Programmable nucleases and artificial transcriptional factors have enabled targeted correction of disease-causing mutations or targeted control over gene regulation. The advent of clustered, regularly interspaced, short palindromic repeats, and CRISPR-associated proteins (CRISPR-Cas9) systems has allowed for efficient RNA-guided targeted insertion, deletion or replacement of DNA sequences. The development of engineered Cys2His2 zinc finger proteins (ZFPs) that can be tuned to recognize specific DNA sequences has allowed for their application in artificial gene modulation. This thesis explores the utility of the CRISPR-Cas9 system and engineered ZFPs for the correction of disease-associated microduplications and for upregulation of a haploinsufficient gene, respectively. In the first part of my thesis, we employ the CRISPR-Cas9 system for correcting frame-shift causing microduplications for two disease targets: Hermansky- Pudlak Syndrome Type I (HPS1) and Limb-Girdle Muscular Dystrophy Type 2G (TCAP). We demonstrate efficient nuclease-mediated deletion of the duplicated segment and reversion to the wild-type allele in patient-derived cell lines. In the second part of my thesis, we describe a novel method for mitigating SpyCas9-based off-target editing at GC rich targets. We demonstrate that inosine substitutions that replace guanosines within the spacer sequence aids in efficient mitigation of editing at active near-cognate sites for two therapeutically relevant targets: HPS1 and HBB. Importantly, we show that inosine guide RNAs confer improved fidelity without reduction in on-target activity even when complexed with a high fidelity Cas9 (HiFiCas9). In the third part of my thesis, we engineer novel ZFPs to recognize the promoter region of SCN1A, which when haploinsufficient results in Dravet Syndrome. These DNA-binding domains fused to a transcriptional activator are designed to enable specific upregulation of SCN1A from the wild-type allele in GABAergic inhibitory interneurons. Taken together, my thesis research aimed to apply and optimize current genome manipulation technologies for targeted gene editing and targeted gene activation for translational applications that could provide a potential therapeutic benefit.