Nanopore Sequencing: Advancing Genomics

An Overview of the Mechanism of Nanopore Sequencing Technologies (ONT)

To begin with, one can say that nanopore sequencing is a state-of-the-art technology that allows nucleic acids to be sequenced through the examination of jon-changes (when the electric current is maintained) as the DNA chain or RNA passes through the nanopore. Nanopore refers to small openings whose shapes are mostly made of biological materials like proteins and other non-biological materials like graphene Quantum Dot. Whenever a DNA or RNA strand is passed through a nanopore, there are baselines (A, T, C,G for DNA, and A, U, C, G for RNA) that cause an interruption/ blockade of the ion current that results into a current change (Johnson et al, 2009). All of these changes are encoded instantaneously, so it becomes possible to sequentially read the thread at the level of its molecule.

This is made possible by the fact that there is no need for amplification and fluorescent tags, which are usually applied in various other sequencing methods. More importantly, the genetic materials can be studied in an immediate, straightforward and non-invasive manner which helps to change the dynamics of genomic studies, diagnostics and even treatment regimens.

Applications of Nanopore Technology

It is well known that nanopore technology is very broad in its applications.

Clinical Diagnostics: With the help of nanotechnology-based portable sequencing devices, onsite detection of various pathogens, profiling of cancer mutations, and submission of genetic material for personalized therapies has become a reality.

Genetic Research: Sequencing with this technology is not dominated by mistakes resulting in assembly gaps, researchers use it to sequence for complete genomes, search out and characterize structural variants and even for those challenging to reach regions in the human genome.

Environmental and Ecological Studies: The portability of these devices means that a researcher can perform in situ sequencing of microbial communities and assess biodiversity or monitor environments within the same timeframe as data gathering.

Agricultural Genomics: The technology enables efficient and high throughput and wide-scale genome sequencing of plants and livestock for purposes of crop improvement and enhancing breeding programs.

Pandemic Surveillance: Real-time sequencing of genetic material of the pathogens such as the COVID-19 pathogen has been useful in helping to monitor changes in the pathogen or its transmission.

Nanopore Design: A Slight Bend towards the Deep End

The design of the nanopore is of utmost importance in nanopore sequencing innovation. Nanopores are structures which contain very tiny pores that can only be described as being a size of one nanometer and therefore, they are suspended by a membrane . Polymer or protein derived biological nanoparticles as well as solid-state structures of the nanopore act as conduits for DNA and RNA molecules.

Ionic current flow through the nanopore is observed. Always when a nucleotide passes through the pore, it causes some disturbance in the ionic current which is well defined. Computational models accurately relate the effects caused by these transitions with the nucleotide composition being defined in real time. It is clear from the above description why this technology has the ability to read long stretches of nucleic acid molecules either RNA or DNA bases, and hence can be used for long-read sequencing needed projects.

Approaches to Nanopore Sequencing Itself

This novel sequencing approach overcomes some traditional sequencing limitations:

Ultra-long Reads: Unlike short-read technologies, it is possible with the help of nanopore sequencing to read whole DNA or RNA molecules which sometimes exceed even 2 million bases in length. This is vital for structural variation analysis, repeat identification and more complete genome assemblies.
Real time sequencing: Nanopore sequencing provides data instantaneously as sequencing reactions are performed. This is advantageous in time-critical situations such as disease outbreaks where timely intervention will be needed or immediate pathogen identification and clinical diagnosis.
Portability and Accessibility: Nanopore devices such as the MinION are hand-held, low cost, and therefore quick and easy to operate. This portability means that genomic sequencing can be performed even in the field or in a mobile device as opposed to just movies that have to be in-house in the hospital. It is therefore feasible to carry out genomic studies whilst out in the field, in areas where genomic sequencing is not available or geographies that may be too far reaching for the conventional sequencing technology.
Direct RNA Sequencing: Unlike other sequencing technologies the nanopore technology is able to sequence RNA directly without first converting it to cDNA. This helps in investigating RNA modifications and gene expressions more efficiently.
Cost Effectivity: Owing to minimal sample preparation and lower dependency on costly reagents, nanopore sequencing is less expensive than several forms of other WHO and this has more utility in more and more projects both clinical and research.
Scalability: On the other hand, nanopore platforms permit throughput modification, thereby scaling up the amount of work done as the user so wishes. This flexibility implies that anything ranging from little gene panels to larger genome projects can make use of nanopore sequencing.
Real Time Error Correction: Some aspects of the Nanopore technology involve error-correction mechanisms in order that the levels of accuracy in long read sequences are gradually improved. And because technology has advanced – especially the software – it is no longer acceptable to ignore nanopore technology because all the chances of errors in sequencing are being curtailed.

Final Remarks

Nanopore sequencing is one of the major breakthroughs in the field of genomics as it provides a well-deserved level of flexibility, speed up and accuracy. It also finds its wide array of applications encompassing disease diagnostics, environmental surveys and even clinical usage because of its unique features such as long reads, real time data availability and portability. Improvements in this technology lead to the conclusion that, in the future, nanopore sequencing will enable progress in catastrophic medicine, genome studies and further.