The methods disclosed herein are of use for the treatment of a wide variety of diseases. In particular, the methods provide for the targeting of a transcription altering agent to a specific target site of a viral genome in order to inactivate the virus. In addition, the methods provide for a triplex-forming oligonucleotide capable of interacting with a target site in a viral genome in order to alter transcription. The methods of the present invention may be used against viral pathogens or agents of bioterrorism.