Do Anions Exert any Structural Changes on Dimeric d(G4T4G4)2 Quadruplex in Aqueous Solution?

Primož Šket(1*), Rok Pirh(2), Janez Plavec(3)

(1) Slovenian NMR center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia., Slovenia
(2) Slovenian NMR center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana., Slovenia
(3) Slovenian NMR center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva cesta 5, SI-1000 Ljubljana, Slovenia and EN-FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia., Slovenia
(*) Corresponding author


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Abstract


It is well known that the presence of cations is necessary for G-quartet formation due to their role in reducing repulsions amongst guanine carbonyl oxygen atoms and additionally enhancing base-base stacking interactions. However, not much is known about the influence of anions on G-quadruplex formation by G-rich oligonucleotides in aqueous solution. In the presence of sodium halides, acetate, nitrate and BPh4- folding was almost complete, while only partial folding has been observed with NaBF4 and NaPF6. Detailed evaluation of 1H NMR spectra of d(G4T4G4)2 in the presence of nine different sodium salts indicates minor differences in loop regions as well as in structure of G-quadruplex core. Comparison of inter-proton distances obtained from NOESY spectra showed slightly different orientations of thymine residues in loop regions and changes in stacking interactions between G-quartets, which are most pronounced in the case of G-quadruplex folded in the presence of NaPF6
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Keywords


Quadruplex; Cations; Anions; NMR Spectroscopy

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References


S. Neidle; S. Balasubramanian, Quadruplex Nucleic Acids (The Royal Society of Chemistry, 2006).

M. A. Keniry, Quadruplex structures in nucleic acids, Biopolymers, Volume 56, (Issue 3), 2001, Pages 123-146.

J. T. Davis, G-quartets 40 years later: from 5 '-GMP to molecular biology and supramolecular chemistry, Angew. Chem.-Int. Edit., Volume 43, (Issue 6), 2004, Pages 668-698.

H. Fernando; S. Sewitz; J. Darot; S. Tavare; J. L. Huppert; S. Balasubramanian, Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression, Nucleic Acids Res., Volume 37, (Issue 20), 2009, Pages 6716-6722.

F. Rosu; V. Gabelica; H. Poncelet; E. De Pauw, Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry, Nucleic Acids Res., Volume 38, (Issue 15), 2010, Pages 5217-5225.

J. Amato; B. Pagano; N. Borbone; G. Oliviero; V. Gabelica; E. D. Pauw; S. D'Errico; V. Piccialli; M. Varra; C. Giancola; G. Piccialli; L. Mayol, Targeting G-quadruplex structure in the human c-Kit promoter with short PNA sequences, Bioconjug. Chem., Volume 22, (Issue 4), 2011, Pages 654-663.

A. Galeone; L. Mayol; A. Virgilio; A. Virno; A. Randazzo, A further contribution to the extreme variability of quadruplex structures from oligodeoxyribonucleotides containing inversion of polarity sites in the G-tract, Mol. Biosyst., Volume 4, (Issue 5), 2008, Pages 426-430.

E. Fadrna; N. Spackova; R. Stefl; J. Koca; T. E. Cheatham; J. Sponer, Molecular dynamics simulations of guanine quadruplex loops: advances and force field limitations, Biophys. J., Volume 87, (Issue 2004, Pages 227-242.

J. Sponer; N. Spackova, Molecular dynamics simulations and their application to four-stranded DNA, Methods, Volume 43, (Issue 4), 2007, Pages 278-290.

X. Cang; J. Sponer; T. E. Cheatham, 3rd, Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes, Nucleic Acids Res., Volume 39, (Issue 10), 2011, Pages 4499-4512.

F. W. Smith; J. Feigon, Quadruplex structure of Oxytricha telomeric DNA oligonucleotides., Nature, Volume 356, (Issue 1992, Pages 164-168.

F. W. Smith; J. Feigon, Strand orientation in the DNA quadruplex formed from the Oxytricha telomere repeat oligonucleotide d(G4T4G4) in solution, Biochemistry, Volume 32, (Issue 33), 1993, Pages 8682-8692.

N. V. Hud; P. Schultze; V. Sklenar; J. Feigon, Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex, J. Mol. Biol., Volume 285, (Issue 1), 1999, Pages 233-243.

P. Sket; M. Crnugelj; W. Kozminski; J. Plavec, 15NH4+ ion movement inside d(G4T4G4)2 G-quadruplex is accelerated in the presence of smaller Na+ ions, Org. Biomol. Chem., Volume 2, (Issue 14), 2004, Pages 1970-1973.

P. Sket; M. Crnugelj; J. Plavec, Identification of mixed di-cation forms of G-quadruplex in solution, Nucleic Acids Res., Volume 33, (Issue 11), 2005, Pages 3691-3697.

P. Sket; J. Plavec, Not all G-quadruplexes exhibit ion-channel-like properties: NMR study of ammonium ion (non)movement within the d(G3T4G4)2 quadruplex, J. Am. Chem. Soc., Volume 129, (Issue 28), 2007, Pages 8794-8800.

M. Trajkovski; P. Sket; J. Plavec, Cation localization and movement within DNA thrombin binding aptamer in solution, Org. Biomol. Chem., Volume 7, (Issue 22), 2009, Pages 4677-4684.

P. Sket; J. Plavec, Tetramolecular DNA Quadruplexes in Solution: Insights into Structural Diversity and Cation Movement, J. Am. Chem. Soc., Volume 132, (Issue 36), 2010, Pages 12724-12732.

D. Gonzalez-Rodriguez; J. L. J. van Dongen; M. Lutz; A. L. Spek; A. P. H. J. Schenning; E. W. Meijer, G-quadruplex self-assembly regulated by Coulombic interactions, Nat. Chem., Volume 1, (Issue 2), 2009, Pages 151-155.

P. Schultze; F. W. Smith; J. Feigon, Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG), Structure, Volume 2, (Issue 3), 1994, Pages 221-233.


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