Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously or under the action of various physical and chemical agents. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of AP sites in synthetic duplexes. We report here on interactions of diastereomerically pure metallo-helical 'flexicate' complexes, bimetallic triple-stranded ferro-helicates [Fe2(NN-NN)3](4+) incorporating the common NN-NN bis(bidentate) helicand, with short DNA duplexes containing AP sites in different sequence contexts. The results show that the flexicates bind to AP sites in DNA duplexes in a shape-selective manner. They preferentially bind to AP sites flanked by purines on both sides and their binding is enhanced when a pyrimidine is placed in opposite orientation to the lesion. Notably, the Λ-enantiomer binds to all tested AP sites with higher affinity than the Δ-enantiomer. In addition, the binding of the flexicates to AP sites inhibits the activity of human AP endonuclease 1, which is as a valid anticancer drug target. Hence, this finding indicates the potential of utilizing well-defined metallo-helical complexes for cancer chemotherapy.

Department of Chemistry University of Warwick Gibbet Hill Road Coventry CV4 7AL UK

Institute of Biophysics Academy of Sciences of the Czech Republic v v i Kralovopolska 135 CZ 61265 Brno Czech Republic

Zobrazit více v PubMed

Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993;362:709–715. PubMed

Nilsen H., Krokan H.E. Base excision repair in a network of defence and tolerance. Carcinogenesis. 2001;22:987–998. PubMed

Tropp B.E. Molecular Biology: Genes to Proteins. Sudbury, MA: Jones & Bartlett Publishers; 2012. p. 455.

Wu F., Sun Y., Shao Y., Xu S., Liu G., Peng J., Liu L. DNA abasic site-selective enhancement of sanguinarine fluorescence with a large emission shift. PLoS One. 2012;7:e48251. PubMed PMC

Xu S., Shao Y., Wu F., Liu G., Liu L., Peng J., Sun Y. Targeting DNA abasic site by myricetin: sequence-dependent ESIPT emission. J. Lumin. 2013;136:291–295.

Wang X., Wang X., Cui S., Wang Y., Chen G., Guo Z. Specific recognition of DNA depurination by a luminescent terbium(III) complex. Chem. Sci. 2013;4:3748–3752.

Rajendran A., Zhao C., Rajendar B., Thiagarajan V., Sato Y., Nishizawa S., Teramae N. Effect of the bases flanking an abasic site on the recognition of nucleobase by amiloride. Biochim. Biophys. Acta. 2010;1800:599–610. PubMed

Sato Y., Nishizawa S., Yoshimoto K., Seino T., Ichihashi T., Morita K., Teramae N. Influence of substituent modifications on the binding of 2-amino-1, 8-naphthyridines to cytosine opposite an AP site in DNA duplexes: thermodynamic characterization. Nucleic Acids Res. 2009;37:1411–1422. PubMed PMC

Sato Y., Zhang Y., Seino T., Sugimoto T., Nishizawa S., Teramae N. Highly selective binding of naphthyridine with a trifluoromethyl group to cytosine opposite an abasic site in DNA duplexes. Org. Biomol. Chem. 2012;10:4003–4006. PubMed

Belmont P., Jourdan M., Demeunynck M., Constant J.F., Garcia J., Lhomme J., Carez D., Croisy A. Abasic site recognition in DNA as a new strategy to potentiate the action of anticancer alkylating drugs. J. Med. Chem. 1999;42:5153–5159. PubMed

Berthet N., Constant J.F., Demeunynck M., Michon P., Lhomme J. Search for DNA repair inhibitors: Selective binding of nucleic bases acridine conjugates to a DNA duplex containing an abasic site. J. Med. Chem. 1997;40:3346–3352. PubMed

Zeglis B.M., Boland J.A., Barton J.K. Targeting abasic sites and single base bulges in DNA with metalloinsertors. J. Am. Chem. Soc. 2008;130:7530–7531. PubMed PMC

Zeglis B.M., Boland J.A., Barton J.K. Recognition of abasic sites and single base bulges in DNA by a metalloinsertor. Biochemistry. 2009;48:839–849. PubMed PMC

Fakhari A., Rokita S.E. A new solvatochromic fluorophore for exploring nonpolar environments created by biopolymers. Chem. Commun. 2011;47:4222–4224. PubMed

Benner K., Bergen A., Ihmels H., Pithan P.M. Selective stabilization of abasic site-containing DNA by insertion of sterically demanding biaryl ligands. Chem. Eur. J. 2014;20:9883–9887. PubMed

Wu F., Shao Y., Ma K., Cui Q., Liu G., Xu S. Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site. Org. Biomol. Chem. 2012;10:3300–3307. PubMed

Berthet N., Michon J., Lhomme J., Teulade-Fichou M.P., Vigneron J.P., Lehn J.M. Recognition of abasic sites in DNA by a cyclobisacridine molecule. Chem. Eur. J. 1999;5:3625–3630.

Barret J.M., Etievant C., Fahy J., Lhomme J., Hill B.T. Novel artificial endonucleases inhibit base excision repair and potentiate the cytotoxicity of DNA-damaging agents on L1210 cells. Anticancer Drugs. 1999;10:55–65. PubMed

Lefrancois M., Bertrand J.R., Malvy C. 9-Amino-ellipticine inhibits the apurinic site-dependent base excision-repair pathway. Mutation Res. 1990;236:9–17. PubMed

Malvy C., Safraoui H., Bloch E., Bertrand J.R. Involvement of apurinic sites in the synergistic action of alkylating and intercalating drugs in Escherichia coli. Anticancer Drug Des. 1988;2:361–370. PubMed

Alarcon K., Demeunynck M., Lhomme J., Carrez D., Croisy A. Diaminopurine-acridine heterodimers for specific recognition of abasic site containing DNA. Influence on the biological activity of the position of the linker on the purine ring. Bioorg. Med. Chem. Lett. 2001;11:1855–1858. PubMed

Alarcon K., Demeunynck M., Lhomme J., Carrez D., Croisy A. Potentiation of BCNU cytotoxicity by molecules targeting abasic lesions in DNA. Bioorg. Med. Chem. Lett. 2001;9:1901–1910. PubMed

Brabec V., Howson S.E., Kaner R.A., Lord R.M., Malina J., Phillips R.M., Abdallah Q.M.A., McGowan P.C., Rodger A., Scott P. Metallohelices with activity against cisplatin-resistant cancer cells; does the mechanism involve DNA binding. Chem. Sci. 2013;4:4407–4416.

Howson S.E., Scott P. Approaches to the synthesis of optically pure helicates. Dalton Trans. 2011;40:10268–10277. PubMed

Howson S.E., Bolhuis A., Brabec V., Clarkson G.J., Malina J., Rodger A., Scott P. Optically pure, water-stable metallo-helical ‘flexicate’ assemblies with antibiotic activity. Nat. Chem. 2012;4:31–36. PubMed

Howson S.E., Allan L.E.N., Chmel N.P., Clarkson G.J., van Gorkum R., Scott P. Self-assembling optically pure Fe(A-B)3 chelates. Chem. Commun. 2009:1727–1729. PubMed

Howson S.E., Allan L.E.N., Chmel N.P., Clarkson G.J., Deeth R.J., Faulkner A.D., Simpson D.H., Scott P. Origins of stereoselectivity in optically pure phenylethaniminopyridine tris-chelates M(NN ‘)3n+ (M = Mn, Fe, Co, Ni and Zn) Dalton Trans. 2011;40:10416–10433. PubMed

Abbotts R., Madhusudan S. Human AP endonuclease 1 (APE1): from mechanistic insights to druggable target in cancer. Cancer Treat. Rev. 2010;36:425–435. PubMed

Freyer M.W., Lewis E.A. Isothermal titration calorimetry: experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions. Methods Cell Biol. 2008;84:79–113. PubMed

Xi Z., Zhang R., Yu Z., Ouyang D., Huang R. Selective interaction between tylophorine B and bulged DNA. Bioorg. Med. Chem. Lett. 2005;15:2673–2677. PubMed

Bai L.P., Cai Z.W., Zhao Z.Z., Nakatani K., Jiang Z.H. Site-specific binding of chelerythrine and sanguinarine to single pyrimidine bulges in hairpin DNA. Anal. Bioanal. Chem. 2008;392:709–716. PubMed

Sielaff A., Mackay H., Brown T., Lee M. 2-aminopurine/cytosine base pair containing oligonucleotides: fluorescence spectroscopy studies on DNA-polyamide binding. Biochem. Biophys. Res. Commun. 2008;369:630–634. PubMed

Patel N., Berglund H., Nilsson L., Rigler R., McLaughlin L.W., Graslund A. Thermodynamics of interaction of a fluorescent DNA oligomer with the anti-tumour drug netropsin. Eur. J. Biochem. 1992;203:361–366. PubMed

Bradrick T.D., Marino J.P. Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA. RNA. 2004;10:1459–1468. PubMed PMC

Lacourciere K.A., Stivers J.T., Marino J.P. Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy. Biochemistry. 2000;39:5630–5641. PubMed

Holz B., Klimasauskas S., Serva S., Weinhold E. 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases. Nucleic Acids Res. 1998;26:1076–1083. PubMed PMC

Rachofsky E.L., Osman R., Ross J.B.A. Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence. Biochemistry. 2001;40:946–956. PubMed

Zhao C.X., Dai Q., Seino T., Cui Y.Y., Nishizawa S., Teramae N. Strong and selective binding of amiloride to thymine base opposite AP sites in DNA duplexes: simultaneous binding to DNA phosphate backbone. Chem. Commun. 2006:1185–1187. PubMed

ITC Data Analysis in OriginH. Tutorial Guide Version 5.0. 1998.

Pyle A.M., Morii T., Barton J.K. Probing microstructures in double-helical DNA with chiral metal complexes: recognition of changes in base-pair propeller twisting in solution. J. Amer. Chem. Soc. 1990;112:9432–9434.

Sitlani A., Long E.C., Pyle A.M., Barton J.K. DNA photocleavage by phenanthrenequinone diimine complexes of rhodium(III): shape-selective recognition and reaction. J. Am. Chem. Soc. 1992;114:2303–2312.

Cuniasse P., Fazakerley G.V., Guschlbauer W., Kaplan B.E., Sowers L.C. The abasic site as a challenge to DNA-polymerase - a nuclear-magnetic-resonance study of G, C and T opposite a model abasic site. J. Mol. Biol. 1990;213:303–314. PubMed

Yoo D.G., Song Y.J., Cho E.J., Lee S.K., Park J.B., Yu J.H., Lim S.P., Kim J.M., Jeon B.H. Alteration of APEI/ref-1 expression in non-small cell lung cancer: The implications of impaired extracellular superoxide dismutase and catalase antioxidant systems. Lung Cancer. 2008;60:277–284. PubMed

Dicobalt(ii) helices kill colon cancer cells via enantiomer-specific mechanisms; DNA damage or microtubule disruption

Glycoconjugated Metallohelices have Improved Nuclear Delivery and Suppress Tumour Growth In Vivo

Discovery of selective, antimetastatic and anti-cancer stem cell metallohelices via post-assembly modification