A new oxygen modification cyclooctaoxygen binds to nucleic acids as sodium crown complex

Abstract

Background: Oxygen exists in two gaseous and six solid allotropic modifications. An additional allotropic modification of oxygen, the cyclooctaoxygen, was predicted to exist in 1990.

Methods: Cyclooctaoxygen sodium was synthesized in vitro from atmospheric oxygen, or catalase effect-generated oxygen, under catalysis of cytosine nucleosides and either ninhydrin or eukaryotic low-molecular weight RNA. Thin-layer chromatographic mobility shift assays were applied on specific nucleic acids and the cyclooctaoxygen sodium complex.

Results: We report the first synthesis and characterization of cyclooctaoxygen as its sodium crown complex, isolated in the form of three cytosine nucleoside hydrochloride complexes. The cationic cyclooctaoxygen sodium complex is shown to bind to nucleic acids (RNA and DNA), to associate with single-stranded DNA and spermine phosphate, and to be essentially non-toxic to cultured mammalian cells at 0.1-1.0mM concentration.

Conclusions: We postulate that cyclooctaoxygen is formed in most eukaryotic cells in vivo from dihydrogen peroxide in a catalase reaction catalyzed by cytidine and RNA. A molecular biological model is deduced for a first epigenetic shell of eukaryotic in vivo DNA. This model incorporates an epigenetic explanation for the interactions of the essential micronutrient selenium (as selenite) with eukaryotic in vivo DNA.

General significance: Since the sperminium phosphate/cyclooctaoxygen sodium complex is calculated to cover the active regions (2.6%) of bovine lymphocyte interphase genome, and 12.4% of murine enterocyte mitotic chromatin, we propose that the sperminium phosphate/cyclooctaoxygen sodium complex coverage of nucleic acids is essential to eukaryotic gene regulation and promoted proto-eukaryotic evolution.

Keywords: Cyclooctaoxygen; DNA; Epigenetics; Oxygen modification; RNA; Selenium.

Graphical abstract

Fig. 1

Molecular modeling of cyclooctaoxygen and its Na⁺ complex. (A) The cyclo-O₈ octagon (top, space-fill model; middle, crown conformation in D_4d symmetry; bottom, octagon). (B) Molecular modeling of the square pyramidal (SPY-4)-cyclo-O₈-Na⁺ crown complex. (C) Molecular modeling of the trigonal prismatic cyclo-O₈-Na⁺ crown complex, the (TPR-6)-aqua(chloro)(octoxocane-κ⁴O¹,O³,O⁵,O⁷)sodium. In comparison to the cyclo-O₈-Na⁺ crown complex (B), a symmetry transition in the O₈ ring can be noted due to the thermodynamic trans-effect of the additional ligands.

Fig. 2

The syntheses of cyclo-O₈-Na⁺-containing complexes. (A) Synthesis of the cyclo-O₈-Na⁺-containing complex NC by refluxing cytidine × HCl with ninhydrin under influence of atmospheric O₂. (B) Synthesis of the cyclo-O₈-Na⁺-containing complex dNC by refluxing 2′-deoxycytidine × HCl with ninhydrin under influence of atmospheric O₂. (C) Biomimetic synthesis of the cyclo-O₈-Na⁺-containing complex RC through reaction with buffered 3% H₂O₂ as catalyzed (catalase effect) by C. utilis low-molecular-weight RNA and NaHCO₃ at ambient temperature and physiological pH. (D) Proposed synthesis mechanism for the generation of cyclo-O₈ from atmospheric O₂ under ninhydrin catalysis over the 10-ring intermediate spiro[indene-2,10′-nonoxecane]-1,3-dione.

Fig. 3

Electrospray ionization mass spectrometry of RC. Magnified (100 ×) section of the ESI–MS spectrum of RC dissolved in H₂O/methanol from m/z 430 to m/z 760. Inset, magnified (20 ×) segment of the ESI–MS spectrum of RC from m/z 370 to m/z 430. The cluster cations of heptoxazocan-8-ium − octoxocane − Na³⁵Cl (1:2:m) are marked (m = 0–6). Not marked are the + 2 isotope peaks resulting from ³⁷Cl instead of one ³⁵Cl (m = 1–6). The origin of the heptoxazocan-8-iumyl − octoxocane (1:2) cluster radical cations (− 2 peaks) is indicated in the inset. The cluster cations of [(cytidine)₂ + Na + (NaCl)_n]⁺ (n = 0–5) are marked with stars.

Fig. 4

Molecular modeling of the postulated first epigenetic shell of in vivo DNA, as exemplified for a single-stranded hexanucleotide, introducing a molecular biological model for sperminium phosphate/cyclo-O₈-Na⁺/ssDNA and sperminium selenite/cyclo-O₈-Na⁺/ssDNA interactions. (A) The molecular model of the lysyl–lysine-coding single-stranded hexanucleotide d(ApApApApApAp) liganded with cyclo-O₈-Na⁺ and sperminium phosphate. (B) The molecular model of d(ApApApApApAp) liganded with cyclo-O₈-Na⁺ and sperminium selenite. Element color codings for (A) and (B): gray, carbon; white, hydrogen; blue, nitrogen; red, oxygen; purple, phosphorus; green, sodium; yellow, selenium.