Transcription start sites are critical switches for converting recognition of chromosomal DNA into synthesis of RNA. We report that antigene peptide nucleic acid (agPNA) oligomers or antigene RNA (agRNA) duplexes can target transcription start sites and block gene expression. Our data suggest that chromosomal DNA within cells is readily accessible to recognition by synthetic agents. agPNAs and agRNAs will be useful tools for silencing gene expression and will provide insights into natural mechanisms for controlling transcription.