Structure of a left-handed DNA G-quadruplex

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 9, 2015, Pages 2729-2733

  Chung, Wan Jun ^a   Heddi, Brahim ^a   Schmitt, Emmanuelle ^b   Lim, Kah Wai ^a   Mechulam, Yves ^b   Phan, Anh Tuân ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b LABORATOIRE DE BIOCHIMIE   (France)

Author keywords

G quadruplex; Left handed helix; NMR; Nucleic acid; X ray crystallography

Indexed keywords

DNA Z; GUANINE QUADRUPLEX; DNA;

ARTICLE; CIRCULAR DICHROISM; CRYSTAL STRUCTURE; DNA HELIX; DNA STRUCTURE; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; X RAY ANALYSIS; CHEMISTRY; CONFORMATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DNA; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID CONFORMATION;

EID: 84924363690     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1418718112     Document Type: Article

References (42)

1. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171(4356):737-738
2. Wang AHJ, et al. (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282(5740):680-686
3. Leontis NB, Stombaugh J, Westhof E (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30(16):3497-3531
4. Nikolova EN, et al. (2011) Transient Hoogsteen base pairs in canonical duplex DNA. Nature 470(7335):498-502
5. Frank-Kamenetskii MD, Mirkin SM (1995) Triplex DNA structures. Annu Rev Biochem 64:65-95
6. Smith FW, Feigon J (1992) Quadruplex structure of Oxytricha telomeric DNA oligonucleotides. Nature 356(6365):164-168
7. Parkinson GN, Lee MPH, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417(6891):876-880
8. Gehring K, Leroy JL, Guéron M (1993) A tetrameric DNA structure with protonated cytosine-cytosine base pairs. Nature 363(6429):561-565
9. Lilley DMJ (2000) Structures of helical junctions in nucleic acids. Q Rev Biophys 33(2): 109-159
10. Siddiqui-Jain A, Grand CL, Bearss DJ, Hurley LH (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc Natl Acad Sci USA 99(18):11593-11598
11. Kumari S, Bugaut A, Huppert JL, Balasubramanian S (2007) An RNA G-quadruplex in the 5' UTR of the NRAS proto-oncogene modulates translation. Nat Chem Biol 3(4): 218-221
12. Cahoon LA, Seifert HS (2009) An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoeae. Science 325(5941):764-767
13. Paeschke K, Capra JA, Zakian VA (2011) DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell 145(5):678-691
14. Lopes J, et al. (2011) G-quadruplex-induced instability during leading-strand replication. EMBO J 30(19):4033-4046
15. Biffi G, Tannahill D, McCafferty J, Balasubramanian S (2013) Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem 5(3):182-186
16. Maizels N, Gray LT (2013) The G4 genome. PLoS Genet 9(4):e1003468
17. Gellert M, Lipsett MN, Davies DR (1962) Helix formation by guanylic acid. Proc Natl Acad Sci USA 48(12):2013-2018
18. Adrian M, Heddi B, Phan AT (2012) NMR spectroscopy of G-quadruplexes. Methods 57(1):11-24
19. Trajkovski M, da Silva MW, Plavec J (2012) Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from the intron of the N-myc gene. J Am Chem Soc 134(9):4132-4141
20. Yatsunyk LA, Mendoza O, Mergny JL (2014) "Nano-oddities": Unusual nucleic acid assemblies for DNA-based nanostructures and nanodevices. Acc Chem Res 47(6):1836-1844
21. Bates PJ, Laber DA, Miller DM, Thomas SD, Trent JO (2009) Discovery and development of the G-rich oligonucleotide AS1411 as a novel treatment for cancer. Exp Mol Pathol 86(3):151-164
22. Dailey MM, Miller MC, Bates PJ, Lane AN, Trent JO (2010) Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence. Nucleic Acids Res 38(14):4877-4888
23. Vorlíčková M, Kejnovská I, Bednářová K, Renčiuk D, Kypr J (2012) Circular dichroism spectroscopy of DNA: From duplexes to quadruplexes. Chirality 24(9):691-698
24. Lech CJ, Heddi B, Phan AT (2013) Guanine base stacking in G-quadruplex nucleic acids. Nucleic Acids Res 41(3):2034-2046
25. Do NQ, Phan AT (2012) Monomer-dimer equilibrium for the 5'-5' stacking of propeller- type parallel-stranded G-quadruplexes: NMR structural study. Chemistry 18(46): 14752-14759
26. Pohl FM, Jovin TM (1972) Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly (dG-dC). J Mol Biol 67(3):375-396
27. Phan AT, et al. (2011) Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction. Nat Struct Mol Biol 18(7):796-804
28. Huang H, et al. (2014) A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol 10(8):686-691
29. Warner KD, et al. (2014) Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol 21(8):658-663
30. Tran PLT, Moriyama R, Maruyama A, Rayner B, Mergny JL (2011) A mirror-image tetramolecular DNA quadruplex. Chem Commun 47(19):5437-5439
31. Virgilio A, et al. (2011) Unprecedented right- and left-handed quadruplex structures formed by heterochiral oligodeoxyribonucleotides. Biochimie 93(7):1193-1196
32. Seeman NC (2010) Nanomaterials based on DNA. Annu Rev Biochem 79:65-87
33. Goddard TD, Kneller DG SPARKY 3 (University of California, San Francisco)
34. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160(1):65-73
35. Case DA, et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668-1688
36. DeLano WL, Bromberg S (2004) PyMOL User's Guide (DeLano Scientific LLC, San Carlos, CA)
37. Kabsch W (2010) XDS. Acta Crystallogr D Biol Crystallogr 66(Pt 2):125-132
38. McCoy AJ, et al. (2007) Phaser crystallographic software. J Appl Cryst 40(Pt 4):658-674
39. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66(Pt 4):486-501
40. Afonine PV, et al. (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 68(Pt 4):352-367
41. Lavery R, Moakher M, Maddocks JH, Petkeviciute D, Zakrzewska K (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res 37(17):5917-5929
42. Schneider B, Neidle S, Berman HM (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42(1):113-124.