Synthesis of peptides anchored to DNA by intercalating chromophores can incorporate the design principle of the naturally occurring peptide based antibiotics. This work is concerned with the synthesis of DNA anchored cysteinyl peptides designed to be potentially nucleotide sequence specific with possible affinity for the AP-l transcription site. Previous work has shown that anthraquinones and anthrapyrazoles (APZs) substituted with cationic side groups are excellent DNA intercalating agents. In this work a series of APZ analogues has been synthesised which are coupled onto the amino terminus of varying peptide sequences. Three derivatives of APZs were prepared namely 2-, 2,5- and 2,7-substituted. Eight short polypeptides (see below), all varying slightly in sequence but all containing the KCR motif (with one exception where a Cys was replaced with Ser) were combined with the APZ chromophore to give a series of intercalator-peptide molecules. Peptides were synthesised using the Fmoc strategy on a solid phase peptide synthesizer (SPPS). The peptides were then isolated by reversed-phase HPLC using a water: acetonitrile gradient. Characterisation of the peptides was carried out by matrix assisted laser desorption ionisation (MALDI) mass spectrometry and two dimensional nmr (i.e. COSY and NOESy). Anthraquinone linked peptide ligands were also synthesised using similar synthetic routes, and tested for their activity. Coupling of the two components was achieved via activation of the carboxylic acid group using PyBOP or via formation of a reactive aziridinium ion. All intercalator-peptides prepared were examined for their DNA binding properties. The methods included the effect of intercalator-peptides on the thermal denaturation of DNA and the competitive displacement of ethidium by fluorimetry. It was shown that the APZ binds to DNA by intercalation. Peptides prepared were: H2N-A-K-C-R-A-C02H; H2N-A-K-C-R-A-CONH2; H2N-A-K-S-R-A-CONH2; H2N-A-K-C-R-N-A-CONH2; H2N-A-K-C-R-K-A-CONH2; H2N-A-K-C-R-N-R-A-CONH2; H2N-A-K-C-R-K-R-ACONH2; H2N-A-A-K-C-R-A-A-CONH2. The biological activities of the intercalatorpeptides were then investigated using an electrophoretic mobility shift assay (EMSA), making use of cell nuclear extracts rich in AP-l and also c-Jun homodimer recombinant proteins. It was shown that most of the intercalatorpeptides were capable of inhibiting AP-l (fos/jun) heterodimer protein from binding to the AP-l DNA consensus sequence. Importantly, the intercalatorpeptides showed superior activity over the intercalator or peptide moieties alone. The order of binding affinity was intercalator-peptide> intercalator» peptide.