PAPER www.rsc.org/pps | Photochemical & Photobiological Sciences Photophysical properties of N-alkylated azahelicene derivatives as DNA intercalators: counterion effects† Rosita Passeri,‡ a Gian Gaetano Aloisi, a Fausto Elisei, a Loredana Latterini,* a Tullio Caronna, b Francesca Fontana b and Isabella Natali Sora b Received 3rd June 2009, Accepted 17th August 2009 First published as an Advance Article on the web 17th September 2009 DOI: 10.1039/b9pp00015a In this work, three compounds having the same organic moiety (N-methyl-5-azahelicenium salts) but different counterions (I - , NO 3 - and COOCF 3 - ) have been investigated in buffered aqueous solutions and in the presence of DNA to give information on the counterion effects on the binding. In particular, the absorption spectra, fluorescence quantum yields and fluorescence lifetimes in aqueous solution for free organic molecules have been determined by steady-state and time-resolved spectrofluorimetric measurements. The obtained values are compared with those of the chromophores in the presence of increasing concentrations of DNA. The results allow determination of the association constants (K a ) and the number of base couples per chromophore molecule (n) by means of the McGhee Von Hippel model. The binding parameters are strongly affected by the nature of counterions since the highest K a value was determined for the compound having COOCF 3 - ; on the other hand the NO 3 - derivative is able to interact with the highest number of binding sites. The morphology and structural properties of the DNA–chromophore complexes were investigated by circular dichroism (CD) and atomic force microscopy (AFM). The data revealed that I - and COOCF 3 - derivatives preferentially form intercalation complexes, while the NO 3 - salt is able to form intercalation and grove binding complexes at the same time. Introduction The interactions of organic or organometallic molecules with DNA has been the subject of intense investigations in recent decades. 1–3 The knowledge of such interactions has provided insight into the biological functions 4 and it is giving the oppor- tunity for the development of new therapeutic agents. 5 Polycyclic aromatic molecules are known to intercalate in double stranded DNA or to adsorb on the biomolecule grooves, leading to complex formation with alteration of DNA structure; this might result in a hidden or suppressed DNA function in physiological processes. Planar aromatic molecules bind to DNA essentially by intercalation between base pairs, 6 while crescent-shaped or flexible molecules bind on the grooves. 7 Although sequence specificity has been delineated in several small molecules’ interactions, 3 further binding studies are building up fundamental data on the structural features of DNA binding for further development of a Dipartimento di Chimica and Centro di Eccellenza Materiali Innovativi Nanostrutturati (CEMIN), Universit` a di Perugia, Via Elce di Sotto, 8, 06123, Perugia, Italy. E-mail: loredana@unipg.it; Fax: +39-75-5855598; Tel: +39-75-5855636 b Dipartimento di Ingegneria Industriale, Universit` a di Bergamo, Viale Marconi, 5, 24044, Dalmine, Bergamo, Italy †Electronic supplementary information (ESI) available: NMR data, Scatchard plot fittings and DNA length distribution obtained by AFM imaging. See DOI: 10.1039/b9pp00015a ‡ Present address: Dipartimento di Biochimica “G. Moruzzi”, S3 center of the National Institute for the Physics of the Matter (CNR), Italian In- teruniversity Consortium for Materials Science and Technology (INSTM), Universit` a di Bologna, Via Irnerio 48, 40126 Bologna, Italy. more effective therapeutic agents and in order to elucidate the parameters affecting the energetics of DNA complexation. 1 “Helicene” is the name introduced by Newman in 1956 to indicate dibenzo[c,g]phenanthrene, a totally aromatic molecule in which the ortho-condensed ring system gives rise to a helical structure. 8 Helicenes constitute a class of aromatic molecules with many intriguing features, such as extended aromaticity, chirality, the capability to self-assemble into columnar solid-state architectures and the ability to behave as organic conductors These helically shaped molecules exhibit unique chiroptical properties, such as large circular dichroism (CD) spectra and large optical rotations. 9 There has also been interest in their application as a new class of DNA-intercalating agents 10 since they display chiral selection in binding Z-DNA. Nitrogen-substituted heteroaromatic molecules are currently gaining increasing interest owing to the fact that their complexes with transition metal ions show interesting behaviour when irradiated in the UV-Vis region. 11 It is commonly established that the introduction of a positive charge 12 on an organic molecule enhances its capacity to bind to DNA, due to ionic interactions between the cation and the phosphate backbone. Azonia-aromatic compounds, in which a bridgehead carbon of polycyclic aromatic compounds is replaced by a quaternary nitrogen, have been widely investigated in connection with their biological activity, because a similar structure is found in natural alkaloids. 1,13 There has also been interest in their application as a new class of DNA-intercalating agents. 10 Many literature data point out that the ionic strength of the medium strongly affects the binding of cationic ligands to anionic 1574 | Photochem. Photobiol. Sci., 2009, 8, 1574–1582 This journal is © The Royal Society of Chemistry and Owner Societies 2009