Bilateral NSF/BIO-BBSRC: Engineering Tunable Portal Hybrid Nanopores for High-Resolution Sequence Mapping

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The identity, structure, and function of each living organism is encoded as a sequence of chemical building blocks (called bases) in DNA. In higher organisms, DNA bases are organized into very long structures called chromosomes; for example, human DNA has 6 billion bases in 23 chromosomes. Despite the advances in reading the sequence of bases along the lengths of the whole chromosomes, in many living species there are parts of chromosomes composed of "difficult-to-read" codes. In this project, we will develop a nanopore device that can read a DNA molecule of exceptionally long length (1 million bases) and inform the user of the position of sequences of interest along that length. A nanopore is a small hole in a membrane that is only a few nanometers thin. We are designing a hybrid nanopore that is made up of a protein molecule that sits inside a man-made membrane in a silicon-based device. The work is a collaboration between a structural biology group at the the UK whose expertise is in protein structure, and a nanofabrication group at Northeastern University. The impact of this work will be manifold: first, it will allow fundamental research on a particular set of DNA regions in organisms (including humans) called microsatellites, are specific loci on genomic DNA in which a sequence of 2-6 nucleotides is repeated numerous times. Alterations in the lengths of these microsatellites directly impact many aspects of cellular function at the DNA, RNA, and protein levels, potentially causing disease. In cereal crops, STRs constitute a much greater proportion of the genome (80%) and can be involved in conferring economically useful traits such as increased yields in less than ideal environments. Therefore, understanding of these microsatellite regions can help in directing disease, as well as having future impact on food supply. Other impacts include the training of early-career personnel at all levels (undergraduates, graduates, and a post-doctoral associate) on molecular biology, nanotechnology, and DNA-related research.