Cystic fibrosis gene repair: correction of ΔF508 using ZFN and CRISPR/Cas9 guide RNA gene editing tools

Cystic Fibrosis (CF) is an autosomal recessive monogenic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene with the ΔF508 mutation accounting for approximately 70% of all CF cases worldwide. This thesis investigates whether existing zinc finger nucleases designed in this lab and CRISPR/gRNAs designed in this thesis can mediate efficient homology-directed repair (HDR) with appropriate donor repair plasmids to correct CF-causing mutations in a CF cell line. Firstly, the most common mutation, ΔF508, was corrected using a pair of existing ZFNs, which cleave in intron 9, and the donor repair plasmid pITR-donor-XC, which contains the correct CTT sequence and two unique restriction sites. HDR was initially determined to be <1% but further analysis by next generation sequencing (NGS) revealed HDR occurred at a level of 2%. This relatively low level of repair was determined to be a consequence of distance from the cut site to the mutation and so rather than designing a new pair of ZFNs, the position of the existing intron 9 ZFNs was exploited and attempts made to correct >80% of CF-causing mutations. The ZFN cut site was used as the site for HDR of a mini-gene construct comprising exons 10-24 from CFTR cDNA (with appropriate splice acceptor and poly A sites) to allow production of full length corrected CFTR mRNA. Finally, the ability to cleave closer to the mutation and mediate repair of CFTR using the latest gene editing tool CRISPR/Cas9 was explored. Two CRISPR gRNAs were tested; CRISPR ex10 was shown to cleave at an efficiency of 15% and CRISPR in9 cleaved at 3%. Both CRISPR gRNAs mediated HDR with appropriate donor plasmids at a rate of ~1% as determined by NGS. This is the first evidence of CRISPR induced HDR in CF cell lines.

Precursor adsorption on copper surfaces as the first step during the deposition of copper: a density functional study with van der Waals correction

Copper dimethylamino-2-propoxide [Cu(dmap)2] is used as a precursor for low-temperature atomic layer deposition (ALD) of copper thin films. Chemisorption of the precursor is the necessary first step of ALD, but it is not known in this case whether there is selectivity for adsorption sites, defects, or islands on the substrate. Therefore, we study the adsorption of the Cu(dmap)2 molecule on the different sites on flat and rough Cu surfaces using PBE, PBE-D3, optB88-vdW, and vdW-DF2 methods. We found the relative order of adsorption energies for Cu(dmap)2 on Cu surfaces is Eads (PBE-D3) > Eads (optB88-vdW) > Eads (vdW-DF2) > Eads (PBE). The PBE and vdW-DF2 methods predict one chemisorption structure, while optB88-vdW predicts three chemisorption structures for Cu(dmap)2 adsorption among four possible adsorption configurations, whereas PBE-D3 predicts a chemisorbed structure for all the adsorption sites on Cu(111). All the methods with and without van der Waals corrections yield a chemisorbed molecule on the Cu(332) step and Cu(643) kink because of less steric hindrance on the vicinal surfaces. Strong distortion of the molecule and significant elongation of Cu–N bonds are predicted in the chemisorbed structures, indicating that the ligand–Cu bonds break during the ALD of Cu from Cu(dmap)2. The molecule loses its initial square-planar structure and gains linear O–Cu–O bonding as these atoms attach to the surface. As a result, the ligands become unstable and the precursor becomes more reactive to the coreagent. Charge redistribution mainly occurs between the adsorbate O–Cu–O bond and the surface. Bader charge analysis shows that electrons are donated from the surface to the molecule in the chemisorbed structures, so that the Cu center in the molecule is partially reduced.