Circular dichroism spectroscopy of DNA: From duplexes to quadruplexes

Chirality

Volumn 24, Issue 9, 2012, Pages 691-698

  Vorlíčková, Michaela ^a,b   Kejnovská, Iva ^a   Bednářová, Klára ^a   Renčiuk, Daniel ^a   Kypr, Jaroslav ^a  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

^b MASARYK UNIVERSITY   (Czech Republic)

Author keywords

A form; B form; circular dichroism; nucleic acid conformations; RNA; structural transitions; trinucleotide repeats; Z form

Indexed keywords

DOUBLE STRANDED DNA; GUANINE QUADRUPLEX; NUCLEIC ACID; PURINE; PYRIMIDINE; TRINUCLEOTIDE;

AMINO ACID SEQUENCE; CIRCULAR DICHROISM; CONFERENCE PAPER; DNA DETERMINATION; ISOMERIZATION; PRIORITY JOURNAL; PROTEIN STRUCTURE; TRINUCLEOTIDE REPEAT;

BASE SEQUENCE; CIRCULAR DICHROISM; DNA; G-QUADRUPLEXES; HUMANS; TRINUCLEOTIDE REPEATS;

EID: 84865630266     PISSN: 08990042     EISSN: 1520636X     Source Type: Journal    
DOI: 10.1002/chir.22064     Document Type: Conference Paper

References (66)

1. Gray DM, Ratliff RL, Vaughan MR,. Circular dichroism spectroscopy of DNA. Methods Enzymol 1992; 211: 389-406.
2. Johnson WC,. CD of nucleic acids. In:, N. Berova, K. Nakanishi, Woody RW, editors. New York: Wiley-VCH; 2000.
3. Johnson WC, Jr., Determination of the conformation of nucleic acids by electronic CD. In:, Fasman GD, editor. Circular dichroism and the conformational analysis of biomolecules. New York: Plenum press; 2000. p 433-468.
4. Kypr J, Kejnovska I, Renciuk D, Vorlickova M,. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 2009; 37: 1713-1725.
5. Bishop GR, Chaires JB,. Characterization of DNA structures by circular dichroism. Current protocols in nucleic acid chemistry: John Wiley & Sons, Inc.; 2003. p 7.11.1-7.11.8.
6. Klug A, Jack A, Viswamitra MA, Kennard O, Shakked Z, Steitz TA,. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J Mol Biol 1979; 131: 669-680.
7. Vorlickova M, Sagi J, Hejtmankova I, Kypr J,. Alkyl substituent in place of the thymine methyl-group controls the A-X conformational bimorphism in poly(dA-dT). J Biomol Struct Dyn 1991; 9: 571-578.
8. Diekmann S, Zarling DA,. Unique poly(dA).poly(dT) B'-conformation in cellular and synthetic DNAs. Nucleic Acids Res 1987; 15: 6063-6074.
9. Trantirek L, Stefl R, Vorlickova M, Koca J, Sklenar V, Kypr J,. An A-type double helix of DNA having B-type puckering of the deoxyribose rings. J Mol Biol 2000; 297: 907-922.
10. Stefl R, Trantirek L, Vorlickova M, Koca J, Sklenar V, Kypr J,. A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC). J Mol Biol 2001; 307: 513-524. (Pubitemid 33027675)
11. Ivanov VI, Minchenkova LE, Schyolkina AK, Poletayev AI,. Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers 1973; 12: 89-110.
12. Ivanov VI, Minchenkova LE, Minyat EE, Frank-Kamenetskii MD, Schyolkina AK,. The B to A transition of DNA in solution. J Mol Biol 1974; 87: 817-833.
13. Pohl FM, Jovin TM,. Salt-induced cooperative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-dC). J Mol Biol 1972; 67: 375-396.
14. Wang AH-J, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A,. Molecular structure a left-handed double helical DNA fragment at atomic resolution. Nature 1979; 282: 680-686. (Pubitemid 10217542)
15. Drew H, Takano T, Tanaka S, Itakura K, Dickerson RE,. High-salt d(CpGpCpG), a left-handed Z' DNA double helix. Nature 1980; 286: 567-573.
16. Drew HR, Wing RM, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE,. Structure of a B-DNA dodecamer: conformation and dynamics. Proc Natl Acad Sci USA 1981; 78: 2179-2183.
17. Ivanov VI, Minyat EE,. The transitions between left- and right-handed forms of poly(dG-dC). Nucleic Acids Res 1981; 9: 4783-4798.
18. Vorlickova M,. Conformational transitions of alternating purine-pyrimidine DNAs in perchlorate ethanol solutions. Biophys J 1995; 69: 2033-2043.
19. 5dC). Proc Natl Acad Sci USA 1981; 78: 1619-1623.
20. 5dC) by substitution of ethyl for the 5-methyl group. Int J Biol Macromol 1991; 13: 329-336.
21. Mazumdar D, Nagraj N, Kim H-K, Meng X, Brown AK, Sun Q, Li W, Lu Y,. Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions. J Am Chem Soc 2009; 131: 5506-5515.
22. 4: parallel, anti-parallel, right-handed and left-handed homoduplexes of a trinucleotide repeat DNA. Biochimica Et Biophysica Acta-General Subjects 2001; 1527: 73-80. (Pubitemid 32566212)
23. Vorlickova M, Kejnovska I, Tumova M, Kypr J,. Conformational properties of DNA fragments containing (GAC) trinucleotide repeats associated with skeletal displasias. Eur Biophys J 2001; 30: 179-185. (Pubitemid 32768851)
24. Renciuk D, Kypr J, Vorlickova M,. CGG repeats associated with Fragile X chromosome form left-handed Z-DNA structure. Biopolymers 2011; 95: 174-181.
25. Hardin CC, Zarling DA, Puglisi JD, Trulson MO, Davis PW, Tinoco IJ,. Stabilization of Z-RNA by chemical bromination and its recognition by anti-Z-DNA antibodies. Biochemistry 1987; 26: 5191-5199.
26. Feng S, Li H, Zhao J, Pervushin K, Lowenhaupt K, Schwartz TU, Droge P,. Alternate rRNA secondary structures as regulators of translation. Nat Struct Mol Biol 2011; 18: 169-176.
27. Vorlickova M, Kypr J, Sklenar V,. Salt-induced conformational transition of poly[d(A-T)]·poly[d(A-T)] J. Mol Biol 1983; 166: 85-92.
28. Bourtayre P, Liquier J, Pizzorni L, Taillandier E,. Z form of poly d(A-T).poly d(A-T) in solution studied by CD and UV spectroscopies. J Biomol Struct Dyn 1987; 5: 97-104.
29. Airoldi M, Gennaro G, Giomini M, Giuliani AM, Giustini M,. Circular dichroism of polynucleotides: Interactions of NiCl2 with poly(dA-dT) ·poly(dA-dT) and poly(dG-dC)·poly(dG-dC) in a water-in-oil microemulsion. Chirality 2008; 20: 951-960.
30. Vorlickova M, Kypr J, Stokrova S, Sponar J,. A Z-like form of poly(dA-dC)-poly(dG-dT) in solution. Nucleic Acids Res 1982; 10: 1071-1080.
31. Kypr J, Stepan J, Chladkova J, Vorlickova M,. Circular dichroism spectroscopy analysis of conformational transitions of a 54 base pair DNA duplex composed of alternating CGCGCG and TATATA blocks. Biospectroscopy 1999; 5: 253-262.
32. Pearson CE, Edamura KN, Cleary JD,. Repeat instability: mechanisms of dynamic mutations. Nat Rev Genet 2005; 6: 729-742. (Pubitemid 41400831)
33. Mirkin SM,. DNA structures, repeat expansions and human hereditary disorders. Curr Opin Struct Biol 2006; 16: 1-8.
34. Mirkin SM,. Expandable DNA repeats and human disease. Nature 2007; 447: 932-940. (Pubitemid 46975760)
35. Pearson CE, Tam M, Wang YH, Montgomery SE, Dar AC, Cleary JD, Nichol K,. Slipped-strand DNAs formed by long (CAG).(CTG) repeats: slipped-out repeats and slip-out junctions. Nucleic Acids Res 2002; 30: 4534-4547.
36. n nucleotide repeats form a stable tetrahelical structure. Proc Natl Acad Sci USA 1994; 91: 4950-4954.
37. Khateb S, Weisman-Shomer P, Hershco-Shani I, Ludwig AL, Fry M,. The tetraplex (CGG)n destabilizing proteins hnRNP A2 and CBF-A enhance the in vivo translation of fragile X premutation mRNA. Nucleic Acids Res 2007; 35: 5775-5788. (Pubitemid 47514486)
38. Fojtik P, Vorlickova M,. The fragile X chromosome (GCC) repeat folds into a DNA tetraplex at neutral pH. Nucleic Acids Res 2001; 29: 4684-4690. (Pubitemid 33095029)
39. Renciuk D, Zemanek M, Kejnovska I, Vorlickova M,. Quadruplex-forming properties of FRAXA (CGG) repeats interrupted by (AGG) triplets. Biochimie 2009; 91: 416-422.
40. Rippe K, Fritsch V, Westhof E, Jovin TM,. Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J 1992; 11: 3777-3786.
41. Vorlickova M, Kejnovska I, Kovanda J, Kypr J,. Dimerization of the guanine-adenine repeat strands of DNA. Nucleic Acids Res 1999; 27: 581-586. (Pubitemid 29210026)
42. n and related oligonucleotide sequences. Prog Nucleic Acid Res Mol Biol 2003; 75:Elsevier; 321-347. (Pubitemid 137639561)
43. Antao VP, Gray DM, Ratliff RL,. CD of six different conformational rearrangements of poly(d(A-G).d(C-T)) induced by low pH. Nucleic Acids Res 1988; 16: 719-738.
44. Gray DM, Hung S-H, Johnson KH,. Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Methods Enzymol 1995; 246: 19-34.
45. Simon P, Cannata F, Concordet JP, Giovannangeli C,. Targeting DNA with triplex-forming oligonucleotides to modify gene sequence. Biochimie 2008; 90: 1109-1116.
46. Jain A, Wang G, Vasquez KM,. DNA triple helices: biological consequences and therapeutic potential. Biochimie 2008; 90: 1117-1130.
47. Neidle S, Balasubramanian S, editors. Quadruplex nucleic acids. London, Cambridge: Royal Society of Chemistry; 2006.
48. Balasubramanian S, Neidle S,. G-quadruplex nucleic acids as therapeutic targets. Curr Opin Chem Biol 2009; 13: 345-353.
49. Han HY, Hurley LH,. G-quadruplex DNA: a potential target for anti-cancer drug design. Trends Pharmacol Sci 2000; 21: 136-142. (Pubitemid 30190138)
50. Balasubramanian S, Hurley LH, Neidle S,. Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat Rev Cancer 2011; 10: 261-275.
51. Alberti P, Mergny JL,. DNA duplex-quadruplex exchange as the basis for a nanomolecular machine. Proc Natl Acad Sci USA 2003; 100: 1569-1573. (Pubitemid 36254488)
52. Paramasivan S, Rujan I, Bolton PH,. Circular dichroism of quadruplex DNAs: applications to structure, cation effects and ligand binding. Methods 2007; 43: 324-331. (Pubitemid 47633205)
53. Mergny JL, Lacroix L, Han X, Leroy J-L, Helene C,. Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif. J Am Chem Soc 1995; 117: 8887-8898.
54. Gueron M, Leroy J-L,. The i-motif in nucleic acids. Curr Opin Struct Biol 2000; 10: 326-331. (Pubitemid 30333102)
55. Simonsson T,. G-quadruplex DNA structures-variations on a theme. Biol Chem 2001; 382: 621-628. (Pubitemid 32472172)
56. Gray DM, Wen J, Gray CV, Repges R, Repges C, Raabe G, Fleischhauer J,. Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities. Chirality 2008; 20: 431-440. (Pubitemid 351303984)
57. Masiero S, Trotta R, Pieraccini S, De Tito S, Perone R, Randazzo A, Spada GP,. A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures. Org Biomol Chem 2010; 8: 2653-2872.
58. Karsisiotis AI, Hessari NM, Novellino E, Spada GP, Randazzo A, da Silva W,. Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism. Angew. Chem.-Int. Edit. 2011; 50: 10645-10648.
59. Neidle S, Parkinson G,. Telomere maintenance as a target for anticancer drug discovery. Nature Reviews 2002; 1: 383-393. (Pubitemid 37361468)
60. Patel DJ, Phan AT, Kuryavyi V,. Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res 2007; 35: 7429-7455.
61. De Cian A, Lacroix L, Douarre C, Temime-Smaali N, Trentesaux C, Riou JF, Mergny JL,. Targeting telomeres and telomerase. Biochimie 2008; 90: 131-155. (Pubitemid 350245369)
62. Vorlickova M, Chladkova J, Kejnovska I, Fialova M, Kypr J,. Guanine tetraplex topology of human telomere DNA is governed by the number of (TTAGGG) repeats. Nucleic Acids Res 2005; 33: 5851-5860. (Pubitemid 41742604)
63. Xu Y, Ishizuka T, Kurabayashi K, Komiyama M,. Consecutive formation of G-quadruplexes in human telomeric-overhang DNA: a protective capping structure for telomere ends. Angew. Chem.-Int. Edit. 2009; 48: 7833-7836.
64. + solutions. Nucleic Acids Res 2009; 37: 6625-6634.
65. Wells RD,. Non-B DNA conformations, mutagenesis and disease. Trends Biochem Sci 2007; 32: 271-278. (Pubitemid 46874927)
66. Mirkin SM,. Discovery of alternative DNA structures: a heroic decade (1979-1989). Front Biosci 2008; 13: 1064-1071. (Pubitemid 351594748)