DinoKnot:核酸与伪结的双重相互作用
IEEE/ACM transactions on computational biology and bioinformatics
|February 12, 2024
概括
我们开发了DinoKnot,这是一个高效的算法,可以预测复杂的核酸相互作用,包括伪结. 这个工具准确地建模了DNA/RNA双重结构,有助于变异查和理解分子相互作用.
科学领域:
- 计算生物学 计算生物学
- 生物技术是生物技术.
- 分子生物学分子生物学
背景情况:
- 核酸相互作用对于细胞功能和生物技术应用至关重要.
- 预测复杂的核酸结构,特别是具有伪结的核酸结构,仍然是一个计算挑战.
研究的目的:
- 介绍DinoKnot,这是一种新且高效的算法,用于预测核酸分子之间的双重相互作用的最小自由能量结构,包括伪结的结构.
- 通过使用等级折叠假设,预测两个相互作用的核酸链 (homo-和 hetero-dimers) 的二次结构.
主要方法:
- DinoKnot算法通过使用分子的相互作用前结构作为指南来预测双重结构.
- 该算法允许在双重形成期间进行基对竞争.
- 根据SARS-CoV-2的实验数据进行评估,初级探针集,临床突变示例和已知的伪结相互作用.
主要成果:
- DinoKnot准确地预测核酸双重结构,包括复杂的伪结结的配置.
- 对实验结果进行了性能验证,并与RNAcofold.fold等现有工具进行了有利的比较.
- 在分析SARS-CoV-2相互作用和影响检测的突变方面证明有用.
结论:
- DinoKnot提供了一种高效准确的方法来预测核酸双重相互作用,包括伪结.
- 该算法可用于选具有潜在检测问题的新变体.
- 支持涉及DNA/RNA相互作用的应用,将功能洞察的结构性考虑纳入其中.
更多相关视频
相关概念视频
Nucleic Acid Structure
6.1K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
DNA Structure
DNA...
6.1K
Single-Strand DNA Binding Proteins
14.1K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
14.1K
Homologous Recombination
50.5K
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
50.5K
Nucleic Acids
44.2K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
44.2K
Proofreading
54.1K
Overview
54.1K
Nucleic acids
162.3K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
162.3K


