assembly toolbox to construct soft materials of arbitrary complexity, through bottom-up approaches including DNA origami, brick, wireframe, and tile-based assemblies. This toolbox can be expanded by incorporating interactions orthogonal to DNA base-pairing such as metal coordination, small molecule hydrogen bonding, π-stacking, fluorophilic interactions, or the hydrophobic effect. These interactions allow for hierarchical and long-range organization in DNA supramolecular assemblies through a DNA-minimal approach: the use of fewer unique DNA sequences to make complex structures. Here we describe our research group's work to integrate these orthogonal interactions into DNA and its supramolecular assemblies. Using automated solid phase techniques, we synthesized equence-defined NA olymers (SDPs) featuring a wide range of functional groups, achieving high yields in the process. These SDPs can assemble into not only isotropic spherical morphologies─such as spherical nucleic acids (SNAs)─but also into anisotropic nanostructures such as 1D nanofibers and 2D nanosheets. Our structural and molecular modeling studies revealed new insights into intermolecular chain packing and intramolecular chain folding, influenced by phosphodiester positioning and SDP sequence. Using these new self-assembly paradigms, we created hierarchical, anisotropic assemblies and developed systems exhibiting polymorphism and chiroptical behavior dependent on the SDP sequence. We could also precisely control the size of our nanofiber assemblies via nucleation-growth supramolecular polymerization and create compartmentalized nanostructures capable of precise surface functionalization.The exquisite control over sequence, composition, and length allowed us to combine our SDPs with nanostructures including DNA wireframe assemblies such as prisms, nanotubes, and cubes to create hybrid, stimuli-responsive assemblies exhibiting emergent structural and functional modes. The spatial control of our assemblies enabled their use as nanoreactors for chemical transformations in several ways: via hybridization chain reaction within SNA coronas, through chemical conjugation within SNA cores, and through a molecular "printing" approach within wireframe assemblies for nanoscale information transfer and the creation of anisotropic "DNA-printed" polymer particles.We have also employed our SDP nanostructures toward biological and therapeutic applications. We demonstrated that our SNAs could serve as both extrinsic and intrinsic therapeutic platforms, with improved cellular internalization and biodistribution profiles, and excellent gene silencing activities. Using SDPs incorporating hydrophobic dendrons, high-affinity and highly specific oligonucleotide binding to human serum albumin was demonstrated. These structures showed an increased stability to nuclease degradation, reduced nonspecific cellular uptake, no toxicity even at high concentrations, and excellent biodistribution beyond the liver, resulting in unprecedented gene silencing activity in various tissues.Control over the sequence has thus presented us with a unique polymeric building block in the form of the SDP, which combines the chemical and structural diversity of polymers with the programmability of DNA. By linking these orthogonal assembly languages, we have discovered new self-assembly rules, created DNA-minimal nanostructures, and demonstrated their utility through a range of applications. Developing this work further will open new avenues in the fields of DNA nanomaterials, nucleic acid therapeutics, as well as block copolymer self-assembly.

摘要

结构DNA纳米技术提供了一个独特的自组装工具箱,通过包括DNA折纸、砖块、线框和基于瓦片的组装等自下而上的方法来构建任意复杂程度的软材料。通过纳入与DNA碱基配对正交的相互作用,如金属配位、小分子氢键、π-堆积、亲氟相互作用或疏水效应,可以扩展这个工具箱。这些相互作用通过一种DNA最小化方法,即使用较少的独特DNA序列来构建复杂结构,实现了DNA超分子组装中的分层和长程组织。在这里,我们描述了我们研究小组将这些正交相互作用整合到DNA及其超分子组装中的工作。使用自动化固相技术,我们合成了具有广泛官能团的序列定义的核酸聚合物(SDPs),并在此过程中实现了高产率。这些SDPs不仅可以组装成各向同性的球形形态,如球形核酸(SNAs),还可以组装成各向异性的纳米结构,如一维纳米纤维和二维纳米片。我们的结构和分子建模研究揭示了受磷酸二酯定位和SDP序列影响的分子间链堆积和分子内链折叠的新见解。利用这些新的自组装范式,我们创建了分层的、各向异性的组装体,并开发了依赖于SDP序列表现出多态性和手性光学行为的系统。我们还可以通过成核-生长超分子聚合精确控制纳米纤维组装体的大小,并创建能够进行精确表面功能化的分隔纳米结构。对序列、组成和长度的精确控制使我们能够将SDPs与包括DNA线框组装体(如棱柱、纳米管和立方体)在内的纳米结构相结合,以创建表现出新兴结构和功能模式的混合、刺激响应组装体。我们组装体的空间控制使其能够以多种方式用作化学转化的纳米反应器:通过SNA冠层内的杂交链式反应、通过SNA核心内的化学共轭,以及通过线框组装体内的分子“打印”方法进行纳米级信息传递和创建各向异性的“DNA打印”聚合物颗粒。我们还将SDP纳米结构应用于生物和治疗应用。我们证明了我们的SNAs既可以作为外在的也可以作为内在的治疗平台,具有改善的细胞内化和生物分布特征,以及出色的基因沉默活性。使用包含疏水性树枝状分子的SDPs,证明了其对人血清白蛋白具有高亲和力和高特异性的寡核苷酸结合。这些结构对核酸酶降解表现出更高的稳定性,减少了非特异性细胞摄取,即使在高浓度下也没有毒性,并且在肝脏以外具有出色的生物分布,从而在各种组织中产生了前所未有的基因沉默活性。因此,对序列的控制为我们提供了一种独特的聚合物构建块,即SDP,它将聚合物的化学和结构多样性与DNA的可编程性结合在一起。通过连接这些正交的组装语言,我们发现了新的自组装规则,创建了DNA最小化纳米结构,并通过一系列应用证明了它们的实用性。进一步开展这项工作将为DNA纳米材料、核酸治疗以及嵌段共聚物自组装领域开辟新的途径。

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