Abstract

Quadruplex structures are higher order structures formed by guanine-rich oligonucleotides. In the present study, temperature-induced conformational changes in the quadruplex structures of aptamers and other guanine-rich oligonucleotides are probed by Raman spectroscopy. In particular, dramatic changes in the fingerprint region are observed in the spectra of thrombin binding aptamer at higher temperatures. These changes are accompanied by a decrease in the intensity of the 1480 cm−1 peak (attributed to C8 = N7-H2), which is diagnostic of the quadruplex structure. We also show that these changes can be reversed (to a certain extent) by addition of K+ ions.

©2010 Optical Society of America

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References

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  2. J. L. Huppert and S. Balasubramanian, “G-quadruplexes in promoters throughout the human genome,” Nucleic Acids Res. 35(2), 406–413 (2006).
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  6. N. de-los-Santos-Álvarez, M. J. Lobo-Castañón, A. J. Miranda-Ordieres, and P. Tuñón-Blanco, “Aptamers as recognition elements for label-free analytical devices,” Trends Analyt. Chem. 27(5), 437–446 (2008).
    [Crossref]
  7. B. J. Hicke, C. Marion, Y.-F. Chang, T. Gould, C. K. Lynott, D. Parma, P. G. Schmidt, and S. Warren, “Tenascin-C aptamers are generated using tumor cells and purified protein,” J. Biol. Chem. 276(52), 48644–48654 (2001).
    [Crossref] [PubMed]
  8. 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).
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  9. 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).
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  28. C. Krafft, J. M. Benevides, and G. J. Thomas., “Secondary structure polymorphism in Oxytricha nova telomeric DNA,” Nucleic Acids Res. 30(18), 3981–3991 (2002).
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  30. J. M. Benevides and G. J. Thomas., “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).
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    [Crossref]
  33. D. Zhang, Y. Xie, M. F. Mrozek, C. Ortiz, V. J. Davisson, and D. Ben-Amotz, “Raman detection of proteomic analytes,” Anal. Chem. 75(21), 5703–5709 (2003).
    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  36. J. M. Benevides, M. A. Weiss, and G. J. Thomas., “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).
    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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2010 (3)

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

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).

2008 (3)

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).
[Crossref] [PubMed]

N. de-los-Santos-Álvarez, M. J. Lobo-Castañón, A. J. Miranda-Ordieres, and P. Tuñón-Blanco, “Aptamers as recognition elements for label-free analytical devices,” Trends Analyt. Chem. 27(5), 437–446 (2008).
[Crossref]

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).
[Crossref] [PubMed]

2007 (2)

M. Webba da Silva, “Geometric formalism for DNA quadruplex folding,” Chemistry 13(35), 9738–9745 (2007).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

2006 (4)

M. R. Guzmán, J. Liquier, S. K. Brahmachari, and E. Taillandier, “Characterization of parallel and antiparallel G-tetraplex structures by vibrational spectroscopy,” Spectrochim. Acta A Mol. Biomol. Spectrosc. 64(2), 495–503 (2006).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

J. L. Huppert and S. Balasubramanian, “G-quadruplexes in promoters throughout the human genome,” Nucleic Acids Res. 35(2), 406–413 (2006).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

2004 (1)

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).
[PubMed]

2003 (4)

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).
[Crossref] [PubMed]

D. Zhang, Y. Xie, M. F. Mrozek, C. Ortiz, V. J. Davisson, and D. Ben-Amotz, “Raman detection of proteomic analytes,” Anal. Chem. 75(21), 5703–5709 (2003).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

2002 (1)

C. Krafft, J. M. Benevides, and G. J. Thomas., “Secondary structure polymorphism in Oxytricha nova telomeric DNA,” Nucleic Acids Res. 30(18), 3981–3991 (2002).
[Crossref] [PubMed]

2001 (3)

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).
[Crossref] [PubMed]

B. J. Hicke, C. Marion, Y.-F. Chang, T. Gould, C. K. Lynott, D. Parma, P. G. Schmidt, and S. Warren, “Tenascin-C aptamers are generated using tumor cells and purified protein,” J. Biol. Chem. 276(52), 48644–48654 (2001).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

2000 (1)

T. Hermann and D. J. Patel, “Adaptive recognition by nucleic acid aptamers,” Science 287(5454), 820–825 (2000).
[Crossref] [PubMed]

1998 (3)

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).
[Crossref] [PubMed]

L. Laporte and G. J. Thomas., “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).
[Crossref] [PubMed]

J.-L. Mergny, A.-T. Phan, and L. Lacroix, “Following G-quartet formation by UV-spectroscopy,” FEBS Lett. 435(1), 74–78 (1998).
[Crossref] [PubMed]

1997 (1)

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).
[Crossref] [PubMed]

1995 (1)

T. Miura and G. J. Thomas., “Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA,” Biochemistry 34(29), 9645–9654 (1995).
[Crossref] [PubMed]

1994 (2)

T. Miura and G. J. Thomas., “Structural polymorphism of telomere DNA: interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy,” Biochemistry 33(25), 7848–7856 (1994).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

1993 (4)

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).
[PubMed]

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

1992 (1)

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).
[Crossref] [PubMed]

1991 (1)

J. M. Benevides, M. A. Weiss, and G. J. Thomas., “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).
[Crossref] [PubMed]

1990 (2)

A. D. Ellington and J. W. Szostak, “In vitro selection of RNA molecules that bind specific ligands,” Nature 346(6287), 818–822 (1990).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

1988 (1)

J. M. Benevides, A. H. J. Wang, G. A. van der Marel, J. H. van Boom, and G. J. Thomas., “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).
[Crossref] [PubMed]

1986 (2)

C. Otto, T. J. J. van den Tweel, F. F. M. de Mul, and J. Greve, “Surface-enhanced Raman spectroscopy of DNA bases,” J. Raman Spectrosc. 17(3), 289–298 (1986).
[Crossref]

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).
[Crossref]

1984 (1)

B. Prescott, W. Steinmetz, and G. J. Thomas., “Characterization of DNA structures by laser Raman spectroscopy,” Biopolymers 23(2), 235–256 (1984).
[Crossref] [PubMed]

1983 (1)

J. M. Benevides and G. J. Thomas., “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).
[Crossref] [PubMed]

Aoki, K.

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).
[Crossref]

Balasubramanian, S.

J. L. Huppert and S. Balasubramanian, “G-quadruplexes in promoters throughout the human genome,” Nucleic Acids Res. 35(2), 406–413 (2006).
[Crossref] [PubMed]

Barhoumi, A.

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).
[Crossref] [PubMed]

Beeson, J.

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).
[Crossref] [PubMed]

Ben-Amotz, D.

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).
[Crossref] [PubMed]

D. Zhang, Y. Xie, M. F. Mrozek, C. Ortiz, V. J. Davisson, and D. Ben-Amotz, “Raman detection of proteomic analytes,” Anal. Chem. 75(21), 5703–5709 (2003).
[Crossref] [PubMed]

Benevides, J. M.

C. Krafft, J. M. Benevides, and G. J. Thomas., “Secondary structure polymorphism in Oxytricha nova telomeric DNA,” Nucleic Acids Res. 30(18), 3981–3991 (2002).
[Crossref] [PubMed]

J. M. Benevides, M. A. Weiss, and G. J. Thomas., “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).
[Crossref] [PubMed]

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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).
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B. J. Hicke, C. Marion, Y.-F. Chang, T. Gould, C. K. Lynott, D. Parma, P. G. Schmidt, and S. Warren, “Tenascin-C aptamers are generated using tumor cells and purified protein,” J. Biol. Chem. 276(52), 48644–48654 (2001).
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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).
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J.-L. Mergny, A.-T. Phan, and L. Lacroix, “Following G-quartet formation by UV-spectroscopy,” FEBS Lett. 435(1), 74–78 (1998).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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B. J. Hicke, C. Marion, Y.-F. Chang, T. Gould, C. K. Lynott, D. Parma, P. G. Schmidt, and S. Warren, “Tenascin-C aptamers are generated using tumor cells and purified protein,” J. Biol. Chem. 276(52), 48644–48654 (2001).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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J. M. Benevides, A. H. J. Wang, G. A. van der Marel, J. H. van Boom, and G. J. Thomas., “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).
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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).
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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).
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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).
[Crossref] [PubMed]

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Warren, S.

B. J. Hicke, C. Marion, Y.-F. Chang, T. Gould, C. K. Lynott, D. Parma, P. G. Schmidt, and S. Warren, “Tenascin-C aptamers are generated using tumor cells and purified protein,” J. Biol. Chem. 276(52), 48644–48654 (2001).
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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).
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M. Webba da Silva, “Geometric formalism for DNA quadruplex folding,” Chemistry 13(35), 9738–9745 (2007).
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J. M. Benevides, M. A. Weiss, and G. J. Thomas., “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).
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Xie, Y.

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).
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D. Zhang, Y. Xie, M. F. Mrozek, C. Ortiz, V. J. Davisson, and D. Ben-Amotz, “Raman detection of proteomic analytes,” Anal. Chem. 75(21), 5703–5709 (2003).
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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).
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Yang, G.

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).
[Crossref] [PubMed]

Zhang, D.

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

D. Zhang, Y. Xie, M. F. Mrozek, C. Ortiz, V. J. Davisson, and D. Ben-Amotz, “Raman detection of proteomic analytes,” Anal. Chem. 75(21), 5703–5709 (2003).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

Zhang, M.

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).
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Anal. Biochem. (1)

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).
[Crossref] [PubMed]

Anal. Chem. (1)

D. Zhang, Y. Xie, M. F. Mrozek, C. Ortiz, V. J. Davisson, and D. Ben-Amotz, “Raman detection of proteomic analytes,” Anal. Chem. 75(21), 5703–5709 (2003).
[Crossref] [PubMed]

Biochem. Biophys. Res. Commun. (1)

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).
[Crossref] [PubMed]

Biochemistry (8)

T. Miura and G. J. Thomas., “Structural polymorphism of telomere DNA: interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy,” Biochemistry 33(25), 7848–7856 (1994).
[Crossref] [PubMed]

T. Miura and G. J. Thomas., “Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA,” Biochemistry 34(29), 9645–9654 (1995).
[Crossref] [PubMed]

L. Laporte and G. J. Thomas., “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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

J. M. Benevides, M. A. Weiss, and G. J. Thomas., “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).
[Crossref] [PubMed]

J. M. Benevides, A. H. J. Wang, G. A. van der Marel, J. H. van Boom, and G. J. Thomas., “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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

Biopolymers (1)

B. Prescott, W. Steinmetz, and G. J. Thomas., “Characterization of DNA structures by laser Raman spectroscopy,” Biopolymers 23(2), 235–256 (1984).
[Crossref] [PubMed]

Chemistry (1)

M. Webba da Silva, “Geometric formalism for DNA quadruplex folding,” Chemistry 13(35), 9738–9745 (2007).
[Crossref] [PubMed]

FEBS Lett. (1)

J.-L. Mergny, A.-T. Phan, and L. Lacroix, “Following G-quartet formation by UV-spectroscopy,” FEBS Lett. 435(1), 74–78 (1998).
[Crossref] [PubMed]

J. Am. Chem. Soc. (4)

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

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).
[Crossref] [PubMed]

J. Biol. Chem. (3)

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).
[PubMed]

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).
[Crossref] [PubMed]

B. J. Hicke, C. Marion, Y.-F. Chang, T. Gould, C. K. Lynott, D. Parma, P. G. Schmidt, and S. Warren, “Tenascin-C aptamers are generated using tumor cells and purified protein,” J. Biol. Chem. 276(52), 48644–48654 (2001).
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Figures (4)

Fig. 1
Fig. 1 Scheme 1a, Guanine quartet (tetrad) formed via Hoogsten-type H-bonding of four guanine molecules, with characteristic vibrational band frequencies. Scheme 1b, Chair (left) and basket (right) intramolecular quadruplex structures consisting of 2 stacks of guanine quartets. Chair type is formed by lateral or edge looping while diagonal looping forms basket type.
Fig. 2
Fig. 2 Top: raw Raman spectra of TBA incubated at 4°C and measured from five different spots in the rim of the drop. Bottom: Temperature dependent TBA Raman spectra. (a) 4°C, (b) 25°C, (c) 60°C, (d) 90°C. The spectra are normalized with respect to the most intense for each trace.
Fig. 3
Fig. 3 Quadruplex Stabilization by K+. Top: Raman spectra of TBA incubated at 25°C without (a) and with (b) 100 mM KCl. Middle: Raman spectra of TBA incubated at 60°C without (a) and with (b) 100 mM KCl. Bottom: Raman spectra of TBA incubated at 90°C without (a) and with (b) 100 mM KCl. The spectra are normalized with respect to the most intense peak for each trace.
Fig. 4
Fig. 4 Raman spectra of oligonucleotides incubated at 4°C. (a) DDCRDL Aptamer, (b) Human Telomeric Sequence 1 (24 nt), (c) Human Telomeric Sequence 2 (22 nt), (d) Bcl-2 promoter sequence, (e) HIV integrase aptamer (T30695), and (f) Thrombin Binding Aptamer (TBA). The spectra are normalized with respect to the most intense peak for each trace.

Tables (2)

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Table 1 DNA sequences of oligonucleotides used in the present study.

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Table 2 Raman Frequencies of Thrombin Binding Aptamer Incubated at Different Temperatures

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