The suppression of neuropeptide Y Y1 receptor gene expression by antisense oligonucleotides targeted to different gene regions was monitored on mRNA and protein level in the human neuroblastoma SK-N-MC cell line. The antisense oligonucleotide targeted to the junction of the first intron and second exon suppressed specifically Y1 receptor subtype number by more than 50%, but only if oligonucleotides were administered by electroporation. Also, the formation of Y1 receptor mRNA as shown by reverse transcription-polymerase chain reaction was markedly blocked in this case. Using the antisense oligonucleotide targeted to the start of translation, no effect, neither on the Y1 receptor number nor on Y1 receptor mRNA, could be observed. This finding suggests that besides sequence-specific effects of antisense oligonucleotides gene site-specific effects play a major role in the efficacy of suppression.