Nanopore sequencing is a unique technique for determining the order in which nucleotides occur on a strand of DNA.
A nanopore is just a small hole whose diameter is 1 nanometer. Although some kind of porous transmembrane cellular proteins behaves like nanopores.The principle of nanopore sequencing is that when a nanopore is immersed in a specific conducting fluid and a voltage is applied the electric current due to conduction of various ions through the nanopore can be found. The magnitude of the electricity is very sensitive to the size and as well as shape of the nanopore. If single nucleotides strands of DNA or other protein molecules pass through the nanopore then a characteristic change in the magnitude of the current is observed.
The electrophoresis might attract the DNA towards the nanopoe and The DNA could be passed through the nanopore. In addition specific enzymes attached to the nanopore also guide DNA towards the above mentioned nanopore. The size of nano pore indicates that the DNA may be guided through the particular hole as a long string like one base at a time. So nucleotide present in the DNA molecule may block the nanopore to a different, characteristic degree. The magnitude of current that can pass through the specific nanopore at a particular moment varies depending on whether the nanopore is blocked by an A, a C, a G or a T or a section of DNA that includes more than one of these bases (kmer). The change in the current through the nanopore as the DNA molecule passes through the nanopore shows a direct reading of the DNA sequence.
Fig 1: Schematic diagram of translocation of a DNA molecule through a paticular nanopore device
Recent recent progress in computational studies on key issues of DNA sequencing focuses on
1.control of the DNA translocation speed and
2.The electronic signature of the identity of bases.
1. The challenge for the 'strand sequencing' method is to refine the method to improve its resolution to be able to detect single bases.
2. A processive enzyme feeds individual bases, in the correct order, into the nanopore, is to integrate the exonuclease and the nanopore detection systems. The problem is that when an exonuclease hydrolyzes the phosphodieseter bonds between nucleotides in DNA, the subsequently released nucleotide is not necessarily guaranteed to directly move in to, say, a nearby alpha-hemolysin nano pore.
3. One of the main challenges in DNA sequencing with a solid-state nanopore is to reduce the speed of the DNA molecule when it passed the nanopore . The DNA translocation speed is excessively high using the currently available solid-state nanopores.
4. Lots theoretical studies significantly improves our realization of base identification for DNA sequencing but practically improvement is very less.
1.Agilent Laboratories was the pioneer develop nanopores but does progress in commercialization.
2. The Oxford Nanopore Technologies company in 2008 get lecence from technologyfrom Harvard, UCSC and other universities and is developing protein and solid state nanopore technology with the aim of sequencing DNA. The Company introduced its pocket-sized sensing device MinION to an early-access community in early 2014.
3.NABsys is researching nanopores as a method of identifying areas of single stranded DNA that have been hybridized with specific DNA probes.
2.DNA: An introduction to nanopore sequencing.