Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)₂as an A-DNA duplex

Abstract

The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACC-GGGG) 2 has been determined at 2.5 Å resolution in the tetragonal space group P4 1 . This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn 2+ ion was identified with direct coordination to the N7 position of G 13 and a water molecule at the major-groove side of the C 2 ÁG 13 base pair.

Structure of d(CCCCGGTACCGGGG)2at 1.65 Å resolution

“…The DNA sequence crystallizes as an Atype double helix. The structure of this sequence has been previously reported at a resolution of 2.5 Å (Mandal et al, 2012). Apart from the higher resolution, which allows identification of the solvent interactions and supports a discussion on the economy of hydration, the present crystal differs in another way from that reported previously.…”

“…The previously reported unit cell for this sequence (Mandal et al, 2012) had unit-cell parameters a = b = 29.34, c = 87.69 Å in space group P4 1 . This is related to the present unit cell by a rotation of 45 about the c axis and extension of the a and b axes by a factor of 2 1/2 .…”

“…The previously reported crystal structure of the present sequence (PDB entry 3v9d; Mandal et al, 2012) was used as the search model. A solution with a correlation coefficient of 89.4 and an R factor of 26.9% was obtained.…”

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

“…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.…”