The presently-disclosed subject matter relates to a compositions and methods that makes use of a CasΦ(CasPhi) that has been modified for effective nuclear targeting. In particular, certain embodiments of the presently-disclosed subject matter relate to unique nucleic acid molecules, compositions, and methods for delivery of CasPhi to the nucleus to effectively modulate expression or otherwise target of a gene of interest. A nucleic acid disclosed herein includes a nucleotide encoding a CasPhi, wherein there are no amino acid substitutions, or wherein proline residues at amino acids 749 and 753 have been substituted; a nucleotide encoding an amino-terminal linker connected to the amino-terminal end of the CasPhi; a nucleotide encoding a carboxy -terminal linker connected to the carboxy-terminal end of the CasPhi; and a nucleotide encoding a nuclear localization signal (NLS) downstream from the CasPhi and carboxy-terminal linker.