Surface area accessibility and the preferred topology of telomeric DNA quadruplex-ligand complexes

Biochimie

Volumn 93, Issue 8, 2011, Pages 1275-1279

  Haider, Shozeb M ^a,b   Autiero, Ida ^a,c   Neidle, Stephen ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^c SECOND UNIVERSITY OF NAPLES   (Italy)

Author keywords

Ligand; Quadruplex; Surface area; Topology

Indexed keywords

GUANINE QUADRUPLEX; SOLVENT;

ARTICLE; CRYSTAL STRUCTURE; DNA STRUCTURE; ENERGY; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID STRUCTURE; TELOMERE;

G-QUADRUPLEXES; HUMANS; LIGANDS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; SOLVENTS; TELOMERE;

EID: 79960700765     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2011.05.014     Document Type: Article

References (31)

1. A. Verma, V.K. Yadav, R. Basundra, A. Kumar, and S. Chowdhury Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells Nucleic Acids Res. 37 2009 4194 4204
2. A.K. Todd, M. Johnston, and S. Neidle Highly prevalent putative quadruplex sequence motifs in human DNA Nucleic Acids Res. 33 2005 2901 2907 (Pubitemid 41511229)
3. J.L. Huppert, and S. Balasubramanian Prevalence of quadruplexes in the human genome Nucleic Acids Res. 33 2005 2908 2916 (Pubitemid 41511230)
4. J. Eddy, and N. Maizels Gene function correlates with potential for G4 DNA formation in the human genome Nucleic Acids Res. 34 2006 3887 3896 (Pubitemid 44391004)
5. L.H. Hurley, D.D. Von Hoff, A. Siddiqui-Jain, and D. Yang Drug targeting of the c-MYC promoter to repress gene expression via a G-quadruplex silencer element Semin. Oncol. 33 2006 498 512 (Pubitemid 44142743)
6. C.M. Lombardo, I.S. Martinez, S. Haider, V. Gabelica, E. De Pauw, J.E. Moses, and S. Neidle Structure-based design of selective high-affinity telomeric quadruplex-binding ligands Chem. Commun. (Camb.) 46 2010 9116 9118
7. M. Read, R.J. Harrison, B. Romagnoli, F.A. Tanious, S.H. Gowan, A.P. Reszka, W.D. Wilson, L.R. Kelland, and S. Neidle Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors Proc. Natl. Acad. Sci. USA 98 2001 4844 4849 (Pubitemid 32397044)
8. M.A. Read, and S. Neidle Structural characterization of a guanine-quadruplex ligand complex Biochemistry 39 2000 13422 13432
9. G.N. Parkinson, M.P. Lee, and S. Neidle Crystal structure of parallel quadruplexes from human telomeric DNA Nature 417 2002 876 880 (Pubitemid 34670337)
10. + solution Nucleic Acids Res. 34 2006 5715 5719 (Pubitemid 44742458)
11. + solution: an intramolecular (3 + 1) G-quadruplex scaffold J. Am. Chem. Soc. 128 2006 9963 9970 (Pubitemid 44147983)
12. + solution Bioorg. Med. Chem. 14 2006 5584 5591 (Pubitemid 43994462)
13. + solution under molecular crowding condition J. Am. Chem. Soc. 129 2007 11185 11191 (Pubitemid 47435722)
14. L. Martino, B. Pagano, I. Fotticchia, S. Neidle, and C. Giancola Shedding light on the interaction between TMPyP4 and human telomeric quadruplexes J. Phys. Chem. B 113 2009 14779 14786
15. G.W. Collie, S. Sparapani, G.N. Parkinson, and S. Neidle Structural basis of telomeric RNA quadruplex-acridine ligand recognition J. Am. Chem. Soc. 133 2010 2721 2728
16. N.H. Campbell, M. Patel, A.B. Tofa, K. Ghosh, G.N. Parkinson, and S. Neidle Selectivity in ligand recognition of G-quadruplex loops Biochemistry 48 2009 1675 1680
17. G.N. Parkinson, F. Cuenca, and S. Neidle Topology conservation and loop flexibility in quadruplex-drug recognition: crystal structures of inter- and intramolecular telomeric DNA quadruplex-drug complexes J. Mol. Biol. 381 2008 1145 1156
18. N.H. Campbell, G.N. Parkinson, A.P. Reszka, and S. Neidle Structural basis of DNA quadruplex recognition by an acridine drug J. Am. Chem. Soc. 130 2008 6722 6724 (Pubitemid 351748405)
19. G.N. Parkinson, R. Ghosh, and S. Neidle Structural basis for binding of porphyrin to human telomeres Biochemistry 46 2007 2390 2397 (Pubitemid 46362413)
20. T.P. Garner, H.E. Williams, K.I. Gluszyk, S. Roe, N.J. Oldham, M.F. Stevens, J.E. Moses, and M.S. Searle Selectivity of small molecule ligands for parallel and anti-parallel DNA G-quadruplex structures Org. Biomol. Chem. 7 2009 4194 4200
21. 4 containing the human telomeric repeat J. Mol. Biol. 334 2003 25 36 (Pubitemid 37330097)
22. J. Dash, P.S. Shirude, S.T. Hsu, and S. Balasubramanian Diarylethynyl amides that recognize the parallel conformation of genomic promoter DNA G-quadruplexes J. Am. Chem. Soc. 130 2008 15950 15956
23. J. Alzeer, and N.W. Luedtke pH-Mediated fluorescence and G-quadruplex binding of amido phthalocyanines Biochemistry 49 2010 4339 4348
24. S.M. Hampel, A. Sidibe, M. Gunaratnam, J.-F. Riou, and S. Neidle Tetrasubstituted naphthalene diimide ligands with selectivity for telomeric G-quadruplexes and cancer cells Bioorg. Med. Chem. Lett. 20 2010 6459 6463
25. S. Sparapani, S.M. Haider, F. Doria, M. Gunaratnam, and S. Neidle Rational design of acridine-based ligands with selectivity for human telomeric quadruplexes J. Am. Chem. Soc. 132 2010 12263 12272
26. J.J. Stewart MOPAC: a semiempirical molecular orbital program J. Comput. Aided Mol. Des. 4 1990 1 105
27. A.D. Moorhouse, S. Haider, M. Gunaratnam, D. Munnur, S. Neidle, and J.E. Moses Targeting telomerase and telomeres: a click chemistry approach towards highly selective G-quadruplex ligands Mol. Biosyst. 4 2008 629 642 (Pubitemid 351706307)
28. F. Cuenca, O. Greciano, M. Gunaratnam, S. Haider, D. Munnur, R. Nanjunda, W.D. Wilson, and S. Neidle Tri- and tetra-substituted naphthalene diimides as potent G-quadruplex ligands Bioorg. Med. Chem. Lett. 18 2008 1668 1673 (Pubitemid 351318241)
29. R.J. Harrison, A.P. Reszka, S.M. Haider, B. Romagnoli, J. Morrell, M.A. Read, S.M. Gowan, C.M. Incles, L.R. Kelland, and S. Neidle Evaluation of disubstituted acridone derivatives as telomerase inhibitors: the importance of G-quadruplex binding Bioorg. Med. Chem. Lett. 14 2004 5845 5849 (Pubitemid 39421529)
30. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-38 (Pubitemid 26152973)
31. N.A. Baker Poisson-Boltzmann methods for biomolecular electrostatics Methods Enzymol. 383 2004 94 118 (Pubitemid 38401788)