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Volumn 2, Issue 2, 2011, Pages 207-217

Conformational changes in quadruplex oligonucleotide structures probed by Raman spectroscopy

Author keywords

[No Author keywords available]

Indexed keywords

POSITIVE IONS; RAMAN SPECTROSCOPY;

EID: 84862019671     PISSN: None     EISSN: 21567085     Source Type: Journal    
DOI: 10.1364/BOE.2.000207     Document Type: Article
Times cited : (29)

References (44)
  • 1
    • 55249109574 scopus 로고    scopus 로고
    • Stability and kinetics of G-quadruplex structures
    • A. N. Lane, J. B. Chaires, R. D. Gray, and J. O. Trent, "Stability and kinetics of G-quadruplex structures, " Nucleic Acids Res. 36(17), 5482-5515 (2008).
    • (2008) Nucleic Acids Res. , vol.36 , Issue.17 , pp. 5482-5515
    • Lane, A.N.1    Chaires, J.B.2    Gray, R.D.3    Trent, J.O.4
  • 2
    • 33846928449 scopus 로고    scopus 로고
    • G-quadruplexes in promoters throughout the human genome
    • J. L. Huppert, and S. Balasubramanian, "G-quadruplexes in promoters throughout the human genome, " Nucleic Acids Res. 35(2), 406-413 (2006).
    • (2006) Nucleic Acids Res. , vol.35 , Issue.2 , pp. 406-413
    • Huppert, J.L.1    Balasubramanian, S.2
  • 3
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • A. D. Ellington, and J. W. Szostak, "In vitro selection of RNA molecules that bind specific ligands, " Nature 346(6287), 818-822 (1990).
    • (1990) Nature , vol.346 , Issue.6287 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 4
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • C. Tuerk, and L. Gold, "Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase, " Science 249(4968), 505-510 (1990).
    • (1990) Science , vol.249 , Issue.4968 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 5
    • 0034603154 scopus 로고    scopus 로고
    • Adaptive recognition by nucleic acid aptamers
    • T. Hermann, and D. J. Patel, "Adaptive recognition by nucleic acid aptamers, " Science 287(5454), 820-825 (2000).
    • (2000) Science , vol.287 , Issue.5454 , pp. 820-825
    • Hermann, T.1    Patel, D.J.2
  • 8
    • 0037430933 scopus 로고    scopus 로고
    • Single-stranded DNA aptamers that bind differentiated but not parental cells: Subtractive systematic evolution of ligands by exponential enrichment
    • C. Wang, M. Zhang, G. Yang, D. Zhang, H. Ding, H. Wang, M. Fan, B. Shen, and N. Shao, "Single-stranded DNA aptamers that bind differentiated but not parental cells: subtractive systematic evolution of ligands by exponential enrichment, " J. Biotechnol. 102(1), 15-22 (2003).
    • (2003) J. Biotechnol. , vol.102 , Issue.1 , pp. 15-22
    • Wang, C.1    Zhang, M.2    Yang, G.3    Zhang, D.4    Ding, H.5    Wang, H.6    Fan, M.7    Shen, B.8    Shao, N.9
  • 9
    • 0032493654 scopus 로고    scopus 로고
    • 2′-Fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain
    • J. Ruckman, L. S. Green, J. Beeson, S. Waugh, W. L. Gillette, D. D. Henninger, L. Claesson-Welsh, and N. Janjić, "2′-Fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain, " J. Biol. Chem. 273(32), 20556-20567 (1998).
    • (1998) J. Biol. Chem. , vol.273 , Issue.32 , pp. 20556-20567
    • Ruckman, J.1    Green, L.S.2    Beeson, J.3    Waugh, S.4    Gillette, W.L.5    Henninger, D.D.6    Claesson-Welsh, L.7    Janjić, N.8
  • 10
    • 0041923790 scopus 로고    scopus 로고
    • Inhibition of heregulin signaling by an aptamer that preferentially binds to the oligomeric form of human epidermal growth factor receptor-3
    • C.-H. B. Chen, G. A. Chernis, V. Q. Hoang, and R. Landgraf, "Inhibition of heregulin signaling by an aptamer that preferentially binds to the oligomeric form of human epidermal growth factor receptor-3, " Proc. Natl. Acad. Sci. U.S.A. 100(16), 9226-9231 (2003).
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , Issue.16 , pp. 9226-9231
    • Chen, C.-H.B.1    Chernis, G.A.2    Hoang, V.Q.3    Landgraf, R.4
  • 11
    • 0026575221 scopus 로고
    • Selection of single-stranded DNA molecules that bind and inhibit human thrombin
    • L. C. Bock, L. C. Griffin, J. A. Latham, E. H. Vermaas, and J. J. Toole, "Selection of single-stranded DNA molecules that bind and inhibit human thrombin, " Nature 355(6360), 564-566 (1992).
    • (1992) Nature , vol.355 , Issue.6360 , pp. 564-566
    • Bock, L.C.1    Griffin, L.C.2    Latham, J.A.3    Vermaas, E.H.4    Toole, J.J.5
  • 12
    • 0027537022 scopus 로고
    • A DNA aptamer which binds to and inhibits thrombin exhibits a new structural motif for DNA
    • K. Y. Wang, S. McCurdy, R. G. Shea, S. Swaminathan, and P. H. Bolton, "A DNA aptamer which binds to and inhibits thrombin exhibits a new structural motif for DNA, " Biochemistry 32(8), 1899-1904 (1993).
    • (1993) Biochemistry , vol.32 , Issue.8 , pp. 1899-1904
    • Wang, K.Y.1    McCurdy, S.2    Shea, R.G.3    Swaminathan, S.4    Bolton, P.H.5
  • 13
    • 0027380687 scopus 로고
    • The tertiary structure of a DNA aptamer which binds to and inhibits thrombin determines activity
    • K. Y. Wang, S. H. Krawczyk, N. Bischofberger, S. Swaminathan, and P. H. Bolton, "The tertiary structure of a DNA aptamer which binds to and inhibits thrombin determines activity, " Biochemistry 32(42), 11285-11292 (1993).
    • (1993) Biochemistry , vol.32 , Issue.42 , pp. 11285-11292
    • Wang, K.Y.1    Krawczyk, S.H.2    Bischofberger, N.3    Swaminathan, S.4    Bolton, P.H.5
  • 14
    • 0027467617 scopus 로고
    • Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution
    • 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(8), 3745-3749 (1993).
    • (1993) Proc. Natl. Acad. Sci. U.S.A. , vol.90 , Issue.8 , pp. 3745-3749
    • Macaya, R.F.1    Schultze, P.2    Smith, F.W.3    Roe, J.A.4    Feigon, J.5
  • 15
    • 0028318093 scopus 로고
    • Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG)
    • P. Schultze, R. F. Macaya, and J. Feigon, "Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG), " J. Mol. Biol. 235(5), 1532-1547 (1994).
    • (1994) J. Mol. Biol. , vol.235 , Issue.5 , pp. 1532-1547
    • Schultze, P.1    Macaya, R.F.2    Feigon, J.3
  • 16
    • 0027172294 scopus 로고
    • The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer
    • K. Padmanabhan, K. P. Padmanabhan, J. D. Ferrara, J. E. Sadler, and A. Tulinsky, "The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer, " J. Biol. Chem. 268(24), 17651-17654 (1993).
    • (1993) J. Biol. Chem. , vol.268 , Issue.24 , pp. 17651-17654
    • Padmanabhan, K.1    Padmanabhan, K.P.2    Ferrara, J.D.3    Sadler, J.E.4    Tulinsky, A.5
  • 17
    • 0035823852 scopus 로고    scopus 로고
    • Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): Stability, heat, and hydration
    • B. I. Kankia, and L. A. Marky, "Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): stability, heat, and hydration, " J. Am. Chem. Soc. 123(44), 10799-10804 (2001).
    • (2001) J. Am. Chem. Soc. , vol.123 , Issue.44 , pp. 10799-10804
    • Kankia, B.I.1    Marky, L.A.2
  • 18
    • 33845294799 scopus 로고    scopus 로고
    • Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions
    • S. Nagatoishi, Y. Tanaka, and K. Tsumoto, "Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions, " Biochem. Biophys. Res. Commun. 352(3), 812-817 (2007).
    • (2007) Biochem. Biophys. Res. Commun. , vol.352 , Issue.3 , pp. 812-817
    • Nagatoishi, S.1    Tanaka, Y.2    Tsumoto, K.3
  • 19
    • 0037425570 scopus 로고    scopus 로고
    • G-quadruplex formation of thrombin-binding aptamer detected by electrospray ionization mass spectrometry
    • M. Vairamani, and M. L. Gross, "G-quadruplex formation of thrombin-binding aptamer detected by electrospray ionization mass spectrometry, " J. Am. Chem. Soc. 125(1), 42-43 (2003).
    • (2003) J. Am. Chem. Soc. , vol.125 , Issue.1 , pp. 42-43
    • Vairamani, M.1    Gross, M.L.2
  • 20
    • 77956098867 scopus 로고    scopus 로고
    • Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry
    • F. Rosu, V. Gabelica, H. Poncelet, and E. De Pauw, "Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry, " Nucleic Acids Res. 38(15), 5217-5225 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , Issue.15 , pp. 5217-5225
    • Rosu, F.1    Gabelica, V.2    Poncelet, H.3    De Pauw, E.4
  • 21
    • 77955791968 scopus 로고    scopus 로고
    • Electrospray mass spectrometry of telomeric RNA (TERRA) reveals the formation of stable multimeric G-quadruplex structures
    • G. W. Collie, G. N. Parkinson, S. Neidle, F. Rosu, E. De Pauw, and V. Gabelica, "Electrospray mass spectrometry of telomeric RNA (TERRA) reveals the formation of stable multimeric G-quadruplex structures, " J. Am. Chem. Soc. 132(27), 9328-9334 (2010).
    • (2010) J. Am. Chem. Soc. , vol.132 , Issue.27 , pp. 9328-9334
    • Collie, G.W.1    Parkinson, G.N.2    Neidle, S.3    Rosu, F.4    De Pauw, E.5    Gabelica, V.6
  • 22
    • 0032508468 scopus 로고    scopus 로고
    • Following G-quartet formation by UV-spectroscopy
    • J.-L. Mergny, A.-T. Phan, and L. Lacroix, "Following G-quartet formation by UV-spectroscopy, " FEBS Lett. 435(1), 74-78 (1998).
    • (1998) FEBS Lett. , vol.435 , Issue.1 , pp. 74-78
    • Mergny, J.-L.1    Phan, A.-T.2    Lacroix, L.3
  • 23
    • 8544229944 scopus 로고    scopus 로고
    • Tetraplex structure formation in the thrombin-binding DNA aptamer by metal cations measured by vibrational spectroscopy
    • J. A. Mondragon-Sanchez, J. Liquier, R. H. Shafer, and E. Taillandier, "Tetraplex structure formation in the thrombin-binding DNA aptamer by metal cations measured by vibrational spectroscopy, " J. Biomol. Struct. Dyn. 22(3), 365-373 (2004).
    • (2004) J. Biomol. Struct. Dyn. , vol.22 , Issue.3 , pp. 365-373
    • Mondragon-Sanchez, J.A.1    Liquier, J.2    Shafer, R.H.3    Taillandier, E.4
  • 25
    • 0028275836 scopus 로고
    • Structural polymorphism of telomere DNA: Interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy
    • T. Miura, and G. J. Thomas, Jr., "Structural polymorphism of telomere DNA: interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy, " Biochemistry 33(25), 7848-7856 (1994).
    • (1994) Biochemistry , vol.33 , Issue.25 , pp. 7848-7856
    • Miura, T.1    Thomas Jr., G.J.2
  • 26
    • 0029148328 scopus 로고
    • Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA
    • T. Miura, and G. J. Thomas, Jr., "Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA, " Biochemistry 34(29), 9645-9654 (1995).
    • (1995) Biochemistry , vol.34 , Issue.29 , pp. 9645-9654
    • Miura, T.1    Thomas Jr., G.J.2
  • 27
    • 0032477893 scopus 로고    scopus 로고
    • Structural basis of DNA recognition and mechanism of quadruplex formation by the beta subunit of the Oxytricha telomere binding protein
    • L. Laporte, and G. J. Thomas, Jr., "Structural basis of DNA recognition and mechanism of quadruplex formation by the beta subunit of the Oxytricha telomere binding protein, " Biochemistry 37(5), 1327-1335 (1998).
    • (1998) Biochemistry , vol.37 , Issue.5 , pp. 1327-1335
    • Laporte, L.1    Thomas Jr., G.J.2
  • 28
    • 0037106459 scopus 로고    scopus 로고
    • Secondary structure polymorphism in Oxytricha nova telomeric DNA
    • C. Krafft, J. M. Benevides, and G. J. Thomas, Jr., "Secondary structure polymorphism in Oxytricha nova telomeric DNA, " Nucleic Acids Res. 30(18), 3981-3991 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , Issue.18 , pp. 3981-3991
    • Krafft, C.1    Benevides, J.M.2    Thomas Jr., G.J.3
  • 29
    • 77949643003 scopus 로고    scopus 로고
    • Raman and surface-enhanced Raman spectroscopic studies of the 15-mer DNA thrombin-binding aptamer
    • C. V. Pagba, S. M. Lane, and S. Wachsmann-Hogiu, "Raman and surface-enhanced Raman spectroscopic studies of the 15-mer DNA thrombin-binding aptamer, " J. Raman Spectrosc. 41, 241-247 (2010).
    • (2010) J. Raman Spectrosc. , vol.41 , pp. 241-247
    • Pagba, C.V.1    Lane, S.M.2    Wachsmann-Hogiu, S.3
  • 30
    • 0021112466 scopus 로고
    • Characterization of DNA structures by Raman spectroscopy: High-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA
    • J. M. Benevides, and G. J. Thomas, Jr., "Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA, " Nucleic Acids Res. 11(16), 5747-5761 (1983).
    • (1983) Nucleic Acids Res. , vol.11 , Issue.16 , pp. 5747-5761
    • Benevides, J.M.1    Thomas Jr., G.J.2
  • 31
    • 0021378939 scopus 로고
    • Characterization of DNA structures by laser Raman spectroscopy
    • B. Prescott, Jr., W. Steinmetz, and G. J. Thomas, Jr., "Characterization of DNA structures by laser Raman spectroscopy, " Biopolymers 23(2), 235-256 (1984).
    • (1984) Biopolymers , vol.23 , Issue.2 , pp. 235-256
    • Prescott Jr., B.1    Steinmetz, W.2    Thomas Jr., G.J.3
  • 32
    • 0000793963 scopus 로고
    • Conformation-sensitive Raman lines of mononucleotides and their use in a structure analysis of polynucleotides: Guanine and cytosine nucleotides
    • Y. Nishimura, M. Tsuboi, T. Sato, and K. Aoki, "Conformation-sensitive Raman lines of mononucleotides and their use in a structure analysis of polynucleotides: guanine and cytosine nucleotides, " J. Mol. Struct. 146(3-4), 123-153 (1986).
    • (1986) J. Mol. Struct. , vol.146 , Issue.3-4 , pp. 123-153
    • Nishimura, Y.1    Tsuboi, M.2    Sato, T.3    Aoki, K.4
  • 34
    • 33646843580 scopus 로고    scopus 로고
    • Validation of the drop coating deposition Raman method for protein analysis
    • C. Ortiz, D. Zhang, Y. Xie, A. E. Ribbe, and D. Ben-Amotz, "Validation of the drop coating deposition Raman method for protein analysis, " Anal. Biochem. 353(2), 157-166 (2006).
    • (2006) Anal. Biochem. , vol.353 , Issue.2 , pp. 157-166
    • Ortiz, C.1    Zhang, D.2    Xie, Y.3    Ribbe, A.E.4    Ben-Amotz, D.5
  • 35
    • 42949134048 scopus 로고    scopus 로고
    • Surface-enhanced Raman spectroscopy of DNA
    • A. Barhoumi, D. Zhang, F. Tam, and N. J. Halas, "Surface-enhanced Raman spectroscopy of DNA, " J. Am. Chem. Soc. 130(16), 5523-5529 (2008).
    • (2008) J. Am. Chem. Soc. , vol.130 , Issue.16 , pp. 5523-5529
    • Barhoumi, A.1    Zhang, D.2    Tam, F.3    Halas, N.J.4
  • 36
    • 0025866678 scopus 로고
    • DNA recognition by the helix-turn-helix motif: Investigation by laser Raman spectroscopy of the phage lambda repressor and its interaction with operator sites OL1 and OR3
    • J. M. Benevides, M. A. Weiss, and G. J. Thomas, Jr., "DNA recognition by the helix-turn-helix motif: investigation by laser Raman spectroscopy of the phage lambda repressor and its interaction with operator sites OL1 and OR3, " Biochemistry 30(24), 5955-5963 (1991).
    • (1991) Biochemistry , vol.30 , Issue.24 , pp. 5955-5963
    • Benevides, J.M.1    Weiss, M.A.2    Thomas Jr., G.J.3
  • 37
    • 0026781438 scopus 로고
    • Conformation of DNA in Vitro and in Vivo from laser Raman scattering
    • (Academic Press, in
    • W. L. Peticolas, E. Evertsz, M. J. L. David, and E. D. James, "[17] Conformation of DNA in Vitro and in Vivo from laser Raman scattering, " in Methods in Enzymology(Academic Press, 1992), pp. 335-352.
    • (1992) Methods in Enzymology , pp. 335-352
    • Peticolas, W.L.1    Evertsz, E.2    David, M.J.L.3    James, E.D.4
  • 38
    • 0024282309 scopus 로고
    • Crystal and solution structures of the B-DNA dodecamer d(CGCAAATTTGCG) probed by Raman spectroscopy: Heterogeneity in the crystal structure does not persist in the solution structure
    • J. M. Benevides, A. H. J. Wang, G. A. van der Marel, J. H. van Boom, and G. J. Thomas, Jr., "Crystal and solution structures of the B-DNA dodecamer d(CGCAAATTTGCG) probed by Raman spectroscopy: heterogeneity in the crystal structure does not persist in the solution structure, " Biochemistry 27(3), 931-938 (1988).
    • (1988) Biochemistry , vol.27 , Issue.3 , pp. 931-938
    • Benevides, J.M.1    Wang, A.H.J.2    van der Marel, G.A.3    van Boom, J.H.4    Thomas Jr., G.J.5
  • 40
    • 37249066753 scopus 로고    scopus 로고
    • Geometric formalism for DNA quadruplex folding
    • M. Webba da Silva, "Geometric formalism for DNA quadruplex folding, " Chemistry 13(35), 9738-9745 (2007).
    • (2007) Chemistry , vol.13 , Issue.35 , pp. 9738-9745
    • Webba da Silva, M.1
  • 41
    • 33750990787 scopus 로고    scopus 로고
    • NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region
    • J. Dai, D. Chen, R. A. Jones, L. H. Hurley, and D. Yang, "NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region, " Nucleic Acids Res. 34(18), 5133-5144 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , Issue.18 , pp. 5133-5144
    • Dai, J.1    Chen, D.2    Jones, R.A.3    Hurley, L.H.4    Yang, D.5
  • 42
    • 0035967879 scopus 로고    scopus 로고
    • A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple
    • V. Kuryavyi, A. Majumdar, A. Shallop, N. Chernichenko, E. Skripkin, R. Jones, and D. J. Patel, "A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple, " J. Mol. Biol. 310(1), 181-194 (2001).
    • (2001) J. Mol. Biol. , vol.310 , Issue.1 , pp. 181-194
    • Kuryavyi, V.1    Majumdar, A.2    Shallop, A.3    Chernichenko, N.4    Skripkin, E.5    Jones, R.6    Patel, D.J.7
  • 43
    • 0030764882 scopus 로고    scopus 로고
    • Ion selective folding of loop domains in a potent anti-HIV oligonucleotide
    • N. Jing, R. F. Rando, Y. Pommier, and M. E. Hogan, "Ion selective folding of loop domains in a potent anti-HIV oligonucleotide, " Biochemistry 36(41), 12498-12505 (1997).
    • (1997) Biochemistry , vol.36 , Issue.41 , pp. 12498-12505
    • Jing, N.1    Rando, R.F.2    Pommier, Y.3    Hogan, M.E.4
  • 44
    • 0026781438 scopus 로고
    • Conformation of DNA in vitro and in vivo from laser Raman scattering
    • in, J. E. D. David, M. J. Lilley, eds. (Academic Press
    • W. L. Peticolas, and E. Evertsz, "Conformation of DNA in vitro and in vivo from laser Raman scattering, " in Methods in Enzymology, J. E. D. David, M. J. Lilley, eds. (Academic Press, 1992), pp. 335-352.
    • (1992) Methods in Enzymology , pp. 335-352
    • Peticolas, W.L.1    Evertsz, E.2


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