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Interaction between a DNA oligonucleotide and a dinuclear iron(II) supramolecular cylinder : an NMR and molecular dynamics study

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Moldrheim, Erlend, Sletten, Einar, Hannon, Michael J., Meistermann, Isabelle and Rodger, Alison. (2002) Interaction between a DNA oligonucleotide and a dinuclear iron(II) supramolecular cylinder : an NMR and molecular dynamics study. Journal of Biological Inorganic Chemistry, Vol.7 (No.7-8). pp. 770-780. ISSN 0949-8257

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Official URL: http://dx.doi.org/10.1007/s00775-002-0354-2

Abstract

A tetracationic supramolecular cylinder, [Fe-2 L-3](4+) (L=C25H20N4), with a triple-helical architecture, is just the right size to fit into the major groove of DNA but too big to fit into the minor groove. A detailed NMR spectroscopic analysis supported by molecular dynamics (MD) calculations shows unambiguously the close fit between the cylinder and a duplex oligonucleotide, [d(GACGGCCGTC)(2)]. Furthermore, only the left-handed enantiomer of the cylinder seems to fit the groove geometry. With both free and complexed species of[Fe2L3](4+) and DNA in solution, the NMR spectra are too complicated for a detailed structure determination. Based on differences in chemical shifts and extensive MD calculations, a realistic qualitative picture of the DNA-cylinder adduct is presented. Several sets of chemical shifts assigned to the protons of the three ligand strands in the cylinder indicate that the iron complex situated in the major groove exhibits restricted rotation on the NMR timescale around the cylindrical axis. The NMR NOE data support a model where the cylinder undergoes both a translational and rotational oscillation in the major groove. The results of an NOE restrained MD calculation indicates that the cylinder induces a 40degrees bend of the double helix, in accordance with linear dichroism measurements. Other distinct features to be noticed are the very low value of the helical twist (16degrees) induced at the G(4)C(5) step.

Item Type:	Journal Article
Subjects:	Q Science > QD Chemistry
Divisions:	Faculty of Science > Chemistry
Library of Congress Subject Headings (LCSH):	Oligonucleotides, Supramolecular chemistry
Journal or Publication Title:	Journal of Biological Inorganic Chemistry
Publisher:	Springer
ISSN:	0949-8257
Date:	2002
Volume:	Vol.7
Number:	No.7-8
Number of Pages:	11
Page Range:	pp. 770-780
Identification Number:	10.1007/s00775-002-0354-2
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Description:	Electronic supplementary material to this paper, comprising Figs. S1-S4 and Tables S1-S4, can be obtained by using the Springer Link server located at http://dx.doi.org/ 10.1007/s00775-002-0354-2.
Funder:	Leverhulme Trust (LT), Norges forskningsråd [Norwegian Research Council], Engineering and Physical Sciences Research Council (EPSRC), University of Warwick
Grant number:	135055/410 (NFR), F/215/BC (LT), GR/M91105 (EPSRC)
References:	1. Hannon MJ, Moreno V, Prieto MJ, Moldrheim E, Sletten E, Meistermann I, Isaac CJ, Sanders KJ, Rodger A (2001) Angew Chem Int Ed 40: 879-884 2. White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB (1998) Nature 391: 468-471 3. Thuong NT, Helene C (1993) Angew Chem Int Ed 32: 666-690 4. Nielsen PE, Haaima G (1997) Chem Soc Rev 26: 73-78 5. Lippert B (ed) (1999) Cis-platin, a leading anti-cancer drug VCH, Weinheim 6. Coggan DZM, Haworth IS, Bates PJ, Robinson A, Rodger A (1999 Inorg Chem 38: 4486-4497 7. Onfelt B, Lincoln P, Norden B (1999) J Am Chem Soc 121: 10846-10847 8. Erkkila KE, Odom DT, Barton JK (1999) Chem Rev 99: 2777-2795 and refs therein 9. Childs LZ, Alcock NW, Hannon MJ (2001)Angew Chem Int Ed 40: 1079-1081 10. Hannon MJ, Painting CL, Alcock NW (1999) Chem Commun 2023-2024 11. Hannon MJ, Bunce S, Clarke AJ, Alcock NW (1999) Angew Chem Int Ed 38: 1277-1278 12. Hannon MJ, Painting CL, Jackson A, Hamblin J, Errington W (1997) Chem Commun 1807-1808 13. Rodger A, Sanders KJ, Hannon MJ, Meistermann I, Parkinson A, Vidler DS, Haworth IS (2000) Chirality 12: 221-236 14. Liu AM, Mao X, Ye C, Huang H, Nicholson JK, Lindon JC (1998) J Magn Res 132: 125-129 15. Hwang T-L, Shaka AJ (1995) J Magn Res Series A 112: 275-279 16. Goddard TD, Kneller DG, SPARKY3, University of California, San Francisco 17. Ewing TJA, Kuntz ID (1997) J Comp Chem 18: 9, 1175-1189 18. Cheatham III TE, Kollman PA (2000) Annu Rev Phys Chem 51: 435-471 19. Hannon MJ, Painting CL, Alcock NW, Childs LJ, Liu Z (manuscript in preparation) 20. Stewart JJP (1989) J Comp Chem 10: 209-220 21. Titan, Wavefunction, Inc, 18401 Von Karman Ave, Ste 370, Irvine, CA 92612 USA 22. Gaussian 98, Revision A9, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery Jr JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA, Gaussian, Inc, Pittsburgh PA, 1998 23. Rassolov VA, Pople JA, Ratner MA, Windus TL (1998) J Chem Phys 109: 1223- 1229 24. Singh UC, Kollman PA (1984) J Comp Chem 5: 129-145 25. Besler BH, Merz KM, Kollman PA (1990) J Comp Chem 11: 431-439 26. Breneman CM, Wiberg KB (1990) J Comp Chem 11: 361-373 27. Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993) J Phys Chem 97: 10269- 10280 28. http://www.amber.ucsf.edu/amber/ff94/contrib/heme/frcmodhemall 29. Wang J, Cieplak P, Kollman PA (2000) J Comp Chem 21: 1049-1074 30. Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA, Amber 6, University of California, San Francisco, (1999) 31. Jorgensen WL, Chandrasekhar J, Madura J, Impey RW, Klein ML (1983) J Chem Phys 79: 926-937 32. Ryckaert JP, Ciccotti G, Berendsen HJC (1997) J Comp Phys 23: 327-341 33. Berendsen HJC, Postma JPM, van Guensteren WF, DiNola A, Haak JR (1984) J Chem Phys 81: 3684-3690 34. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) J Chem Phys 103: 8577-8593 35. Spakova N, Berger I, Sponer J (2001) J Am Chem Soc 123: 3295-3307 36. Humphrey W, Dalke A, Schulten K, “VMD – Visual Molecular Dynamics” (1996) J Mol Graph 14: 1, 33-38 37. Lu X-J, Shakked Z, Olson WK (2000) J Mol Biol 300: 819-840 38. Lavery R, Sklenar H, Curves 5.3 (http://apex.ibpc.fr/UPR9080/CurForm_bis.html) 39. Delbarre A, Delepierre M, Langlois d’Estaintot B, Igolen J, Roques BP (1987) Biopolymers 26: 1001-1033 40. Frøystein NÅ, Sletten E (1994) J Am Chem Soc 116: 3240-3250 41. Bostock-Smith CE, Harris SA, Laughton CA, Searle MS (2001) Nucl Acid Res 29: 3, 693-702 42. Kumar RA, Ikemoto N, Patel DJ (1997) J Mol Biol 265: 173-186 43. Chen H, Patel DJ (1995) J Mol Biol 246: 164-179 44. Wijmenga SS, Kruithof M, Hilbers CW (1997) J Biomol NMR 10: 337-350 45. Fouchet MH, Guittet E, Cognet JAH, Kozelka J, Gauthier C, Bret ML, Zimmermann K, Chottard JC (1997) J Biol Inorg Chem 2: 83-92 46. Marzilli LG, Saad JS, Kuklenyik Z, Keating KA, Xu Y (2001) 123: 2764-2770 47. Packer MJ, Dauncey MP, Hunter CA (2000) J Mol Biol 295: 71-83 48. Dickerson RE (1998) Nucl Acid Res 26: 8, 1906-1926 49. Bolshoy A, McNamara P, Harrington RE, Trifonov EN (1991) Proc Natl Acad Sci 88: 2312-2316 50. Hannon MJ, Meistermann I, Isaac CJ, Blomme C, Aldrich-Wright JR, Rodger A (2001) Chem Commun, 1078-1079 51. Meng EC, Shoichet BK, Kuntz ID (1992) J Comp Chem 13: 504-524 52. Merrit EA, Bacon DJ (1997) Meth Enzym 277: 505-524
URI:	http://wrap.warwick.ac.uk/id/eprint/10533