ORIGINAL PAPER The role of carboxymethyl substituents in the interaction of tetracationic porphyrins with DNA Oxana A. Kovaleva • Vladimir B. Tsvetkov • Anna K. Shchyolkina • Olga F. Borisova • Valentina A. Ol’shevskaya • Anton V. Makarenkov • Alexander S. Semeikin • Alexander A. Shtil • Dmitry N. Kaluzhny Received: 23 May 2012 / Revised: 10 July 2012 / Accepted: 1 August 2012 Ó European Biophysical Societies’ Association 2012 Abstract Cationic porphyrin-based compounds capable of interacting with DNA are currently under extensive inves- tigation as prospective anticancer and anti-infective drugs. One of the approaches to enhancing the DNA-binding affinity of these ligands is chemical modification of func- tional groups of the porphyrin macrocycle. We analyzed the interaction with DNA of novel derivatives containing carboxymethyl and ethoxycarbonylmethyl substituents at quaternary nitrogen atoms of pyridinium groups at the periphery of the porphyrin macrocycle. The parameters of binding of 5,10,15,20-tetrakis(N-carboxymethyl-4-pyridinium) porphyrin (P1) and 5,10,15,20-tetrakis(N-ethoxycarbonyl- methyl-4-pyridinium)porphyrin (P2) to double-stranded DNA sequences of different nucleotide content were deter- mined using optical spectroscopy. The association constant of P1 interaction with calf thymus DNA (K = 3.4 9 10 6 M -1 ) was greater than that of P2 (K = 2.8 9 10 5 M -1 ). Preferential binding of P1 to GC- rather than AT-rich oli- gonucleotides was detected. In contrast, P2 showed no preference for particular nucleotide content. Modes of binding of P1 and P2 to GC and AT duplexes were verified using the induced circular dichroism spectra. Molecular modeling confirmed an intercalative mode of interaction of P1 and P2 with CpG islands. The carboxyl groups of the peripheral substituent in P1 determine the specific interac- tions with GC-rich DNA regions, whereas ethoxycarbon- ylmethyl substituents disfavor binding to DNA. This study contributes to the understanding of the impact of peripheral substituents on the DNA-binding affinity of cationic por- phyrins, which is important for the design of DNA-targeting drugs. Keywords DNA  Porphyrins  Affinity  Absorption  Fluorescence  Molecular docking Introduction Porphyrins and their derivatives are widely used in pho- todynamic therapy of tumors (Luo et al. 1996; Shieh et al. 2010; Tada-Oikawa et al. 2009) and beyond, also exerting antibacterial and antiviral effects (Ding et al. 1992; Stee- nkeste et al. 2010). Due to their unique photochemical properties, individual porphyrin-based compounds can be used as artificial endonucleases (Haeubl et al. 2009). O. A. Kovaleva  A. K. Shchyolkina  O. F. Borisova  D. N. Kaluzhny (&) Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia e-mail: uzhny@mail.ru O. A. Kovaleva Moscow Institute of Physics and Technology, State University, Dolgoprudny 141700, Russia V. B. Tsvetkov Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow 119121, Russia V. B. Tsvetkov Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow 119991, Russia V. A. Ol’shevskaya  A. V. Makarenkov Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia A. S. Semeikin Ivanovo State University of Chemistry and Technology, Ivanovo 153000, Russia A. A. Shtil Blokhin Cancer Center, Russian Academy of Medical Sciences, Moscow 115478, Russia 123 Eur Biophys J DOI 10.1007/s00249-012-0848-y