DNA设计:通过突变对合成DNA的芯片设计具有特征意识
Yingfei Wang1, Jinsen Li1, Tsu-Pei Chiu1
1Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, United States.
Bioinformatics (Oxford, England)
|February 1, 2025
概括
DNAdesign是一个通过考虑序列和形状来设计DNA突变的网络工具. 它有助于理解基因调节和合成生物学应用.
科学领域:
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
- 结构生物学 结构生物学
背景情况:
- 蛋白质-DNA识别涉及不同的序列和形状读取机制.
- 现有的计算工具无法同时分析DNA突变的序列和形状变化.
研究的目的:
- 开发一个基于网络的工具,DNAdesign,用于比较和设计DNA突变.
- 为突变设计整合DNA序列和形状特征.
主要方法:
- DNAdesign使用Deep DNAshape进行快速的DNA形状预测,使用扩展的k-mers.
- 它支持各种核酸序列编码方法,包括物理化学性质.
- 该工具可视化突变候选人与野生类型DNA进行比较.
主要成果:
- DNAdesign提供了跨序列和形状维度的全面突变候选.
- 交互式可视化使得设计突变与野生类型DNA的比较更容易.
- 该工具支持对基因调节和合成生物学应用的研究.
结论:
- DNAdesign通过整合序列和形状数据,为突变设计提供了一种新的方法.
- 它对合成生物学中的应用非常有价值,例如设计增强剂和转录因子结合部位.
- 网络服务器可以自由访问,用于研究和开发.
相关概念视频
Synthetic Biology
4.7K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
4.7K
Conservative Site-specific Recombination and Phase Variation
5.9K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
5.9K
In-vitro Mutagenesis
13.7K
To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.
13.7K
Genome Copying Errors
4.1K
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.
4.1K
Proofreading
6.1K
Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore, it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase...
Errors During Replication are Corrected by the DNA Polymerase...
6.1K
Mismatch Repair
39.9K
Overview
39.9K


