Preparing and sequencing ultra-long DNA molecules from single chromosomes

• Main Author: Bauer, David L. V.
• Published: University of Oxford 2013
• Subjects: 572.8
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.640151

In this thesis, I describe the development of a single-molecule platform for analysing long DNA molecules that captures haplotype and large-scale structural variation (SV) in addition to DNA sequence. Cunent DNA sequencing methods cannot adequately examine haplotype and SV - both contribute to biological function and disease and are candidates for the location of "missing heritability" in the genome. Both haplotype and SV fundamentally relate to the structure of single chromosomes. Using a lab-on-a-chip nanofluidic device, SV was analysed on stretched (> 2 Mb) DNA fragments. In order to integrate this larger-scale SV information with the base-by-base sequence of the molecule being analysed, the DNA molecule was amplified and sequenced. I developed algorithms to handle the unique features of sequence data from amplified single DNA molecules. I obtained sequence and genotyping data, confirmed successful isolation of single DNA fragments from the chip, and validated the barcoding method used to detect SV. This lab-on-a-chip device for handling long DNAs can also serve as a 'reaction chamber' to answer more fundamental biological questions regarding chromosome structure as a whole. Using a microfluidic chip, I was able to provide the first direct images of DNA catenation within metaphase chromosomes and demonstrate that DNA catenation, in addition to proteins, plays a crucial role in metaphase chromosome architecture. The fluidic platform can be adapted to future 'third-generation' single-molecule sequencing applications that intenogate single DNA molecules directly. I have demonstrated this potential in two ways: First, I used intercalating dyes to form an optical waveguide along DNA to improve single-molecule detection. Secondly, I I engineered E. coli RNA Polymerase to detect single base translocation events along a DNA substrate. Such a polymerase could be used in future third-generation sequencing schemes based upon base-stepping motion or energy transfer to dye-modified nucleotides as the polymerase processes on a long DNA template.