max 150 words) 9Oligonucleotides and nucleic acid analogues that alter gene expression are showing 10 therapeutic promise for selected human diseases. The modification of synthetic nucleic acids 11 to protect against nuclease degradation and to influence drug function is common practice, 12 however, such modifications may also confer unexpected physicochemical and biological 13properties. Here we report backbone-specific effects of modified oligonucleotides on 14 subnuclear organelles, altered distribution of nuclear proteins, the appearance of novel 15 structured nuclear inclusions, and modification of RNA processing in cultured cells 16 transfected with antisense oligonucleotides on a phosphorothioate backbone. Phosphodiester 17 and phosphorodiamidate morpholino oligomers elicited no such consequences. Disruption 18 of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by 19 transcriptomic analysis of fibroblasts exhibiting such disruption. These data suggest that the 20 toxic effects and adverse events reported after clinical evaluation of phosphorothioate 21 nucleic acid drugs may be mediated, at least in part, by non-specific interaction of nuclear 22 components with the phosphorothioate backbone. 23 24 25