The long-term objective of this project is rapid, highly accurate, and inexpensive sequencing of long (up to 150 kb) single DNA strands with a nanopore based DNA sequencing device. Meeting this long-term objective requires precise control of DNA movement past a nanopore sequence detector, and improvement of nanopore sequence detector resolution between DNA bases.
The specific aims of this proposal build upon progress made to date in these two areas by laboratories at the University of California, Santa Cruz (Akeson), University of Washington (Gundlach) and the University of Pennsylvania (Drndic). Individual laboratory expertise and knowledge will be integrated to accomplish four specific aims.
Specific aim one extends promising results at UCSC with DNA polymerase Phi29, a "molecular step motor" able to precisely control DNA movement through a nanopore sequencer. This work will employ existing personnel and 12 years of success at UCSC with alpha hemolysin protein nanopores to extend understanding of Phi29 DNA polymerase function in a nanopore.
Specific aim two evaluates Phi29 DNA polymerase function with two nanopores selected for their potentially superior base resolution to the alpha hemolysin nanopore. The first is MspA, a protein nanopore, which will be evaluated with Phi29 DNA polymerase by U of Washington and UCSC teams. This collaboration takes advantage of expertise with use of Phi29 DNAP at UCSC and expertise with MspA at U of Washington. The second nanopore, a solid state ultrathin silicon nitride pore with fluorescence detection, will be evaluated with Phi29 DNA polymerase by U of Penn (makers of the solid-state nanopore) and UCSC teams. The third specific aim improves DNA base resolution through increased differences in current signals from individual bases. This will be achieved by increased salt concentrations in the nanopore combined with use of salt tolerant DNA Polymerases. DNA polymerases from salt tolerant organisms will be isolated by extremophile experts currently at UCSC.
Specific aim 4 will use all information gathered to generate proof of concept through sequencing of long (up to 48 KB) DNA strands using a nanopore sequencing device. Realization of this technology will provide the basis for a more complete understanding of individual genetic traits and predispositions in human and other populations.
This proposal develops nanopore based DNA sequencing for significant improvement in speed and fidelity of DNA sequencing over current technologies. The ultimate goal is sufficient speed and cost reduction to permit routine sequencing of individual genomes and ultimately provide the basis for a detailed understanding of individual genetic traits and predispositions. This understanding and technology are needed for personalized medicine in the 21st century.
|Laszlo, Andrew H; Derrington, Ian M; Ross, Brian C et al. (2014) Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol 32:829-33|
|Ivankin, Andrey; Henley, Robert Y; Larkin, Joseph et al. (2014) Label-free optical detection of biomolecular translocation through nanopore arrays. ACS Nano 8:10774-81|
|Ivankin, Andrey; Carson, Spencer; Kinney, Shannon R M et al. (2013) Fast, label-free force spectroscopy of histone-DNA interactions in individual nucleosomes using nanopores. J Am Chem Soc 135:15350-2|
|Stoloff, Daniel H; Wanunu, Meni (2013) Recent trends in nanopores for biotechnology. Curr Opin Biotechnol 24:699-704|
|Nivala, Jeff; Marks, Douglas B; Akeson, Mark (2013) Unfoldase-mediated protein translocation through an ?-hemolysin nanopore. Nat Biotechnol 31:247-50|
|Cherf, Gerald M; Lieberman, Kate R; Rashid, Hytham et al. (2012) Automated forward and reverse ratcheting of DNA in a nanopore at 5-A precision. Nat Biotechnol 30:344-8|
|Manrao, Elizabeth A; Derrington, Ian M; Laszlo, Andrew H et al. (2012) Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol 30:349-53|