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X-ray crystal structure of rac-[Ru(phen)2dppz]2+ with d(ATGCAT)2 shows enantiomer orientations and water ordering.

Hall JP, Cook D, Morte SR, McIntyre P, Buchner K, Beer H, Cardin DJ, Brazier JA, Winter G, Kelly JM, Cardin CJ
J Am Chem Soc 135 12652-9 (2013)
Cited: 38 times
EuropePMC logo PMID: 23875832

Abstract

We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz](2+) with the d(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.

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  1. Transition Metal Intercalators as Anticancer Agents-Recent Advances. Deo KM, Pages BJ, Ang DL, Gordon CP, Aldrich-Wright JR. Int J Mol Sci 17 E1818 (2016)

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  4. The Critical Role of 12-Methyl Group of Anthracycline Dutomycin to Its Antiproliferative Activity. Xu R, Hu D, Lin J, Tang J, Zhan R, Liu G, Sun L. Molecules 27 3348 (2022)


Reviews citing this publication (5)

  1. The development of ruthenium(ii) polypyridyl complexes and conjugates for in vitro cellular and in vivo applications. Poynton FE, Bright SA, Blasco S, Williams DC, Kelly JM, Gunnlaugsson T. Chem Soc Rev 46 7706-7756 (2017)
  2. Ruthenium(ii) complexes with dppz: from molecular photoswitch to biological applications. Li G, Sun L, Ji L, Chao H. Dalton Trans 45 13261-13276 (2016)
  3. RutheniumII complexes bearing fused polycyclic ligands: from fundamental aspects to potential applications. Troian-Gautier L, Moucheron C. Molecules 19 5028-5087 (2014)
  4. Ruthenium polypyridine complexes combined with oligonucleotides for bioanalysis: a review. Zhang S, Ding Y, Wei H. Molecules 19 11933-11987 (2014)
  5. Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)₂dppz]2+ and [Ru(phen)₂dppz]2+ with a DNA Molecule. Jia F, Wang S, Man Y, Kumar P, Liu B. Molecules 24 E769 (2019)

Articles citing this publication (28)

  1. Metal complex interactions with DNA. Pages BJ, Ang DL, Wright EP, Aldrich-Wright JR. Dalton Trans 44 3505-3526 (2015)
  2. Binding Behaviors for Different Types of DNA G-Quadruplexes: Enantiomers of [Ru(bpy)2(L)](2+) (L=dppz, dppz-idzo). Shi S, Xu JH, Gao X, Huang HL, Yao TM. Chemistry 21 11435-11445 (2015)
  3. Thread insertion of a bis(dipyridophenazine) diruthenium complex into the DNA double helix by the extrusion of AT base pairs and cross-linking of DNA duplexes. Boer DR, Wu L, Lincoln P, Coll M. Angew Chem Int Ed Engl 53 1949-1952 (2014)
  4. Reversal of a Single Base-Pair Step Controls Guanine Photo-Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex. Keane PM, Poynton FE, Hall JP, Sazanovich IV, Towrie M, Gunnlaugsson T, Quinn SJ, Cardin CJ, Kelly JM. Angew Chem Int Ed Engl 54 8364-8368 (2015)
  5. Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex. Almaqwashi AA, Paramanathan T, Lincoln P, Rouzina I, Westerlund F, Williams MC. Nucleic Acids Res 42 11634-11641 (2014)
  6. Delta chirality ruthenium 'light-switch' complexes can bind in the minor groove of DNA with five different binding modes. Hall JP, Keane PM, Beer H, Buchner K, Winter G, Sorensen TL, Cardin DJ, Brazier JA, Cardin CJ. Nucleic Acids Res 44 9472-9482 (2016)
  7. Supramolecular activation of a molecular photocatalyst. Pfeffer MG, Pehlken C, Staehle R, Sorsche D, Streb C, Rau S. Dalton Trans 43 13307-13315 (2014)
  8. From intercalation to groove binding: switching the DNA-binding mode of isostructural transition-metal complexes. Ahmad H, Wragg A, Cullen W, Wombwell C, Meijer AJ, Thomas JA. Chemistry 20 3089-3096 (2014)
  9. Ru(II)-polypyridyl surface functionalised gold nanoparticles as DNA targeting supramolecular structures and luminescent cellular imaging agents. Martínez-Calvo M, Orange KN, Elmes RB, la Cour Poulsen B, Williams DC, Gunnlaugsson T. Nanoscale 8 563-574 (2016)
  10. Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen)2(dppz)]2+ light-switch compound in solution and when bound to DNA. Poynton FE, Hall JP, Keane PM, Schwarz C, Sazanovich IV, Towrie M, Gunnlaugsson T, Cardin CJ, Cardin DJ, Quinn SJ, Long C, Kelly JM. Chem Sci 7 3075-3084 (2016)
  11. Luminescent ruthenium polypyridyl complexes with extended 'dppz' like ligands as DNA targeting binders and cellular agents. Poulsen BC, Estalayo-Adrián S, Blasco S, Bright SA, Kelly JM, Williams DC, Gunnlaugsson T. Dalton Trans 45 18208-18220 (2016)
  12. Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation. Almaqwashi AA, Andersson J, Lincoln P, Rouzina I, Westerlund F, Williams MC. Biophys J 110 1255-1263 (2016)
  13. Binding of Ru(terpyridine)(pyridine)dipyridophenazine to DNA studied with polarized spectroscopy and calorimetry. Mårtensson AK, Lincoln P. Dalton Trans 44 3604-3613 (2015)
  14. Competitive DNA binding of Ru(bpy)2dppz2+ enantiomers studied with isothermal titration calorimetry (ITC) using a direct and general binding isotherm algorithm. Mårtensson AKF, Lincoln P. Phys Chem Chem Phys 20 7920-7930 (2018)
  15. Guanine Can Direct Binding Specificity of Ru-dipyridophenazine (dppz) Complexes to DNA through Steric Effects. Hall JP, Gurung SP, Henle J, Poidl P, Andersson J, Lincoln P, Winter G, Sorensen T, Cardin DJ, Brazier JA, Cardin CJ. Chemistry 23 4981-4985 (2017)
  16. Inosine Can Increase DNA's Susceptibility to Photo-oxidation by a RuII Complex due to Structural Change in the Minor Groove. Keane PM, Hall JP, Poynton FE, Poulsen BC, Gurung SP, Clark IP, Sazanovich IV, Towrie M, Gunnlaugsson T, Quinn SJ, Cardin CJ, Kelly JM. Chemistry 23 10344-10351 (2017)
  17. Monitoring guanine photo-oxidation by enantiomerically resolved Ru(II) dipyridophenazine complexes using inosine-substituted oligonucleotides. Keane PM, Poynton FE, Hall JP, Clark IP, Sazanovich IV, Towrie M, Gunnlaugsson T, Quinn SJ, Cardin CJ, Kelly JM. Faraday Discuss 185 455-469 (2015)
  18. Effect of the Ancillary Ligands on the Spectral Properties and G-Quadruplexes DNA Binding Behavior: A Combined Experimental and Theoretical Study. Shi S, Gao X, Huang H, Zhao J, Yao T. Chemistry 21 13390-13400 (2015)
  19. Ruthenium Polypyridyl Complex Bound to a Unimolecular Chair-Form G-Quadruplex. McQuaid KT, Takahashi S, Baumgaertner L, Cardin DJ, Paterson NG, Hall JP, Sugimoto N, Cardin CJ. J Am Chem Soc 144 5956-5964 (2022)
  20. Three thymine/adenine binding modes of the ruthenium complex Λ-[Ru(TAP)2(dppz)]2+ to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography. McQuaid K, Hall JP, Baumgaertner L, Cardin DJ, Cardin CJ. Chem Commun (Camb) 55 9116-9119 (2019)
  21. Binding Modes and Selectivity of Ruthenium Complexes to Human Telomeric DNA G-Quadruplexes. Rubio-Magnieto J, Kajouj S, Di Meo F, Fossépré M, Trouillas P, Norman P, Linares M, Moucheron C, Surin M. Chemistry 24 15577-15588 (2018)
  22. The Structure of Linkers Affects the DNA Binding Properties of Tethered Dinuclear Ruthenium(II) Metallo-Intercalators. Saeed HK, Saeed IQ, Buurma NJ, Thomas JA. Chemistry 23 5467-5477 (2017)
  23. Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides. Keane PM, O'Sullivan K, Poynton FE, Poulsen BC, Sazanovich IV, Towrie M, Cardin CJ, Sun XZ, George MW, Gunnlaugsson T, Quinn SJ, Kelly JM. Chem Sci 11 8600-8609 (2020)
  24. X-ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru-dppz Complexes. McQuaid K, Hall JP, Brazier JA, Cardin DJ, Cardin CJ. Chemistry 24 15859-15867 (2018)
  25. Study of picosecond processes of an intercalated dipyridophenazine Cr(III) complex bound to defined sequence DNAs using transient absorption and time-resolved infrared methods. Devereux SJ, Keane PM, Vasudevan S, Sazanovich IV, Towrie M, Cao Q, Sun XZ, George MW, Cardin CJ, Kane-Maguire NA, Kelly JM, Quinn SJ. Dalton Trans 43 17606-17609 (2014)
  26. Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers. Jabak AA, Bryden N, Westerlund F, Lincoln P, McCauley MJ, Rouzina I, Williams MC, Paramanathan T. Biophys J 121 3745-3752 (2022)
  27. Photoinduced interactions of two dirhodium complexes with d(GTCGAC)2 probed by 2D NOESY. Palmer AM, Knoll JD, Turro C. Dalton Trans 44 3640-3646 (2015)
  28. Two ruthenium complexes capable of storing multiple electrons on a single ligand - photophysical, photochemical and electrochemical properties of [Ru(phen)2(TAPHAT)]2+ and [Ru(phen)2(TAPHAT)Ru(phen)2]4. Troian-Gautier L, Marcélis L, De Winter J, Gerbaux P, Moucheron C. Dalton Trans 46 15287-15300 (2017)


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