Unlocking G-quadruplex: Effect of unlocked nucleic acid on G-quadruplex stability

Biochimie

Volumn 93, Issue 10, 2011, Pages 1694-1700

  Agarwal, Tani ^a   Kumar, Santosh ^a   Maiti, Souvik ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

Aptamer; G quadruplex; Serum stability assay; Thermodynamic analysis; Unlocked nucleic acids (UNA)

Indexed keywords

GUANINE QUADRUPLEX; LOCKED NUCLEIC ACID; UNCLASSIFIED DRUG; UNLOCKED NUCLEIC ACID;

AMINO ACID SUBSTITUTION; ARTICLE; CIRCULAR DICHROISM; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA MODIFICATION; DNA SEQUENCE; DNA STRUCTURE; MOLECULAR STABILITY; THERMOSTABILITY; ULTRAVIOLET SPECTROSCOPY;

ANIMALS; APTAMERS, NUCLEOTIDE; CATTLE; CIRCULAR DICHROISM; G-QUADRUPLEXES; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS;

EID: 80052090761     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2011.05.036     Document Type: Article

References (37)

1. P.J. Joshi, T.S. Fisher, and V.R. Prasad Anti-HIV inhibitors based on nucleic acids: emergence of aptamers as potent antivirals Curr. Drug Targets Infect. Disord. 3 2003 383 400 (Pubitemid 38016625)
2. S.M. Nimjee, C.P. Rusconi, and B.A. Sullenger Aptamers: an emerging class of therapeutics Annu. Rev. Med. 56 2005 555 583 (Pubitemid 40299797)
3. C. Pestourie, B. Tavitian, and F. Duconge Aptamers against extracellular targets for in vivo applications Biochimie 87 2005 921 930 (Pubitemid 41297819)
4. C.R. Ireson, and L.R. Kelland Discovery and development of anticancer aptamers Mol. Cancer Ther. 5 2006 2957 2962 (Pubitemid 46092036)
5. J.D. Wen, and D.M. Gray The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex Biochemistry 41 2002 11438 11448
6. C. Wilson, and J.W. Szostak Isolation of a fluorophore-specific DNA aptamer with weak redox activity Chem. Biol. 5 1998 609 617 (Pubitemid 28519448)
7. T.W. Wiegand, P.B. Williams, S.C. Dreskin, M.H. Jouvin, J.P. Kinet, and D.I. Tasset High-affinity oligonucleotide ligands to human IgE inhibit binding to Fc epsilon receptor I J. Immunol. 157 1996 221 230
8. C.T. Lauhon, and J.W. Szostak RNA aptamers that bind flavin and nicotinamide redox cofactors J. Am. Chem. Soc. 117 1995 1246 1257
9. D.E. Huizenga, and J.W. Szostak A DNA aptamer that binds adenosine and ATP Biochemistry 34 1995 656 665
10. R.F. Macaya, P. Schultze, F.W. Smith, J.A. Roe, and J. Feigon Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution Proc. Natl. Acad. Sci. U S A 90 1993 3745 3749 (Pubitemid 23111444)
11. J.L. Huppert Four-stranded DNA: cancer, gene regulation and drug development Philos. Transact. A. Math. Phys. Eng. Sci. 365 2007 2969 2984
12. T. Agarwal, S. Roy, T.K. Chakraborty, and S. Maiti Furan based cyclic homo-oligopeptides bind G-quadruplex selectively and repress c-MYC transcription Bioorg. Med. Chem. Lett. 20 2010 4346 4349
13. T. Agarwal, S. Roy, T.K. Chakraborty, and S. Maiti Selective targeting of G-quadruplex using furan-based cyclic homooligopeptides: effect on c-MYC expression Biochemistry 49 2010 8388 8397
14. H. Bartz, Y. Mendoza, M. Gebker, T. Fischborn, K. Heeg, and A. Dalpke Poly-guanosine strings improve cellular uptake and stimulatory activity of phosphodiester CpG oligonucleotides in human leukocytes Vaccine 23 2004 148 155 (Pubitemid 39505083)
15. A.H. Dalpke, S. Zimmermann, I. Albrecht, and K. Heeg Phosphodiester CpG oligonucleotides as adjuvants: polyguanosine runs enhance cellular uptake and improve immunostimulative activity of phosphodiester CpG oligonucleotides in vitro and in vivo Immunology 106 2002 102 112 (Pubitemid 34437883)
16. J.S. Bishop, J.K. Guy-Caffey, J.O. Ojwang, S.R. Smith, M.E. Hogan, P.A. Cossum, R.F. Rando, and N. Chaudhary Intramolecular G-quartet motifs confer nuclease resistance to a potent anti-HIV oligonucleotide J. Biol. Chem. 271 1996 5698 5703 (Pubitemid 26084455)
17. P.J. Bates, D.A. Laber, D.M. Miller, S.D. Thomas, and J.O. Trent Discovery and development of the G-rich oligonucleotide AS1411 as a novel treatment for cancer Exp. Mol. Pathol. 86 2009 151 164
18. A. Rhodes, A. Deakin, J. Spaull, B. Coomber, A. Aitken, P. Life, and S. Rees The generation and characterization of antagonist RNA aptamers to human oncostatin M J. Biol. Chem. 275 2000 28555 28561
19. C. Da Pieve, P. Williams, D.M. Haddleton, R.M. Palmer, and S. Missailidis Modification of thiol functionalized aptamers by conjugation of synthetic polymers Bioconjug. Chem. 21 2010 169 174
20. B. Saccà, L. Lacroix, and J.L. Mergny The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides Nucleic Acids Res. 33 2005 1182 1192 (Pubitemid 41439911)
21. Y. Merle, E. Bonneil, L. Merle, J. Sági, and A. Szemzö Acyclic oligonucleotide analogues Int. J. Biol. Macromol. 17 1995 239 246
22. L. Merle, G. Spach, Y. Merle, J. Sági, and A. Szemzö Some biochemical properties of an acyclic oligonucleotide analogue. A plausible ancestor of the DNA? Orig. Life Evol. Biosph. 23 1993 91 103
23. T.B. Jensen, N. Langkjaer, and J. Wengel Unlocked nucleic acid (UNA) and UNA derivatives: thermal denaturation studies Nucleic Acids Symp. Ser. (Oxf) 52 2008 133 134
24. N. Langkjaer, A. Pasternak, and J. Wengel UNA (unlocked nucleic acid): a flexible RNA mimic that allows engineering of nucleic acid duplex stability Bioorg. Med. Chem. 17 2009 5420 5425
25. M.B. Laursen, M.M. Pakula, S. Gao, K. Fluiter, O.R. Mook, F. Baas, N. Langkjaer, S.L. Wengel, J. Wengel, J. Kjems, and J.B. Bramsen Utilization of unlocked nucleic acid (UNA) to enhance siRNA performance in vitro and in vivo Mol. Biosyst. 6 2010 862 870
26. A. Pasternak, F.J. Hernandez, L.M. Rasmussen, B. Vester, and J. Wengel Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer Nucleic Acids Res. 39 3 2011 1155 1164
27. G.R. Bishop, J. Ren, B.C. Polander, B.D. Jeanfreau, J.O. Trent, and J.B. Chaires Energetic basis of molecular recognition in a DNA aptamer Biophys. Chem. 126 2007 165 175 (Pubitemid 46186647)
28. P.M. Mc Tigue, R.J. Peterson, and J.D. Kahn Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation Biochemistry 43 2004 5388 5405 (Pubitemid 38620931)
29. A. Arora, and S. Maiti Stability and molecular recognition of quadruplexes with different loop length in the absence and presence of molecular crowding agents J. Phys. Chem. B 113 2009 8784 8792
30. M. Tomasko, M. Vorlícková, and J. Sagi Substitution of adenine for guanine in the quadruplex-forming human telomere DNA sequence G(3)(T(2)AG(3))(3) Biochimie 91 2009 171 179
31. P. Schultze, R.F. Macaya, and J. Feigon Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) J. Mol. Biol. 235 1993 1532 1547
32. I. Smirnov, and R.H. Shafer Effect of loop sequence and size on DNA aptamer stability Biochemistry 39 2000 1462 1468 (Pubitemid 30090716)
33. A. Risitano, and K.R. Fox Influence of loop size on the stability of intramolecular DNA quadruplexes Nucleic Acids Res. 32 2004 2598 2606 (Pubitemid 38854813)
34. C.G. Peng, and M.J. Damha G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-d-arabinonucleic acids (2′F-ANA) Nucleic Acids Res. 35 2007 4977 4988 (Pubitemid 47394184)
35. M. Zaitseva, D. Kaluzhny, A. Shchyolkina, O. Borisova, I. Smirnov, and G. Pozmogova Conformation and thermostability of oligonucleotide d(GGTTGGTGTGGTTGG) containing thiophosphoryl internucleotide bonds at different positions Biophys. Chem. 146 2010 1 6
36. V. Esposito, L. Martino, G. Citarella, A. Virgilio, L. Mayol, C. Giancola, and A. Galeone Effects of abasic sites on structural, thermodynamic and kinetic properties of quadruplex structures Nucleic Acids Res. 38 2010 2069 2080
37. P. Skoláková, K. Bednárová, M. Vorlícková, and J. Sagi Quadruplexes of human telomere dG3(TTAG3)3 sequences containing guanine abasic sites Biochem. Biophys. Res. Commun. 399 2010 203 208