Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Azadi Square, Hezar Jerib Avenue, 8174673441, Isfahan, Iran.
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Nucleic Acids Res. 2022 Jul 5;50(W1):W261-W265. doi: 10.1093/nar/gkac269.
Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize. In spite of their attractiveness, the choice of which DNAzyme should be used to cleave a given substrate is far from obvious, and requires expert knowledge as well as in-depth literature scrutiny. DNAzymeBuilder enables fast and automatic assembly of DNAzymes for the first time, superseding the manual design of DNAzymes. DNAzymeBuilder relies on an internal database with information on RNA and DNA cleaving DNAzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNAzyme. Based on this information and the input sequence provided by the user, DNAzymeBuilder provides a list of DNAzymes to carry out the cleavage reaction and detailed information for each of them, including the expected yield, reaction products and optimal reaction conditions. DNAzymeBuilder is a resource to help researchers introduce DNAzymes in their day-to-day research, and is publicly available at https://iimcb.genesilico.pl/DNAzymeBuilder.
核酸切割 DNA 酶是一种多功能且稳健的催化剂，在化学稳定性、价格和合成容易度方面，优于核酶和蛋白质酶。尽管它们具有吸引力，但选择哪种 DNA 酶来切割给定的底物远非显而易见，这需要专业知识以及深入的文献研究。DNAzymeBuilder 首次实现了 DNA 酶的快速自动组装，取代了 DNA 酶的手动设计。DNAzymeBuilder 依赖于一个内部数据库，其中包含有关 RNA 和 DNA 切割 DNA 酶的信息，包括它们最佳运行的反应条件、动力学参数、催化的切割反应类型、DNA 酶识别的特定序列、该序列内的切割位点以及可能对 DNA 酶的最佳活性所必需的特殊设计特征。基于这些信息和用户提供的输入序列，DNAzymeBuilder 提供了执行切割反应的 DNA 酶列表以及它们各自的详细信息，包括预期产量、反应产物和最佳反应条件。DNAzymeBuilder 是一个帮助研究人员在日常研究中引入 DNA 酶的资源，可在 https://iimcb.genesilico.pl/DNAzymeBuilder 上公开获取。
