Author ORCID Identifier

0000-0002-0775-5452

Date of Graduation

4-2026

Document Type

Thesis (MS)

Program Affiliation

Genetics and Epigenetics

Degree Name

Masters of Science (MS)

Advisor/Committee Chair

Fabien Delerue

Committee Member

Richard Behringer

Committee Member

Amiee Stablewski

Committee Member

George Calin

Committee Member

Guillermina Lozano

Abstract

The development of programmable endonucleases and improved transgene-delivery methods has revolutionized genome editing in mice. One such strategy is CRISPR-READI, which combines adeno-associated virus (AAV)-mediated gene delivery with electroporation of Cas9-RNPs. The AAV delivers transgenes (up to 4.7 kb) as ssDNA to the zygotes, which is followed by electroporation of Cas9-RNPs. This results in improved and precise genome editing. However, a thorough quality control (QC) process for the targeted site following this method has yet to be developed, and as a result, unwanted mutations may go undetected. To this end, we targeted two mouse genes, Ace2 and Foxg1, via CRISPR-READI, and generated three GM mouse lines. Next, we employed Nanopore-Cas9-targeted sequencing (nCATS) to analyze the targeted sites and observed concatemer formation, along with unintended insertion of AAV’s inverted terminal repeat (ITR) sequences. Both of these bystander mutations were missed by standard genotyping. This highlights the need for more thorough validation and development of improved transgene delivery methods. Therefore, we further investigated alternative delivery methods, including DNA origami (DO), elastin-like polypeptides (ELPs), and sperm-mediated delivery. We showed that DO nanostructures were efficiently taken up by zygotes and crossed both the ZP and plasma membrane. In contrast, ELPs and mouse sperm failed to deliver the gene editing components into zygotes. Overall, viii these results emphasize the importance of long-read sequencing for QC and support DO as a promising alternative for large, safer, and more reliable gene delivery.

Keywords

Genetically Modified Mice, Adeno Associated Viruses, Genome Editing, Long Read Sequencing, DNA Origami, Electroporation, Elastin Like Peptides, Endosomal Escape Peptides, Mouse Sperm, Gene Delivery, Cas9

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Available for download on Thursday, April 22, 2027

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