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Volumn 5, Issue MAR, 2014, Pages

Anomeric DNA quadruplexes: Modified thrombin aptamers

Author keywords

Anomer; Anticoagulant properties; Nuclease resistance; Quadruplex; Thombin binding aptamer

Indexed keywords

APTAMER; GUANINE QUADRUPLEX; THROMBIN; THROMBIN BINDING APTAMER; UNCLASSIFIED DRUG; GUANINE; NUCLEASE; NUCLEOTIDE; OLIGOMER; ANTICOAGULANT AGENT; THROMBIN APTAMER;

EID: 84899451974     PISSN: 1949095X     EISSN: 19490968     Source Type: Journal    
DOI: 10.4161/adna.28422     Document Type: Article
Times cited : (15)

References (41)
  • 1
    • 47849105417 scopus 로고    scopus 로고
    • Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions
    • PMID: 18355457
    • Qin Y, Hurley LH. Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie 2008; 90: 1149-71; PMID: 18355457; http://dx. doi. org/10. 1016/j. biochi. 2008. 02. 020.
    • (2008) Biochimie , vol.90 , pp. 1149-1171
    • Qin, Y.1    Hurley, L.H.2
  • 2
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • PMID: 2200121
    • Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990; 249: 505-10; PMID: 2200121; http://dx. doi. org/10. 1126/science. 2200121.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 3
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • PMID: 1697402
    • Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature 1990; 346: 818-22; PMID: 1697402; http://dx. doi. org/10. 1038/346818a0.
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 4
    • 84860122883 scopus 로고    scopus 로고
    • G-quadruplex DNA aptamers and their ligands: Structure, function and application
    • PMID: 22376117
    • Tucker WO, Shum KT, Tanner JA. G-quadruplex DNA aptamers and their ligands: structure, function and application. Curr Pharm Des 2012; 18: 2014-26; PMID: 22376117; http://dx. doi. org/10. 2174/138161212799958477.
    • (2012) Curr Pharm Des , vol.18 , pp. 2014-2026
    • Tucker, W.O.1    Shum, K.T.2    Tanner, J.A.3
  • 5
    • 0029980523 scopus 로고    scopus 로고
    • Reconciliation of the X-ray and NMR structures of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG)
    • PMID: 8604127
    • Kelly JA, Feigon J, Yeates TO. Reconciliation of the X-ray and NMR structures of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG). J Mol Biol 1996; 256: 417-22; PMID: 8604127; http://dx. doi. org/10. 1006/jmbi. 1996. 0097.
    • (1996) J Mol Biol , vol.256 , pp. 417-422
    • Kelly, J.A.1    Feigon, J.2    Yeates, T.O.3
  • 6
    • 0028318093 scopus 로고
    • Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG)
    • PMID: 8107090
    • Schultze P, Macaya RF, Feigon J. Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). J Mol Biol 1994; 235: 1532-47; PMID: 8107090; http://dx. doi. org/10. 1006/jmbi. 1994. 1105.
    • (1994) J Mol Biol , vol.235 , pp. 1532-1547
    • Schultze, P.1    Macaya, R.F.2    Feigon, J.3
  • 8
    • 84870535712 scopus 로고    scopus 로고
    • High-resolution structures of two complexes between thrombin and thrombinbinding aptamer shed light on the role of cations in the aptamer inhibitory activity
    • PMID: 22669903
    • Russo Krauss I, Merlino A, Randazzo A, Novellino E, Mazzarella L, Sica F. High-resolution structures of two complexes between thrombin and thrombinbinding aptamer shed light on the role of cations in the aptamer inhibitory activity. Nucleic Acids Res 2012; 40: 8119-28; PMID: 22669903; http://dx. doi. org/10. 1093/nar/gks512.
    • (2012) Nucleic Acids Res , vol.40 , pp. 8119-8128
    • Russo Krauss, I.1    Merlino, A.2    Randazzo, A.3    Novellino, E.4    Mazzarella, L.5    Sica, F.6
  • 9
    • 84860203819 scopus 로고    scopus 로고
    • Thrombin binding aptamer, more than a simple aptamer: Chemically modified derivatives and biomedical applications
    • PMID: 22376107
    • Avino A, Fabrega C, Tintore M, Eritja R. Thrombin binding aptamer, more than a simple aptamer: chemically modified derivatives and biomedical applications. Curr Pharm Des 2012; 18: 2036-47; PMID: 22376107; http://dx. doi. org/10. 2174/138161212799958387.
    • (2012) Curr Pharm Des , vol.18 , pp. 2036-2047
    • Avino, A.1    Fabrega, C.2    Tintore, M.3    Eritja, R.4
  • 10
    • 84155174679 scopus 로고    scopus 로고
    • Enzymatic recognition of 2′-modified ribonucleoside 5′-triphosphates: Towards the evolution of versatile aptamers
    • PMID: 22162282
    • Lauridsen LH, Rothnagel JA, Veedu RN. Enzymatic recognition of 2′-modified ribonucleoside 5′-triphosphates: towards the evolution of versatile aptamers. Chembiochem 2012; 13: 19-25; PMID: 22162282; http://dx. doi. org/10. 1002/cbic. 201100648.
    • (2012) Chembiochem , vol.13 , pp. 19-25
    • Lauridsen, L.H.1    Rothnagel, J.A.2    Veedu, R.N.3
  • 11
    • 38349044104 scopus 로고    scopus 로고
    • Stability and binding properties of a modified thrombin binding aptamer
    • PMID: 17890401
    • Pagano B, Martino L, Randazzo A, Giancola C. Stability and binding properties of a modified thrombin binding aptamer. Biophys J 2008; 94: 562-9; PMID: 17890401; http://dx. doi. org/10. 1529/biophysj. 107. 117382.
    • (2008) Biophys J , vol.94 , pp. 562-569
    • Pagano, B.1    Martino, L.2    Randazzo, A.3    Giancola, C.4
  • 12
    • 36849040452 scopus 로고    scopus 로고
    • A mini-library of TBA analogues containing 3′-3′ and 5′-5′ inversion of polarity sites
    • PMID: 18058554
    • Esposito V, Galeone A, Mayol L, Randazzo A, Virgilio A, Virno A. A mini-library of TBA analogues containing 3′-3′ and 5′-5′ inversion of polarity sites. Nucleosides Nucleotides Nucleic Acids 2007; 26: 1145-9; PMID: 18058554; http://dx. doi. org/10. 1080/15257770701526978.
    • (2007) Nucleosides Nucleotides Nucleic Acids , vol.26 , pp. 1145-1149
    • Esposito, V.1    Galeone, A.2    Mayol, L.3    Randazzo, A.4    Virgilio, A.5    Virno, A.6
  • 13
    • 34548563975 scopus 로고    scopus 로고
    • G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-D-arabinonucleic acids (2'F-ANA)
    • PMID: 17636049
    • Peng CG, Damha MJ. G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-D-arabinonucleic acids (2'F-ANA). Nucleic Acids Res 2007; 35: 4977-88; PMID: 17636049; http://dx. doi. org/10. 1093/nar/gkm520.
    • (2007) Nucleic Acids Res , vol.35 , pp. 4977-4988
    • Peng, C.G.1    Damha, M.J.2
  • 14
    • 66149120170 scopus 로고    scopus 로고
    • Combinatorial synthesis of thrombin-binding aptamers containing iso-guanine
    • PMID: 19243167
    • Nallagatla SR, Heuberger B, Haque A, Switzer C. Combinatorial synthesis of thrombin-binding aptamers containing iso-guanine. J Comb Chem 2009; 11: 364-9; PMID: 19243167; http://dx. doi. org/10. 1021/cc800178m.
    • (2009) J Comb Chem , vol.11 , pp. 364-369
    • Nallagatla, S.R.1    Heuberger, B.2    Haque, A.3    Switzer, C.4
  • 15
    • 41649095687 scopus 로고    scopus 로고
    • Effect of locked-nucleic acid on a biologically active g-quadruplex. A structure-activity relationship of the thrombin aptamer
    • PMID: 19325759
    • Bonifacio L, Church FC, Jarstfer MB. Effect of locked-nucleic acid on a biologically active g-quadruplex. A structure-activity relationship of the thrombin aptamer. Int J Mol Sci 2008; 9: 422-33; PMID: 19325759; http://dx. doi. org/10. 3390/ijms9030422.
    • (2008) Int J Mol Sci , vol.9 , pp. 422-433
    • Bonifacio, L.1    Church, F.C.2    Jarstfer, M.B.3
  • 16
    • 84962361002 scopus 로고    scopus 로고
    • Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer
    • PMID: 19620215
    • Saneyoshi H, Mazzini S, Aviñó A, Portella G, González C, Orozco M, Marquez VE, Eritja R. Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer. Nucleic Acids Res 2009; 37: 5589-601; PMID: 19620215; http://dx. doi. org/10. 1093/nar/gkp598.
    • (2009) Nucleic Acids Res , vol.37 , pp. 5589-5601
    • Saneyoshi, H.1    Mazzini, S.2    Aviñó, A.3    Portella, G.4    González, C.5    Orozco, M.6    Marquez, V.E.7    Eritja, R.8
  • 17
    • 52449112689 scopus 로고    scopus 로고
    • 4-thio-deoxyuridylate-modified thrombin aptamer and its inhibitory effect on fibrin clot formation, platelet aggregation and thrombus growth on subendothelial matrix
    • PMID: 18665927
    • Mendelboum Raviv S, Horváth A, Aradi J, Bagoly Z, Fazakas F, Batta Z, Muszbek L, Hársfalvi J. 4-thio-deoxyuridylate-modified thrombin aptamer and its inhibitory effect on fibrin clot formation, platelet aggregation and thrombus growth on subendothelial matrix. J Thromb Haemost 2008; 6: 1764-71; PMID: 18665927; http://dx. doi. org/10. 1111/j. 1538-7836. 2008. 03106. x.
    • (2008) J Thromb Haemost , vol.6 , pp. 1764-1771
    • Mendelboum Raviv, S.1    Horváth, A.2    Aradi, J.3    Bagoly, Z.4    Fazakas, F.5    Batta, Z.6    Muszbek, L.7    Hársfalvi, J.8
  • 18
    • 70449525152 scopus 로고    scopus 로고
    • Conformation and thermostability of oligonucleotide d(GGTTGGTGTGGTTGG) containing thiophosphoryl internucleotide bonds at different positions
    • PMID: 19846249
    • Zaitseva M, Kaluzhny D, Shchyolkina A, Borisova O, Smirnov I, Pozmogova G. Conformation and thermostability of oligonucleotide d(GGTTGGTGTGGTTGG) containing thiophosphoryl internucleotide bonds at different positions. Biophys Chem 2010; 146: 1-6; PMID: 19846249; http://dx. doi. org/10. 1016/j. bpc. 2009. 09. 011.
    • (2010) Biophys Chem , vol.146 , pp. 1-6
    • Zaitseva, M.1    Kaluzhny, D.2    Shchyolkina, A.3    Borisova, O.4    Smirnov, I.5    Pozmogova, G.6
  • 19
    • 77949683441 scopus 로고    scopus 로고
    • From anionic to cationic alpha-anomeric oligodeoxynucleotides
    • PMID: 20232324
    • Morvan F, Debart F, Vasseur JJ. From anionic to cationic alpha-anomeric oligodeoxynucleotides. Chem Biodivers 2010; 7: 494-535; PMID: 20232324; http://dx. doi. org/10. 1002/cbdv. 200900220.
    • (2010) Chem Biodivers , vol.7 , pp. 494-535
    • Morvan, F.1    Debart, F.2    Vasseur, J.J.3
  • 21
    • 27144440078 scopus 로고    scopus 로고
    • Thermal difference spectra: A specific signature for nucleic acid structures
    • PMID: 16157860
    • Mergny JL, Li J, Lacroix L, Amrane S, Chaires JB. Thermal difference spectra: a specific signature for nucleic acid structures. Nucleic Acids Res 2005; 33: e138; PMID: 16157860; http://dx. doi. org/10. 1093/nar/gni134.
    • (2005) Nucleic Acids Res , vol.33
    • Mergny, J.L.1    Li, J.2    Lacroix, L.3    Amrane, S.4    Chaires, J.B.5
  • 22
    • 64549099313 scopus 로고    scopus 로고
    • Circular dichroism and conformational polymorphism of DNA
    • PMID: 19190094
    • Kypr J, Kejnovská I, Renciuk D, Vorlícková M. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 2009; 37: 1713-25; PMID: 19190094; http://dx. doi. org/10. 1093/nar/gkp026.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1713-1725
    • Kypr, J.1    Kejnovská, I.2    Renciuk, D.3    Vorlícková, M.4
  • 23
    • 39749116244 scopus 로고    scopus 로고
    • Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities
    • PMID: 17853398
    • Gray DM, Wen JD, Gray CW, 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: 431-40; PMID: 17853398; http://dx. doi. org/10. 1002/chir. 20455.
    • (2008) Chirality , vol.20 , pp. 431-440
    • Gray, D.M.1    Wen, J.D.2    Gray, C.W.3    Repges, R.4    Repges, C.5    Raabe, G.6    Fleischhauer, J.7
  • 25
    • 0033955928 scopus 로고    scopus 로고
    • Structural polymorphism of oligo(dC) with mixed alpha, beta-anomeric backbone
    • PMID: 10698103
    • Timofeev EN, Borisova OF, Shchyolkina AK. Structural polymorphism of oligo(dC) with mixed alpha, beta-anomeric backbone. J Biomol Struct Dyn 2000; 17: 655-64; PMID: 10698103; http://dx. doi. org/10. 1080/07391102. 2000. 10506556.
    • (2000) J Biomol Struct Dyn , vol.17 , pp. 655-664
    • Timofeev, E.N.1    Borisova, O.F.2    Shchyolkina, A.K.3
  • 26
    • 77952538407 scopus 로고    scopus 로고
    • Fluorescence polarization/anisotropy in diagnostics and imaging
    • PMID: 20232898
    • Jameson DM, Ross JA. Fluorescence polarization/anisotropy in diagnostics and imaging. Chem Rev 2010; 110: 2685-708; PMID: 20232898; http://dx. doi. org/10. 1021/cr900267p.
    • (2010) Chem Rev , vol.110 , pp. 2685-2708
    • Jameson, D.M.1    Ross, J.A.2
  • 27
    • 84865078986 scopus 로고    scopus 로고
    • NMR spectroscopy of G-quadruplexes
    • PMID: 22633887
    • Adrian M, Heddi B, Phan AT. NMR spectroscopy of G-quadruplexes. Methods 2012; 57: 11-24; PMID: 22633887; http://dx. doi. org/10. 1016/j. ymeth. 2012. 05. 003.
    • (2012) Methods , vol.57 , pp. 11-24
    • Adrian, M.1    Heddi, B.2    Phan, A.T.3
  • 28
    • 0031101168 scopus 로고    scopus 로고
    • NMR diffusion measurements to characterise membrane transport and solute binding
    • Waldeck AR, Kuchel PW, Lennon AJ, Chapman BE. NMR diffusion measurements to characterise membrane transport and solute binding. Prog Nucl Magn Reson Spectrosc 1997; 30: 39-68; http://dx. doi. org/10. 1016/S0079-6565(96)01034-5.
    • (1997) Prog Nucl Magn Reson Spectrosc , vol.30 , pp. 39-68
    • Waldeck, A.R.1    Kuchel, P.W.2    Lennon, A.J.3    Chapman, B.E.4
  • 29
    • 34250675727 scopus 로고    scopus 로고
    • Diffusion-ordered nuclear magnetic resonance spectroscopy for analysis of DNA secondary structural elements
    • PMID: 17570331
    • Ambrus A, Yang D. Diffusion-ordered nuclear magnetic resonance spectroscopy for analysis of DNA secondary structural elements. Anal Biochem 2007; 367: 56-67; PMID: 17570331; http://dx. doi. org/10. 1016/j. ab. 2007. 04. 025.
    • (2007) Anal Biochem , vol.367 , pp. 56-67
    • Ambrus, A.1    Yang, D.2
  • 30
    • 33644775730 scopus 로고    scopus 로고
    • Nuclease resistance of telomere-like oligonucleotides monitored in live cells by fluorescence anisotropy imaging
    • PMID: 16503597
    • Cao Z, Huang CC, Tan W. Nuclease resistance of telomere-like oligonucleotides monitored in live cells by fluorescence anisotropy imaging. Anal Chem 2006; 78: 1478-84; PMID: 16503597; http://dx. doi. org/10. 1021/ac0517601.
    • (2006) Anal Chem , vol.78 , pp. 1478-1484
    • Cao, Z.1    Huang, C.C.2    Tan, W.3
  • 31
    • 29244466487 scopus 로고    scopus 로고
    • Tetraplex DNA transitions within the human c-myc promoter detected by multivariate curve resolution of fluorescence resonance energy transfer
    • PMID: 16342935
    • Kumar P, Verma A, Maiti S, Gargallo R, Chowdhury S. Tetraplex DNA transitions within the human c-myc promoter detected by multivariate curve resolution of fluorescence resonance energy transfer. Biochemistry 2005; 44: 16426-34; PMID: 16342935; http://dx. doi. org/10. 1021/bi051452x.
    • (2005) Biochemistry , vol.44 , pp. 16426-16434
    • Kumar, P.1    Verma, A.2    Maiti, S.3    Gargallo, R.4    Chowdhury, S.5
  • 33
    • 0026832826 scopus 로고
    • Stereochemical studies on nucleic acid analogues. I. Conformations of alphanucleosides and alpha-nucleotides: Interconversion of sugar puckers via O4′-exo
    • PMID: 1581546
    • Latha YS, Yathindra N. Stereochemical studies on nucleic acid analogues. I. Conformations of alphanucleosides and alpha-nucleotides: interconversion of sugar puckers via O4′-exo. Biopolymers 1992; 32: 249-69; PMID: 1581546; http://dx. doi. org/10. 1002/bip. 360320306.
    • (1992) Biopolymers , vol.32 , pp. 249-269
    • Latha, Y.S.1    Yathindra, N.2
  • 34
    • 37249066753 scopus 로고    scopus 로고
    • Geometric formalism for DNA quadruplex folding
    • PMID: 17972263
    • Webba da Silva M. Geometric formalism for DNA quadruplex folding. Chemistry 2007; 13: 9738-45; PMID: 17972263; http://dx. doi. org/10. 1002/chem. 200701255.
    • (2007) Chemistry , vol.13 , pp. 9738-9745
    • Webba da Silva, M.1
  • 35
    • 11144269746 scopus 로고    scopus 로고
    • NMR study of the foldingunfolding mechanism for the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG)
    • PMID: 15617822
    • Mao XA, Gmeiner WH. NMR study of the foldingunfolding mechanism for the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). Biophys Chem 2005; 113: 155-60; PMID: 15617822; http://dx. doi. org/10. 1016/j. bpc. 2004. 09. 003.
    • (2005) Biophys Chem , vol.113 , pp. 155-160
    • Mao, X.A.1    Gmeiner, W.H.2
  • 36
    • 79951575374 scopus 로고    scopus 로고
    • Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer
    • PMID: 20870750
    • Pasternak A, Hernandez FJ, Rasmussen LM, Vester B, Wengel J. Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer. Nucleic Acids Res 2011; 39: 1155-64; PMID: 20870750; http://dx. doi. org/10. 1093/nar/gkq823.
    • (2011) Nucleic Acids Res , vol.39 , pp. 1155-1164
    • Pasternak, A.1    Hernandez, F.J.2    Rasmussen, L.M.3    Vester, B.4    Wengel, J.5
  • 37
    • 0014441011 scopus 로고
    • The effects of energy transfer and rotational diffusion upon the fluorescence polarization of macromolecules
    • PMID: 5777333
    • Weber G, Anderson SR. The effects of energy transfer and rotational diffusion upon the fluorescence polarization of macromolecules. Biochemistry 1969; 8: 361-71; PMID: 5777333; http://dx. doi. org/10. 1021/bi00829a050.
    • (1969) Biochemistry , vol.8 , pp. 361-371
    • Weber, G.1    Anderson, S.R.2
  • 38
    • 0034702766 scopus 로고    scopus 로고
    • Parallel-stranded DNA with mixed AT/GC composition: Role of trans G. C base pairs in sequence dependent helical stability
    • PMID: 10955991
    • Shchyolkina AK, Borisova OF, Livshits MA, Pozmogova GE, Chernov BK, Klement R, Jovin TM. Parallel-stranded DNA with mixed AT/GC composition: role of trans G. C base pairs in sequence dependent helical stability. Biochemistry 2000; 39: 10034-44; PMID: 10955991; http://dx. doi. org/10. 1021/bi9913909.
    • (2000) Biochemistry , vol.39 , pp. 10034-10044
    • Shchyolkina, A.K.1    Borisova, O.F.2    Livshits, M.A.3    Pozmogova, G.E.4    Chernov, B.K.5    Klement, R.6    Jovin, T.M.7
  • 39
    • 0347359145 scopus 로고    scopus 로고
    • Diffusion ordered nuclear magnetic resonance spectroscopy: Principles and applications
    • Johnson CS Jr. Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications. Prog Nucl Magn Reson Spectrosc 1999; 34: 203-56; http://dx. doi. org/10. 1016/S0079-6565(99)00003-5.
    • (1999) Prog Nucl Magn Reson Spectrosc , vol.34 , pp. 203-256
    • Johnson Jr., C.S.1
  • 40
    • 58149362694 scopus 로고
    • An improved diffusion ordered spectroscopy experiment incorporating bipolar gradient pulses
    • Wu D, Chen A, Johnson CS Jr. An improved diffusion ordered spectroscopy experiment incorporating bipolar gradient pulses. J Magn Reson A 1995; 115: 260-4; http://dx. doi. org/10. 1006/jmra. 1995. 1176.
    • (1995) J Magn Reson A , vol.115 , pp. 260-264
    • Wu, D.1    Chen, A.2    Johnson Jr., C.S.3
  • 41
    • 33745551242 scopus 로고
    • Rapid physiological coagulation method in determination of fibrinogen
    • PMID: 13434757
    • Clauss A. [Rapid physiological coagulation method in determination of fibrinogen]. Acta Haematol 1957; 17: 237-46; PMID: 13434757; http://dx. doi. org/10. 1159/000205234.
    • (1957) Acta Haematol , vol.17 , pp. 237-246
    • Clauss, A.1


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