Development of a system to protect and concentrate large DNA for genome analysis - PROJECT SUMMARY/ABSTRACT
Structural variation alters approximately 3.4 times more base pairs than point mutations within the human
genome. Structural variations, such as amplification, deletion, inversions, or translocations, alter genes and
non-genic regions in several different diseases, such as Huntington’s, Parkinson’s, Charcot-Marie-Tooth,
cancer, chromoplexia, and undiagnosed genetic diseases. Long molecule read lengths are beneficial for
studying complex disease genetics. Many diseases involve multiple genetic variants and regulatory elements,
and longer reads provide a more comprehensive view of the genomic regions associated with disease
susceptibility, enabling the identification of variants and potential disease mechanisms. A significant obstacle in
the field is DNA length prior to sequencing and physical mapping. Longer molecules are necessary to span
large variations, with enough unique information on each side to determine the size and genetic information
within the variation. Our long-term goal is to develop a system to protect and concentrate huge DNA molecules
for physical mapping or sequencing systems to analyze genomes for structural variations. The overall objective
of this application is to protect and concentrate whole S. cerevisiae and E. coli chromosomes. Once the system
is tested with S. cerevisiae and E. coli, this system will be used for more complex samples. Our central
hypothesis is that sizeable DNA molecules can be protected in an inverted insert and concentrated in a 3D-
printed device with an acrylamide roadblock. The rationale for this project is to create a method to protect and
concentrate huge DNA molecules since no available system currently exists. To accomplish this, we put forth
the following specific aims: 1) Develop an inverted insert to protect DNA during cell lysis. 2) Develop a
roadblock to concentrate chromosomal DNA. This project is innovative as it a) utilizes 3D printing to create a
device and allows rapid modifications to the device, b) uses a roadblock to slow down the progression of DNA
so DNA can be concentrated in the solution, c) protects DNA inside the inverted insert during cell lysis, so the
DNA remains full length, and d) develops a system to protect and concentrate large DNA molecules (200 kb -
5 Mb). The significance of this project is devising a system to concentrate large DNA molecules that can span
large variations within a genome with enough unique information on either side of the variation to discern
variations associated with different diseases, enhance sequencing efficiency, improve genome assembly, and
aid in phasing and haplotype reconstruction.
