纳米孔链特定不匹配使得细菌DNA修饰的新检测成为可能
Xudong Liu1, Ying Ni2,3,4, Lianwei Ye1
1Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China.
Genome research
|October 2, 2024
概括
细菌DNA甲基化导致纳米孔测序中的链特异错误. 一个新的管道,Hammerhead,检测这些修改没有原始信号分析,改善细菌基因组组装.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- 细菌DNA的修改具有功能意义.
- 现有的纳米孔测序方法用于检测DNA修饰依赖于原始信号比较和无甲基化对照.
- 这些方法可能很复杂,需要特定的实验设置.
研究的目的:
- 用纳米孔测序数据发现一种用于检测细菌DNA修饰的新方法.
- 开发一条绕过原始信号分析和无甲基化控制的计算管道.
- 通过纠正修改引起的错误来提高细菌基因组组合的准确性.
主要方法:
- 通过纳米孔读数中的细菌DNA修改引入的被调查的链特异性错误.
- 从FASTQ/FASTA文件直接开发了Hammerhead管道,用于新的甲基化发现.
- 实施了使用双重读取来纠正组装错误的抛光策略.
主要成果:
- 发现细菌DNA的修改会在纳米孔测序中诱导链特异性错误.
- 在没有原始信号推断的情况下,Hammerhead成功识别了16个已知的细菌甲基化动机中的14个.
- 双重阅读抛光策略将基因组组合中的修改诱导的错误减少了超过85%.
结论:
- 头提供了一种有效的方法,可以从标准的纳米孔测序阅读中定位细菌DNA甲基化位点.
- 该管道消除了对原始信号数据和控制样本的需求,简化了DNA修饰分析.
- 头显示了在各种纳米孔测序应用中常规使用的潜力,包括基因组组装和元基因组学.
更多相关视频
07:16Author Spotlight: Advancements in DNA Nanosensors – Addressing Sensitivity and Selectivity Challenges in Molecular Detection
Published on: February 9, 2024
903
10:01The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform
Published on: September 27, 2016
7.6K
相关概念视频
Mismatch Repair
40.0K
Overview
40.0K
Homologous Recombination
50.3K
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...
50.3K
Proofreading
6.2K
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...
6.2K
Labeling DNA Probes
8.1K
DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
8.1K
Nucleotide Excision Repair
36.9K
Overview
36.9K
Sanger Sequencing
753.8K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
753.8K
