Duplex Structure of a Minimal Nucleic Acid

Abstract

The crystal structure of an 8-mer (S)-GNA duplex is presented. As a tool for phasing, the anomalous diffraction of two copper(II) ions within two artificial metallo-base pairs was employed. The duplex structure confirms a canonical Watson−Crick base pairing scheme of GNA with antiparallel strands. The duplex secondary structure is distinct from canonical A- and B-form nucleic acids and can be described as a right-handed helical ribbon wrapped around the helix axis, resulting in a large hollow core. Most intriguingly, neighboring base pairs slide strongly against each other, resulting in extensive interstrand base−base hydrophobic interactions along with unusual hydrophobic intrastrand interactions of nucleobases with their backbone. These results reveal how a minimal nucleic acid backbone can support highly stable Watson−Crick-like duplex formation.

The Spermine Phosphate-Bound Cyclooctaoxygen Sodium Epigenetic Shell of Euchromatin DNA Is Destroyed by the Epigenetic Poison Glyphosate

“…The monohydrogen phosphate bridges the cyclo-O8-Na + with the sperminium cation, and the cyclo-O8-Na + has an inverted alternating orientation ( Figure 3A). Interestingly, the sperminium tetracation cannot bind alone to DNA in this model, since the distances [d (N 1 ,N 4 ) = 490 pm; d (N 4 ,N 9 ) = 620 pm; d (N 1 ,N 12 ) = 1,600 pm] between the four ammonium nitrogens do not fit the intrastrand phosphate-phosphate distance of dsDNA (B-DNA: dØ = 700 pm [36,37]; A-DNA: dØ = 590-600 pm [37][38][39][40]; Z-DNA: dØ = 590 pm (step pCp), dØ = 600 pm (step pGp) [40]). Therefore, it is quite remarkable that in our model for the first epigenetic shell of in vivo DNA ( Figure 3A) a repeating unit is formed from cyclo-O8-Na + and spermine phosphate that perfectly fits both the triplet nature of the genetic code [41] and the repeating distance of the phosphate anion backbone of DNA.…”

The Spermine Phosphate-Bound Cyclooctaoxygen Sodium Epigenetic Shell of Euchromatin DNA is Destroyed by the Epigenetic Poison Glyphosate

“…Cluster cations of heptoxazocan-8-ium -octoxocane -Na 35 Cl (1:2:m) (m = 0-6) were observed, together with characteristic +2 isotope peaks resulting from substitution of one 37 Cl for 35 Cl (m = 1-6), and together with -2 peaks of heptoxazocan-8-iumyl -octoxocane (1:2) cluster radical cations (m = 0-6) ( Figure 5). Clusters of [(cytidine)2 + Na + (NaCl)n] + (n = 0-5) were also observed ( Figure 5).…”

“…The cluster cations of heptoxazocan-8-ium -octoxocane -Na 35 Cl (1:2:m) are marked (m = 0-6). Not marked are the +2 isotope peaks resulting from 37 Cl instead of one 35 Cl (m = 1-6). The origin of the heptoxazocan-8-iumyl -octoxocane (1:2) cluster radical cations (-2 peaks) is indicated in the inset.…”

Artificial DNA Base Pairing Mediated by Diverse Metal Ions

“…Also interesting to note is that the HCu II H base pair was additionally incorporated into a glycol nucleic acid (GNA). 71,72 Single-crystal X-ray diffraction analysis of the metallo-GNA duplex revealed that two H nucleobases coordinated to the central Cu 2+ ion in a square-planar fashion with only a slight propeller twist (ca. 15°).…”