Effect of the ribose versus 2’-deoxyribose residue in guanosine-5’-monophosphates on the formation of G-quartets stabilized by K+ and Na+

Kateřina Mudroňová1, Václav Římal2 and Peter Mojzeš1

1Institute of Physics, 2Department of Low Temperature Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-12116 Prague 2, Czech Republic

Guanine quadruplexes [1] are widely studied because of their role in various biological processes including gene expression and cell immortalization, and possible nanotechnological applications2. G-quadruplexes can be formed under specific physico-chemical conditions from DNA as well as RNA oligo- or polynucleotides containing repetitive sequences of several consecutive guanosine residues. DNA quadruplexes exhibit greater structural polymorphism than RNA, as they can adopt antiparallel, various hybride (3+1) and parallel folds, whereas RNA quadruplexes seem to be restricted simply to parallel form. Basic building blocks of G-quadruplex consist of four guanines interconnected by Hoogsteen hydrogen bonding to form G-quartet, stabilized by coordinated metal cation, especially Na+ or K+. G-quartets are stacked one upon the other.

            However, G-quartets and their supramolecular self-associates resembling G-quadruplexes can be formed also from monomeric guanosine-phosphates. Although G-quartets and self-associates of 5’-rGMP have been thoroughly studied in the presence of various alkali metals by various methods, notably NMR6, similar studies of deoxyribonucleotide 5’-dGMP are still rare. In particular a direct comparison of the ability of monomeric 5’-rGMPs and 5’-dGMPs to constitute G-quartets and self-associates stabilized by the most common alkali ions Na+ and K+ is missing, although it may contribute for better understanding of the reasons of different polymorphism of DNA and RNA G-quadruplexes in Na+ and K+ solutions.

            Here we report results of a systematic study of the effect of the ribose versus 2’-deoxyribose on the 5’-GMP self-assembling in pH-neutral or slightly basic Na+ and K+ solutions by means of Raman and 1H and 31P NMR spectroscopy. Although not yet frequently used in the G-quadruples research, Raman spectroscopy is especially suitable for the task, since it can be conveniently used at high 5’-GMP concentrations favorable to self-aggregation. Moreover, Raman spectra provide well-established spectral markers sensitive to nucleotide conformation, formation of hydrogen bonds and stacking interactions3,4. In the present study, the nucleotide concentration, nature, concentration and stochiometry of alkali cations, and temperature were systematically varied to find that ability of 5’-dGMP to constitute G-quartets and ordered supramolecular structures stabilized by Na+ is substantially lower than that of 5’-rGMP. As shown on Fig. 1, 5’-dGMP remained in Na+ solution as monomer even at 800 mM concentration where Na25’-rGMP clearly form firmly stacked G-quartets. On the other hand, after introduction of K+ ions both guanosine-monophosphates readily form self-stacking G-quartets, although self-association of 5’-rGMP was still greater than that of 5’-dGMP (Fig. 2). Possible consequences for G-quadruplex polymorphism will be discussed.

Figure 1. Raman spectra of 800 mM Na25’-rGMP and Na25’-dGMP at 5 and 80°C.

Figure 2. Raman spectra of 100 mM Na25’-rGMP and 400 mM Na25’-dGMP in the absence and presence of additional 500 mM K+. T=10°C.


This work was supported by the Grant Agency of the Charles University in Prague (No. 388615) and the Czech Science Foundation (No. 15-06785S).

1.         Chaires J.B., Graves D., (eds.), Quadruplex Nucleic Acids, Springer-Verlag, Berlin 2013.

2.         Davis J.T., Angew. Chem. Int. Ed. 43 (2004) 668-698.

3.         Benevides J.M., Overman S.A., Thomas G.J., Jr., J. Raman Spectrosc. 36 (2005) 279-299.

4.         Palacký J., Vorlíčková M., Kejnovská I., Mojzeš P., Nucleic Acids Res. 41 (2013) 1005-1016.

5.         Kim K.W., Kim S.K., Kim M.S., Suh, S.W., Biopolymers 25 (1986) 753–762.

6.         Wong A., Ida R., Spindler L., Wu G., J. Am. Chem. Soc. 127 (2005) 6990-6998.