Eight novel polyamides containing N-methylpyrrole were designed to target the sequence (5′-CTGCATATAAGCAG-3′/5′-CTGCTTATATGCAG-3′) of the TATA box element of the HIV-1 promoter DNA. The non-covalent complexes of the promoter DNA and the polyamides were investigated by electrospray ionization (ESI) mass spectrometry, which provided strong evidence for the binding of the novel polyamides to the sequence of the TATA box element. It also revealed that polyamide 2 (PyPyPyPyβDp), a potent binder of HIV-1 promoter DNA and a lead molecule for the design of new anti-HIV-1 drugs, had the highest binding affinity with the TATA box element DNA among these polyamides by examining the stoichiometry and the selectivity. Copyright © 2006 John Wiley & Sons, Ltd.