TY - JOUR
T1 - Nanopore sequencing
T2 - Electrical measurements of the code of life
AU - Timp, Winston
AU - Mirsaidov, Utkur M.
AU - Wang, Deqiang
AU - Comer, Jeff
AU - Aksimentiev, Aleksei
AU - Timp, Gregory
N1 - Funding Information:
Manuscript received May 31, 2009. Date of publication March 1, 2010; date of current version May 14, 2010. This work was supported by the National Institutes of Health under Grant R01 HG003713A and Grant PHS 5 P41-RR05969 and by the National Science Foundation under Grants TH 2008-01040 ANTC and PHY0822613. The supercomputer time was provided through TeraGrid via a Large Resources Allocation Grant MCA055S028. The review of this paper was arranged by Associate Editor C. Zhou.
PY - 2010/5
Y1 - 2010/5
N2 - Sequencing a single molecule of deoxyribonucleic acid (DNA) using a nanopore is a revolutionary concept because it combines the potential for long read lengths (>5 kbp) with high speed (1 bp/10 ns), while obviating the need for costly amplification procedures due to the exquisite single molecule sensitivity. The prospects for implementing this concept seem bright. The cost savings from the removal of required reagents, coupled with the speed of nanopore sequencing places the $1000 genome within grasp. However, challenges remain: high fidelity reads demand stringent control over both the molecular configuration in the pore and the translocation kinetics. The molecular configuration determines how the ions passing through the pore come into contact with the nucleotides, while the translocation kinetics affect the time interval in which the same nucleotides are held in the constriction as the data is acquired. Proteins like α-hemolysin and its mutants offer exquisitely precise self-assembled nanopores and have demonstrated the facility for discriminating individual nucleotides, but it is currently difficult to design protein structure ab initio, which frustrates tailoring a pore for sequencing genomic DNA. Nanopores in solid-state membranes have been proposed as an alternative because of the flexibility in fabrication and ease of integration into a sequencing platform. Preliminary results have shown that with careful control of the dimensions of the pore and the shape of the electric field, control of DNA translocation through the pore is possible. Furthermore, discrimination between different base pairs of DNA may be feasible. Thus, a nanopore promises inexpensive, reliable, high-throughput sequencing, which could thrust genomic science into personal medicine.
AB - Sequencing a single molecule of deoxyribonucleic acid (DNA) using a nanopore is a revolutionary concept because it combines the potential for long read lengths (>5 kbp) with high speed (1 bp/10 ns), while obviating the need for costly amplification procedures due to the exquisite single molecule sensitivity. The prospects for implementing this concept seem bright. The cost savings from the removal of required reagents, coupled with the speed of nanopore sequencing places the $1000 genome within grasp. However, challenges remain: high fidelity reads demand stringent control over both the molecular configuration in the pore and the translocation kinetics. The molecular configuration determines how the ions passing through the pore come into contact with the nucleotides, while the translocation kinetics affect the time interval in which the same nucleotides are held in the constriction as the data is acquired. Proteins like α-hemolysin and its mutants offer exquisitely precise self-assembled nanopores and have demonstrated the facility for discriminating individual nucleotides, but it is currently difficult to design protein structure ab initio, which frustrates tailoring a pore for sequencing genomic DNA. Nanopores in solid-state membranes have been proposed as an alternative because of the flexibility in fabrication and ease of integration into a sequencing platform. Preliminary results have shown that with careful control of the dimensions of the pore and the shape of the electric field, control of DNA translocation through the pore is possible. Furthermore, discrimination between different base pairs of DNA may be feasible. Thus, a nanopore promises inexpensive, reliable, high-throughput sequencing, which could thrust genomic science into personal medicine.
KW - Deoxyribonucleic acid (DNA)
KW - Nanopore
KW - Protein
KW - Sequencing
KW - Solid state
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U2 - 10.1109/TNANO.2010.2044418
DO - 10.1109/TNANO.2010.2044418
M3 - Article
C2 - 21572978
AN - SCOPUS:77952611899
SN - 1536-125X
VL - 9
SP - 281
EP - 294
JO - IEEE Transactions on Nanotechnology
JF - IEEE Transactions on Nanotechnology
IS - 3
M1 - 5422648
ER -