Our understanding of pluripotency remains limited: iPSC generation has only been established for a few species, pluripotent stem cell lines exhibit inconsistent developmental potential, and germline transmission has only been demonstrated for mice and rats.

By swapping structural elements between Sox2 and Sox17, we created a chimeric super-reprogramming factor, Sox2-17, which enhanced iPSC generation in five tested species: mice, humans, cynomolgus monkeys, cows, and pigs. The most crucial gain-of-function came from a single residue swap, alanine to valine at position 61 of the Sox2-HMG domain facing Oct4. Our computer simulations, biochemistry, and ChIP-seq experiments demonstrated that Sox2-A61V stabilizes Sox2/Oct4 dimerization on SoxOct DNA motif that controls the pluripotency fate. The point mutant markedly boosted the developmental potential of OSKM iPSCs, as evidenced by their much-improved capacity to support the generation of healthy all-iPSC mice in tetraploid complementation experiments. Sox2/Oct4 dimer emerged as the core driver of naïve pluripotency both during development and in vitro, with the dimer levels diminishing upon priming. Transient overexpression of episomal SK (super-SOX+KLF4 cocktail) restores endogenous Sox2/Oct4 dimerization, enhancing the developmental potential of existing pluripotent stem cell lines across different species. Our research provides a powerful tool for advancing iPSC technology, presents a universal approach for the naive reset across species, and addresses the long-standing question of what dictates the developmental potential or “quality” of pluripotent stem cells. By enabling the generation of high-quality naive pluripotent cells, our findings could enhance the production of tissues and organs and pave the way for precision mammalian germline engineering beyond the mouse model.