Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany.
Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
Molecules. 2020 Jul 7;25(13):3100. doi: 10.3390/molecules25133100.
Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and cleave the RNA sequence of interest. The RNA substrate is cleaved between central purine and pyrimidine nucleotides. The activity of this DNAzyme in vitro is considerably higher than in vivo, which was suggested to be related to its divalent cation dependency. Understanding the mechanism of DNAzyme catalysis is hindered by the absence of structural information. Numerous biological studies, however, provide comprehensive insights into the role of particular deoxynucleotides and functional groups in DNAzymes. Here we provide an overview of the thermodynamic properties, the impact of nucleobase modifications within the catalytic loop, and the role of different metal ions in catalysis. We point out features that will be helpful in developing novel strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. Consideration of these features will enable to develop improved strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. These insights provide the basis for improving activity in cells and pave the way for developing DNAzyme applications.
具有 RNA 水解活性的脱氧核酶 (DNAzyme) 在作为治疗应用的基因抑制剂方面具有巨大的潜力。研究最广泛的代表性代表是由催化环和两个底物结合臂组成的 10-23 DNAzyme，可设计为结合和切割感兴趣的 RNA 序列。RNA 底物在中心嘌呤和嘧啶核苷酸之间被切割。这种 DNAzyme 的体外活性明显高于体内活性，这被认为与其二价阳离子依赖性有关。由于缺乏结构信息，DNAzyme 催化机制的理解受到阻碍。然而，许多生物学研究提供了对 DNAzyme 中特定脱氧核苷酸和官能团作用的全面了解。在这里，我们提供了对热力学性质、催化环中核碱基修饰的影响以及不同金属离子在催化中的作用的概述。我们指出了有助于开发新型结构确定策略和理解 10-23 DNAzyme 机制的特征。考虑这些特征将能够开发出改进的结构确定策略，并理解 10-23 DNAzyme 的机制。这些见解为提高细胞内的活性提供了基础，并为开发 DNAzyme 应用铺平了道路。
