Abstract
We report identification of the binding sites for an organometallic ruthenium anticancer complex [(η 6-biphenyl)Ru(en)Cl][PF6] (1; en = ethylenediamine) on the 15-mer single-stranded oligodeoxynucleotides (ODNs), 5′-CTCTCTX7G8Y9CTTCTC-3′ [X = Y = T (I); X = C and Y = A (II); X = A and Y = T (III); X = T and Y = A (IV)] by electrospray ionization mass spectrometry (ESI-MS) in conjunction with enzymatic digestion or tandem mass spectrometry (top-down MS). ESI-MS combined with enzymatic digestion (termed MS-based ladder-sequencing), is effective for identification of the thermodynamically-favored G-binding sites, but not applicable to determine the thermodynamically unstable T-binding sites because the T-bound adducts dissociate during enzymatic digestion. In contrast, top-down MS is efficient for localization of the T binding sites, but not suitable for mapping ruthenated G bases, due to the facile fragmentation of G bases from ODN backbones prior to the dissociation of the phosphodiester bonds. The combination of the two MS approaches reveals that G8 in each ODN is the preferred binding site for 1, and that the T binding sites of 1 are either T7 or T11 on I and IV, and either T6 or T11 on II and III, respectively. These findings not only demonstrate for the first time that T-bases in single-stranded oligonucleotides are kinetically competitive with guanine for such organoruthenium complexes, but also illustrate the relative merits of the combination of ladder-sequencing and top-down MS approaches to elucidate the interactions of metal anticancer complexes with DNA.
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References
Bruijnincx, P.C.A., Sadler, P.J.: New trends for metal complexes with anticancer activity. Curr. Opin. Chem. Biol. 12, 197–206 (2008)
Jung, Y.W., Lippard, S.J.: Direct cellular responses to platinum-induced DNA damage. Chem. Rev. 107, 1387–1407 (2007)
Liu, H.K., Berners-Price, S.J., Wang, F.Y., Parkinson, J.A., Xu, J.J., Bella, J., Sadler, P.J.: Diversity in guanine-selective DNA binding modes for an organometallic ruthenium arene complex. Angew. Chem. Int. Ed. 45, 8153–8156 (2006)
Novakova, O., Kasparkova, J., Bursova, V., Hofr, C., Vojtiskova, M., Chen, H.M., Sadler, P.J., Brabec, V.: Conformation of DNA modified by monofunctional Ru(II) arene complexes: recognition by DNA binding proteins and repair. Relationship to cytotoxicity. Chem. Biol. 12, 121–129 (2005)
van Rijt, S.H., Sadler, P.J.: Current applications and future potential for bioinorganic chemistry in the development of anticancer drugs. Drug Discov. Today 14, 1089–1097 (2009)
Barry, C.G., Baruah, H., Bierbach, U.: Unprecedented monofunctional metallation of adenine nucleobase in guanine- and thymine-containing dinucleotide sequences by a cytotoxic platinum-acridine hybrid agent. J. Am. Chem. Soc. 125, 9629–9637 (2003)
Beck, J.L., Colgrave, M.L., Ralph, S.F., Sheil, M.M.: Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins. Mass Spectrom. Rev. 20, 61–87 (2001)
Gonnet, F., Kocher, F., Blais, J.C., Bolbach, G., Tabet, J.C., Chottard, J.C.: Kinetic analysis of the reaction between d(TTGGCCAA) and [Pt(NH3)3(H2O)]2+ by enzymatic degradation of the products and ESI and MALDI mass spectrometries. J. Mass Spectrom. 31, 802–809 (1996)
Morris, R.E., Aird, R.E., Murdoch, P.D., Chen, H.M., Cummings, J., Hughes, N.D., Parsons, S., Parkin, A., Boyd, G., Jodrell, D.I., Sadler, P.J.: Inhibition of cancer cell growth by ruthenium(II) arene complexes. J. Med. Chem. 44, 3616–3621 (2001)
Wang, F.Y., Bella, J., Parkinson, J.A., Sadler, P.J.: competitive reactions of a ruthenium arene anticancer complex with histidine, cytochrome c and an oligonucleotide. J. Biol. Inorg. Chem. 10, 147–155 (2005)
Wu, K., Luo, Q., Hu, W.B., Li, X.C., Wang, F.Y., Xiong, S.X., Sadler, P.J.: Mechanism of interstrand migration of organoruthenium anticancer complexes within a DNA duplex. Metallomics 4, 139–148 (2012)
Banoub, J.H., Newton, R.P., Esmans, E., Ewing, D.F., Mackenzie, G.: Recent developments in mass spectrometry for the characterization of nucleosides, nucleotides, oligonucleotides, and nucleic acids. Chem. Rev. 105, 1869–1915 (2005)
Taucher, M., Breuker, K.: Top-down mass spectrometry for sequencing of larger (up to 61 nt) RNA by CAD and EDD. J. Am. Soc. Mass Spectrom. 21, 918–929 (2010)
Wan, K.X., Gross, J., Hillenkamp, F., Gross, M.L.: Fragmentation mechanisms of oligodeoxynucleotides studied by H/D exchange and electrospray ionization tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 12, 193–205 (2001)
Wang, Z., Wan, K.X., Ramanathan, R., Taylor, J.S., Gross, M.L.: Structure and fragmentation mechanisms of isomeric T-rich oligodeoxynucleotides: a comparison of four tandem mass spectrometric methods. J. Am. Soc. Mass Spectrom. 9, 683–691 (1998)
Brodbelt, J.S.: Evaluation of DNA/ligand interactions by electrospray ionization mass spectrometry. Annu. Rev. Anal. Chem. 3, 67–87 (2010)
Wang, Y.S., Taylor, J.S., Gross, M.L.: Fragmentation of electrospray-produced oligodeoxynucleotide ions adducted to metal ions. J. Am. Soc. Mass Spectrom. 12, 550–556 (2001)
Nordhoff, E., Kirpekar, F., Roepstorff, P.: Mass spectrometry of nucleic acids. Mass Spectrom. Rev. 15, 67–138 (1996)
McLafferty, F.W., Breuker, K., Jin, M., Han, X.M., Jiang, H.H.: Top-down identification and characterization of biomolecules by mass spectrometry. J. Am. Soc. Mass Spectrom. 19, 1045–1053 (2008)
McLuckey, S.A., Vanberkel, G.J., Glish, G.L.: Tandem mass-spectrometry of small, multiply charged oligonucleotides. J. Am. Soc. Mass Spectrom. 3, 60–70 (1992)
McLuckey, S.A., Habibigoudarzi, S.: Decompositions of multiply-charged oligonucleotide anions. J. Am. Chem. Soc. 115, 12085–12095 (1993)
Ni, J.S., Pomerantz, S.C., Rozenski, J., Zhang, Y.H., McCloskey, J.A.: Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry. Anal. Chem. 68, 1989–1999 (1996)
Hartinger, C.G., Egger, A.E., Ben Hamidane, H., Tsybin, Y.O., Keppler, B.K., Dyson, P.J.: High resolution mass spectrometry for studying the interactions of cisplatin with oligonucleotides. Inorg. Chem. 47, 10626–10633 (2008)
Wu, J., McLuckey, S.A.: Gas-phase fragmentation of oligonucleotide ions. Int. J. Mass Spectrom. 237, 197–241 (2004)
Groessl, M., Tsybin, Y.O., Hartinger, C.G., Keppler, B.K., Dyson, P.J.: Ruthenium versus platinum: interactions of anticancer metallodrugs with duplex oligonucleotides characterized by electrospray ionization mass spectrometry. J. Biol. Inorg. Chem. 15, 677–688 (2010)
Stucki, S.R., Nyakas, A., Schurch, S.: Tandem mass spectrometry of platinated quadruplex DNA. J. Mass Spectrom. 46, 1288–1296 (2011)
Chen, H.M., Parkinson, J.A., Morris, R.E., Sadler, P.J.: Highly selective binding of organometallic ruthenium ethylenediamine complexes to nucleic acids: novel recognition mechanisms. J. Am. Chem. Soc. 125, 173–186 (2003)
Jamieson, E.R., Lippard, S.J.: Structure, recognition, and processing of cisplatin-DNA adducts. Chem. Rev. 99, 2467–2498 (1999)
Chen, H.M., Parkinson, J.A., Parsons, S., Coxall, R.A., Gould, R.O., Sadler, P.J.: Organometallic ruthenium(II) diamine anticancer complexes: arene-nucleobase stacking and stereospecific hydrogen-bonding in guanine adducts. J. Am. Chem. Soc. 124, 3064–3082 (2002)
Cheng, X.D., Blumenthal, R.M.: Finding a basis for flipping bases. Structure 4, 639–645 (1996)
Klimasauskas, S., Kumar, S., Roberts, R.J., Cheng, X.D.: Hhal methyltransferase flips its target base out of the DNA helix. Cell 76, 357–369 (1994)
Priyakumar, U.D., MacKerell, A.D.: Computational approaches for investigating base flipping in oligonucleotides. Chem. Rev. 106, 489–505 (2006)
Marzilli, L.G., Kistenmacher, T.J.: Stereoselectivity in binding of transition-metal chelate complexes to nucleic-acid constituents: bonding and nonbonding effects. Acc. Chem. Res. 10, 146–152 (1977)
Wang, F., Chen, H.M., Parsons, S., Oswald, L.D.H., Davidson, J.E., Sadler, P.J.: Kinetics of aquation and anation of ruthenium(II) arene anticancer complexes, acidity and X-ray structures of aqua adducts. Chem. Eur. J. 9, 5810–5820 (2003)
Wang, F.Y., Weidt, S., Xu, J.J., Mackay, C.L., Langridge-Smith, P.R.R., Sadler, P.J.: Identification of clusters from reactions of ruthenium arene anticancer complex with glutathione using nanoscale liquid chromatography fourier transform ion cyclotron mass spectrometry combined with 18O-labeling. J. Am. Soc. Mass Spectrom. 19, 544–549 (2008)
Wang, B., Sayer, J.M., Yagi, H., Frank, H., Seidel, A., Jerina, D.M.: Facile interstrand migration of the hydrocarbon moiety of a dibenzo[a, l]pyrene 11,12-diol 13,14-epoxide adduct at N2 of deoxyguanosine in a duplex oligonucleotide. J. Am. Chem. Soc. 128, 10079–10084 (2006)
Redon, S., Bombard, S., Elizondo-Riojas, M.A., Chottard, J.C.: Platinum cross-linking of adenines and guanines on the quadruplex structures of the AG3(T2AG3)3 and (T2AG3)4 human telomere sequences in Na+ and K+ solutions. Nucleic Acids Res. 31, 1605–1613 (2003)
Phillips, D.R., McCloskey, J.A.: A comprehensive study of the low energy collision-induced dissociation of dinucleoside monophosphates. Int. J. Mass Spectrom. Ion Processes 128, 61–82 (1993)
Rosu, F., Pirotte, S., De Pauw, E., Gabelica, V.: Positive and negative ion mode ESI-MS and MS/MS for studying drug–DNA complexes. Int. J. Mass Spectrom. 253, 156–171 (2006)
Vrkic, A.K., O'Hair, R.A.J., Foote, S., Reid, G.E.: Fragmentation reactions of all 64 protonated trimer oligodeoxynucleotides and 16 mixed base tetramer oligodeoxynucleotides via tandem mass spectrometry in an ion trap. Int. J. Mass Spectrom. 194, 145–164 (2000)
Xiang, Y., Abliz, Z., Li, L.J., Takayama, M.: Characteristic Fragmentation Behavior of Deoxytetranucleotides by Positive Ion Electrospray Ionization Tandem Mass Spectrometry. Rapid Commun. Mass Spectrom. 17, 1220–1224 (2003)
Hu, W.B., Luo, Q., Ma, X.Y., Wu, K., Liu, J.A., Chen, Y., Xiong, S.X., Wang, J.P., Sadler, P.J., Wang, F.Y.: Arene control over thiolate to sulfinate oxidation in albumin by organometallic ruthenium anticancer complexes. Chem. Eur. J. 15, 6586–6594 (2009)
Will, J., Kyas, A., Sheldrick, W.S., Wolters, D.: Identification of (η6-arene) ruthenium(II) protein binding sites in E. coli cells by combined multidimensional liquid chromatography and ESI tandem mass spectrometry: specific binding of [(η 6-p-cymene)RuCl2(DMSO)] to stress-regulated proteins and to helicases. J. Biol. Inorg. Chem. 12, 883–894 (2007)
Dorcier, A., Dyson, P.J., Gossens, C., Rothlisberger, U., Scopelliti, R., Tavernelli, I.: Binding of organometallic ruthenium(II) and osmium(II) complexes to an oligonucleotide: a combined mass spectrometric and theoretical study. Organometallics 24, 2114–2123 (2005)
Scolaro, C., Geldbach, T.J., Rochat, S., Dorcier, A., Gossens, C., Bergamo, A., Cocchietto, M., Tavernelli, I., Sava, G., Rothlisberger, U., Dyson, P.J.: Influence of hydrogen-bonding substituents on the cytotoxicity of RAPTA compounds. Organometallics 25, 756–765 (2006)
Hagemeister, T., Linscheid, M.: Mass Spectrometry of Cis-diamminedichloroplatinum(II) adducts with the dinucleosidemonophosphates d(ApG), d(GpG) and d(TpC) in an ion trap. J. Mass Spectrom. 37, 731–747 (2002)
Iannitti-Tito, P., Weimann, A., Wickham, G., Sheil, M.M.: Structural analysis of drug-DNA adducts by tandem mass spectrometry. Analyst 125, 627–633 (2000)
Wan, K.X., Gross, M.L.: Fragmentation mechanisms of oligodeoxynucleotides: effects of replacing phosphates with methylphosphonates and thymines with other bases in T-rich sequences. J. Am. Soc. Mass Spectrom. 12, 580–589 (2001)
Boschenok, J., Sheil, M.M.: Electrospray tandem mass spectrometry of nucleotides. Rapid Commun. Mass Spectrom. 10, 144–149 (1996)
Sykfont, A., Ericson, A., Elmroth, S.K.C.: Non-uniform rate for platination of guanine-N7 located in short DNA oligomers. Chem. Commun. 1190–1191 (2001)
Keenea, F.R., Smith, J.A., Collins, J.G.: Metal Complexes as structure-selective binding agents for nucleic acids. Coord. Chem. Rev. 253, 2021–2035 (2009)
Acknowledgments
The authors thank NSFC (grant nos. 90713020, 21020102039, 21135006, and 2112790), ERC (grant 247450), and the Chinese Academy of Sciences (Hundred Talent Program) for support.
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Wu, K., Hu, W., Luo, Q. et al. Competitive Binding Sites of a Ruthenium Arene Anticancer Complex on Oligonucleotides Studied by Mass Spectrometry: Ladder-Sequencing versus Top-Down. J. Am. Soc. Mass Spectrom. 24, 410–420 (2013). https://doi.org/10.1007/s13361-012-0539-z
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DOI: https://doi.org/10.1007/s13361-012-0539-z