Sánchez López, Mateo IsidroVázquez Vázquez, OlallaVázquez Sentís, Marco EugenioMascareñas Cid, José Luis2019-03-272019-03-272013Sánchez, M. I., Vázquez, O. , Vázquez, M. E. and Mascareñas, J. L. (2013), Sequence‐Selective DNA Recognition with Peptide–Bisbenzamidine Conjugates. Chem. Eur. J., 19: 9923-9929. doi:10.1002/chem.201300519http://hdl.handle.net/10347/18484This is the peer reviewed version of the following article: Sánchez, M. I., Vázquez, O. , Vázquez, M. E. and Mascareñas, J. L. (2013), Sequence‐Selective DNA Recognition with Peptide–Bisbenzamidine Conjugates. Chem. Eur. J., 19: 9923-9929, which has been published in final form at https://doi.org/10.1002/chem.201300519. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsTranscription factors (TFs) are specialized proteins that play a key role in the regulation of genetic expression. Their mechanism of action involves the interaction with specific DNA sequences, which usually takes place through specialized domains of the protein. However, achieving an efficient binding usually requires the presence of the full protein. This is the case for bZIP and zinc finger TF families, which cannot interact with their target sites when the DNA binding fragments are presented as isolated monomers. Herein it is demonstrated that the DNA binding of these monomeric peptides can be restored when conjugated to aza‐bisbenzamidines, which are readily accessible molecules that interact with A/T‐rich sites by insertion into their minor groove. Importantly, the fluorogenic properties of the aza‐benzamidine unit provide details of the DNA interaction that are eluded in electrophoresis mobility shift assays (EMSA). The hybrids based on the GCN4 bZIP protein preferentially bind to composite sequences containing tandem bisbenzamidine–GCN4 binding sites (TCAT⋅AAATT). Fluorescence reverse titrations show an interesting multiphasic profile consistent with the formation of competitive nonspecific complexes at low DNA/peptide ratios. On the other hand, the conjugate with the DNA binding domain of the zinc finger protein GAGA binds with high affinity (KD≈12 nM) and specificity to a composite AATTT⋅GAGA sequence containing both the bisbenzamidine and the TF consensus binding siteseng© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsDNA recognitionFluorescenceMolecular recognitionOlligonucleotidesPeptidesjournal article10.1002/chem.2013005191521-3765open access