Investigation of quadruplex structure under physiological conditions using in-cell NMR

Topics in Current Chemistry

Volumn 330, Issue , 2013, Pages 47-66

  Hänsel, Robert ^a   Foldynová Trantírková, Silvie ^b   Dötsch, Volker ^a   Trantírek, Lukáš ^c  

^a GOETHE UNIVERSITY   (Germany)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c UTRECHT UNIVERSITY   (Netherlands)

Author keywords

G quadruplex; In vivo; In cell NMR; Molecular crowding; Xenopus laevis

Indexed keywords

GUANINE QUADRUPLEX; NUCLEIC ACID;

ANIMAL; CHEMISTRY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; OOCYTE; REVIEW; XENOPUS LAEVIS;

ANIMALS; G-QUADRUPLEXES; HUMANS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACIDS; OOCYTES; XENOPUS LAEVIS;

EID: 84875902527     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128-2012-332     Document Type: Review

References (59)

1. Huppert JL, Balasubramanian S (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res 33:2908
2. Huppert JL, Balasubramanian S (2007) G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res 35:406
3. Brooks TA, Kendrick S, Hurley L (2010) Making sense of G-quadruplex and i-motif functions in oncogene promoters. FEBS J 277:3459
4. Wu Y, Brosh RM Jr (2010) G-quadruplex nucleic acids and human disease. FEBS J 277:3470
5. Bacolla A, Wells RD (2009) Non-B DNA conformations as determinants of mutagenesis and human disease. Mol Carcinog 48:273
6. Heckel A, Famulok M (2008) Building objects from nucleic acids for a nanometer world. Biochimie 90:1096
7. Collie GW, Parkinson GN (2011) The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 40:5867
8. Sedoris KC, Thomas SD, Clarkson CR, Muench D, Islam A, Singh R, Miller DM (2012) Genomic c-Myc quadruplex DNA selectively kills leukemia. Mol Cancer Ther 11:66
9. Li J, Correia JJ, Wang L, Trent JO, Chaires JB (2005) Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Res 33:4649
10. Phan AT (2010) Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J 277:1107
11. Dai J, Carver M, Yang D (2008) Polymorphism of human telomeric quadruplex structures. Biochimie 90:1172
12. Hansel R, Lohr F, Foldynova-Trantirkova S, Bamberg E, Trantirek L, Dotsch V (2011) The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions. Nucleic Acids Res 39:5768
13. Heddi B, Phan AT (2011) Structure of human telomeric DNA in crowded solution. J Am Chem Soc 133:9824
14. Inoue M, Miyoshi D, Sugimoto N (2005) Structural switch of telomere DNA by pH and monovalent cation. Nucleic Acids Symp Ser (Oxf) 243
15. Karimata H, Miyoshi D, Sugimoto N (2005) Structure and stability of DNA quadruplexes under molecular crowding conditions. Nucleic Acids Symp Ser (Oxf) 239
16. Lim KW, Amrane S, Bouaziz S, Xu W, Mu Y, Patel DJ, Luu KN, Phan AT (2009) Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers. J Am Chem Soc 131:4301
17. Miller MC, Buscaglia R, Chaires JB, Lane AN, Trent JO (2010) Hydration is a major determinant of the G-quadruplex stability and conformation of the human telomere 3' sequence of d[AG(3)[TTAG(3)](3)]. J Am Chem Soc 132:17105-17107
18. Miyoshi D, Matsumura S, Li W, Sugimoto N (2003) Structural polymorphism of telomeric DNA regulated by pH and divalent cation. Nucleosides Nucleotides Nucleic Acids 22:203
19. Parkinson GN, Lee MP, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417:876
20. Rencluk D, Kejnovska I, Skolakova P, Bednarova K, Motlova J, Vorlickova M (2009) Arrangements of human telomere DNA quadruplex in physiologically relevant K+ solutions. Nucleic Acids Res 37:6625
21. Xue Y, Kan ZY, Wang Q, Yao Y, Liu J, Hao YH, Tan Z (2007) Human telomeric DNA forms parallel-stranded intramolecular G-quadruplex in K+ solution under molecular crowding condition. J Am Chem Soc 129:11185
22. Li W, Wu P, Ohmichi T, Sugimoto N (2002) Characterization and thermodynamic properties of quadruplex/duplex competition. FEBS Lett 526:77
23. Miyoshi D, Matsumura S, Nakano S, Sugimoto N (2004) Duplex dissociation of telomere DNAs induced by molecular crowding. J Am Chem Soc 126:165
24. Luu KN, Phan AT, Kuryavyi V, Lacroix L, Patel DJ (2006) Structure of the human telomere in K+ solution: an intramolecular (3+1) G-quadruplex scaffold. J Am Chem Soc 128:9963
25. Dai J, Carver M, Punchihewa C, Jones RA, Yang D (2007) Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence. Nucleic Acids Res 35:4927
26. Wang Y, Patel DJ (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure 1:263
27. Serber Z, Dotsch V (2001) In-cell NMR spectroscopy. Biochemistry 40:14317
28. Serber Z, Keatinge-Clay AT, Ledwidge R, Kelly AE, Miller SM, Dotsch V (2001) Highresolution macromolecular NMR spectroscopy inside living cells. J Am Chem Soc 123:2446
29. Serber Z, Ledwidge R, Miller SM, Dotsch V (2001) Evaluation of parameters critical to observing proteins inside living Escherichia coli by in-cell NMR spectroscopy. J Am Chem Soc 123:8895
30. Selenko P, Serber Z, Gadea B, Ruderman J, Wagner G (2006) Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes. Proc Natl Acad Sci USA 103:11904
31. Serber Z, Selenko P, Hansel R, Reckel S, Lohr F, Ferrell JE Jr, Wagner G, Dotsch V (2006) Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopy. Nat Protoc 1:2701
32. Hansel R, Foldynova-Trantirkova S, Lohr F, Buck J, Bongartz E, Bamberg E, Schwalbe H, Dotsch V, Trantirek L (2009) Evaluation of parameters critical for observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR spectroscopy. J Am Chem Soc 131:15761
33. Sakakibara D, Sasaki A, Ikeya T, Hamatsu J, Hanashima T, Mishima M, Yoshimasu M, Hayashi N, Mikawa T, Walchli M, Smith BO, Shirakawa M, Guntert P, Ito Y (2009) Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 458:102
34. Chin DJ, Green GA, Zon G, Szoka FC Jr, Straubinger RM (1990) Rapid nuclear accumulation of injected oligodeoxyribonucleotides. New Biol 2:1091
35. Clarenc JP, Lebleu B, Leonetti JP (1993) Characterization of the nuclear binding sites of oligodeoxyribonucleotides and their analogs. J Biol Chem 268:5600
36. Fisher TL, Terhorst T, Cao X, Wagner RW (1993) Intracellular disposition and metabolism of fluorescently-labeled unmodified and modified oligonucleotides microinjected into mammalian cells. Nucleic Acids Res 21:3857
37. Leonetti JP, Mechti N, Degols G, Gagnor C, Lebleu B (1991) Intracellular distribution of microinjected antisense oligonucleotides. Proc Natl Acad Sci USA 88:2702
38. Lukacs GL, Haggie P, Seksek O, Lechardeur D, Freedman N, Verkman AS (2000) Sizedependent DNA mobility in cytoplasm and nucleus. J Biol Chem 275:1625
39. Bement WM, Capco DG (1990) Transformation of the amphibian oocyte into the egg: structural and biochemical events. J Electron Microsc Tech 16:202
40. Grandin N, Charbonneau M (1991) Cycling of intracellular free calcium and intracellular pH in Xenopus embryos: a possible role in the control of the cell cycle. J Cell Sci 99(Pt 1):5
41. Grandin N, Charbonneau M (1991) Intracellular free calcium oscillates during cell division of Xenopus embryos. J Cell Biol 112:711
42. Grandin N, Charbonneau M (1991) Changes in intracellular free calcium activity in Xenopus eggs following imposed intracellular pH changes using weak acids and weak bases. Biochim Biophys Acta 1091:242
43. Ito Y, Selenko P (2010) Cellular structural biology. Curr Opin Struct Biol 20:640
44. Guigas G, Kalla C, Weiss M (2007) The degree of macromolecular crowding in the cytoplasm and nucleoplasm of mammalian cells is conserved. FEBS Lett 581:5094
45. Guigas G, Kalla C, WeissM(2007) Probing the nanoscale viscoelasticity of intracellular fluids in living cells. Biophys J 93:316
46. Speil J, Kubitscheck U (2010) Single ovalbumin molecules exploring nucleoplasm and nucleoli of living cell nuclei. Biochim Biophys Acta 1803:396
47. Williams SP, Haggie PM, Brindle KM (1997) 19F NMR measurements of the rotational mobility of proteins in vivo. Biophys J 72:490
48. Zhang JL, Fu Y, Zheng L, Li W, Li H, Sun Q, Xiao Y, Geng F (2009) Natural isoflavones regulate the quadruplex-duplex competition in human telomeric DNA. Nucleic Acids Res 37:2471
49. Miyoshi D, Sugimoto N (2008) Molecular crowding effects on structure and stability of DNA. Biochimie 90:1040
50. Elcock AH (2010) Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol 20:196
51. Borman S (2011) DNA Folding in 'crowded' conditions. Chem Eng News 89:6
52. Xue Y, Liu JQ, Zheng KW, Kan ZY, Hao YH, Tan Z (2011) Kinetic and thermodynamic control of G-quadruplex folding. Angew Chem Int Ed Engl 50:8046-8050
53. Petraccone L, Spink C, Trent JO, Garbett NC, Mekmaysy CS, Giancola C, Chaires JB (2011) Structure and stability of higher-order human telomeric quadruplexes. J Am Chem Soc 133:20951
54. Wu Z, Delaglio F, Tjandra N, Zhurkin VB, Bax A (2003) Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy. J Biomol NMR 26:297
55. Ogino S, Kubo S, Umemoto R, Huang S, Nishida N, Shimada I (2009) Observation of NMR signals from proteins introduced into living mammalian cells by reversible membrane permeabilization using a pore-forming toxin, streptolysin O. J Am Chem Soc 131:10834
56. Inomata K, Ohno A, Tochio H, Isogai S, Tenno T, Nakase I, Takeuchi T, Futaki S, Ito Y, Hiroaki H, Shirakawa M (2009) High-resolution multi-dimensional NMR spectroscopy of proteins in human cells. Nature 458:106
57. Fiala R, Spackova N, Foldynova-Trantirkova S, Sponer J, Sklenar V, Trantirek L (2011) NMR cross-correlated relaxation rates reveal ion coordination sites in DNA. J Am Chem Soc 133:13790
58. Azarkh M, Okle O, Singh V, Seemann IT, Hartig JS, Dietrich DR, Drescher M (2011) Longrange distance determination in a DNA model system inside Xenopus laevis oocytes by in-cell spin-label EPR. Chembiochem 12:1992
59. Krstic I, Hansel R, Romainczyk O, Engels JW, Dotsch V, Prisner TF (2011) Long-range distance measurements on nucleic acids in cells by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 50:5070