The present disclosure relates to targeted genome editing in eukaryotic cells or organisms. More particularly, the present disclosure provides for compositions and methods that may induce modifications in target endogenous nucleic acid sequences in nucleuses of eukaryotic cells. For example, disclosed herein are methods of modifying a target endogenous nucleic acid sequence in a nucleus of a eukaryotic cell in vitro or ex vivo, comprising: preparing a composition comprising a recombinant Cas9 protein, a single guide RNA, and a Cas9/RNA complex formed by at least a part of said recombinant Cas9 protein and single guide RNA, and introducing a Cas9/RNA complex into the eukaryotic cell in vitro or ex vivo, wherein in the composition, the single guide RNA is at least two-fold molar excess over the recombinant Cas9 protein, wherein the Cas9/RNA complex is a combination of the recombinant Cas9 protein and the single guide RNA, and wherein the Cas9/RNA complex is complexed prior to being introduced into the eukaryotic cell; wherein the single guide RNA is in vitro transcribed RNA or synthetic RNA, wherein the combination of the recombinant Cas9 protein and the single guide RNA produces a modification of the target endogenous nucleic acid sequence in the nucleus of the eukaryotic cell.