Oxford nanopore sequencing technology: Difference between revisions

Latest revision as of 22:45, 15 December 2024

Oxford Nanopore Sequencing Technology

Oxford Nanopore sequencing technology is a cutting-edge method for DNA and RNA sequencing that utilizes nanopore-based devices to read nucleotide sequences. This technology is known for its ability to sequence long strands of DNA or RNA in real-time, offering significant advantages over traditional sequencing methods.

Principle of Operation[edit]

Oxford Nanopore sequencing operates on the principle of passing a single strand of DNA or RNA through a nanopore, which is a tiny hole, typically in a synthetic membrane. As the nucleic acid strand passes through the nanopore, it disrupts an ionic current that flows through the pore. Each of the four nucleotides (adenine, thymine, cytosine, and guanine) causes a characteristic change in the current, allowing the sequence of the strand to be determined in real-time.

Nanopore Structure[edit]

The nanopores used in Oxford Nanopore sequencing are typically made from proteins or synthetic materials. The most common protein used is alpha-hemolysin, which forms a stable pore in a lipid bilayer. Synthetic nanopores can be made from materials such as silicon nitride.

Sequencing Process[edit]

1. Sample Preparation: DNA or RNA is extracted from the sample and prepared for sequencing. This may involve fragmentation, adapter ligation, and other steps to ensure compatibility with the nanopore device. 2. Loading the Sample: The prepared nucleic acid is loaded onto a flow cell that contains multiple nanopores. 3. Sequencing: An electric potential is applied across the membrane, causing the nucleic acid to be drawn through the nanopore. As the strand passes through, the changes in ionic current are measured and recorded. 4. Data Analysis: The recorded current changes are analyzed using sophisticated algorithms to determine the sequence of nucleotides.

Advantages[edit]

Oxford Nanopore sequencing offers several advantages over traditional sequencing technologies:

Long Reads: It can produce very long reads, often exceeding 100 kilobases, which is beneficial for assembling genomes and identifying structural variants.
Real-Time Sequencing: The technology allows for real-time data acquisition, enabling rapid sequencing and analysis.
Portability: Devices such as the MinION are portable and can be used in field settings, making them ideal for on-site sequencing applications.
Versatility: It can sequence both DNA and RNA, and is capable of direct RNA sequencing without the need for reverse transcription.

Applications[edit]

Oxford Nanopore sequencing is used in a variety of applications, including:

Genomics: Whole genome sequencing, metagenomics, and de novo assembly.
Transcriptomics: RNA sequencing and expression analysis.
Clinical Diagnostics: Pathogen detection, cancer genomics, and genetic disease screening.
Environmental Monitoring: Detection of microbial communities in environmental samples.

Challenges[edit]

Despite its advantages, Oxford Nanopore sequencing faces some challenges:

Error Rates: Historically, nanopore sequencing has had higher error rates compared to other technologies, though improvements are continually being made.
Data Analysis: The large volume of data generated requires robust computational tools for analysis and interpretation.

Also see[edit]

Template:DNA technology

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-'''Oxford Nanopore Sequencing Technology''' is an innovative next-generation DNA sequencing method developed by Oxford Nanopore Technologies. Unlike many other sequencing methods, this technique directly sequences DNA molecules by detecting them as they traverse a nanopore. The process is facilitated by the principle of electrophoresis, which drives the movement of the DNA molecule through the nanopore. Nanopore sequencing offers a unique approach to DNA sequencing by measuring changes in electrical conductivity as individual DNA strands pass through a nanopore. The alterations in the current correspond to specific DNA bases (adenine, cytosine, guanine, thymine), allowing for real-time DNA sequencing.
+Oxford Nanopore Sequencing Technology
-== Technology ==
+Oxford Nanopore sequencing technology is a cutting-edge method for DNA and RNA sequencing that utilizes nanopore-based devices to read nucleotide sequences. This technology is known for its ability to sequence long strands of DNA or RNA in real-time, offering significant advantages over traditional sequencing methods.
-The primary components of Oxford Nanopore Sequencing Technology include:
-* '''Nanopore''': A protein pore embedded in an electrically resistant synthetic membrane.
+==Principle of Operation==
-* '''Electrophoresis''': Uses an electric field to drive the DNA molecule through the nanopore.
+Oxford Nanopore sequencing operates on the principle of passing a single strand of DNA or RNA through a nanopore, which is a tiny hole, typically in a synthetic membrane. As the nucleic acid strand passes through the nanopore, it disrupts an ionic current that flows through the pore. Each of the four nucleotides (adenine, thymine, cytosine, and guanine) causes a characteristic change in the current, allowing the sequence of the strand to be determined in real-time.
-* '''Signal Processing''': As the DNA strand passes through the nanopore, it disrupts the current flowing through the pore. This disruption is unique to each of the four DNA bases and is interpreted by sophisticated algorithms to determine the DNA sequence.
-== Advantages ==
-Oxford Nanopore Sequencing Technology offers several advantages over traditional sequencing methods:
-* '''Long Reads''': It can produce very long sequencing reads, which can be crucial for assembling complex genomes and identifying structural variations.
+===Nanopore Structure===
-* '''Portability''': The MinION device developed by Oxford Nanopore Technologies is a pocket-sized sequencer, making sequencing feasible in field conditions and point-of-care settings.
+The nanopores used in Oxford Nanopore sequencing are typically made from proteins or synthetic materials. The most common protein used is alpha-hemolysin, which forms a stable pore in a lipid bilayer. Synthetic nanopores can be made from materials such as silicon nitride.
-* '''Real-time Analysis''': The technology allows for real-time data analysis, enabling faster decision-making and timely insights.
-* '''Cost-Effective''': The technology offers a lower barrier of entry in terms of equipment cost, especially for smaller labs or individual research projects.
-== Applications ==
-Beyond standard genome sequencing, Oxford Nanopore's technology finds applications in:
-* '''Environmental Monitoring''': Given its portability, it can be used for on-site biodiversity assessments or pathogen monitoring.
+===Sequencing Process===
-* '''Clinical Diagnostics''': Potential applications in real-time infectious disease diagnosis and monitoring.
+. '''[[Sample Preparation]]''': DNA or RNA is extracted from the sample and prepared for sequencing. This may involve fragmentation, adapter ligation, and other steps to ensure compatibility with the nanopore device.
-* '''Agricultural Research''': Used in the study of plant genomes and understanding plant pathogens.
+. '''[[Loading the Sample]]''': The prepared nucleic acid is loaded onto a flow cell that contains multiple nanopores.
-== Challenges and Limitations ==
+. '''[[Sequencing]]''': An electric potential is applied across the membrane, causing the nucleic acid to be drawn through the nanopore. As the strand passes through, the changes in ionic current are measured and recorded.
-While the technology offers numerous benefits, there are also challenges:
+. '''[[Data Analysis]]''': The recorded current changes are analyzed using sophisticated algorithms to determine the sequence of nucleotides.
-* '''Accuracy''': Earlier iterations of nanopore sequencing faced concerns regarding accuracy, but continuous improvements have been made over time.
+==Advantages==
-* '''Data Analysis''': The massive amounts of data produced require robust computational resources and sophisticated algorithms for analysis.
+Oxford Nanopore sequencing offers several advantages over traditional sequencing technologies:
-== Future Directions ==
-With continuous improvements in accuracy, nanopore sequencing is poised to become a significant player in the sequencing landscape. Its ability to deliver long reads and provide real-time data makes it a strong candidate for numerous applications, from research to clinical diagnostics.
-== External Links ==
+* '''[[Long Reads]]''': It can produce very long reads, often exceeding 100 kilobases, which is beneficial for assembling genomes and identifying structural variants.
+* '''[[Real-Time Sequencing]]''': The technology allows for real-time data acquisition, enabling rapid sequencing and analysis.
+* '''[[Portability]]''': Devices such as the MinION are portable and can be used in field settings, making them ideal for on-site sequencing applications.
+* '''[[Versatility]]''': It can sequence both DNA and RNA, and is capable of direct RNA sequencing without the need for reverse transcription.
-* [https://nanoporetech.com/ Oxford Nanopore Technologies Official Website]
+==Applications==
-== References ==
+Oxford Nanopore sequencing is used in a variety of applications, including:
+* '''[[Genomics]]''': Whole genome sequencing, metagenomics, and de novo assembly.
+* '''[[Transcriptomics]]''': RNA sequencing and expression analysis.
+* '''[[Clinical Diagnostics]]''': Pathogen detection, cancer genomics, and genetic disease screening.
+* '''[[Environmental Monitoring]]''': Detection of microbial communities in environmental samples.
+==Challenges==
+Despite its advantages, Oxford Nanopore sequencing faces some challenges:
+* '''[[Error Rates]]''': Historically, nanopore sequencing has had higher error rates compared to other technologies, though improvements are continually being made.
+* '''[[Data Analysis]]''': The large volume of data generated requires robust computational tools for analysis and interpretation.
+==Also see==
+* [[DNA Sequencing]]
+* [[RNA Sequencing]]
+* [[Next-Generation Sequencing]]
+* [[Genomics]]
+* [[Proteomics]]
+{{DNA technology}}
+{{Genomics}}
-* ''Nanopore sequencing: The advantages of long reads for genome assembly''. Rhoads, A., & Au, K. F. (2015). Research in Computational Molecular Biology, 255-271.
-{{DEFAULTSORT:Oxford Nanopore Sequencing Technology}}
-{{stub}}
 [[Category:DNA sequencing]]
 [[Category:Genomics]]
 [[Category:Biotechnology]]