A conformational B-Z DNA study monitored with phosphatemethylated DNA as a model for epigenetic dynamics focused on 5-(hydroxy)methylcytosine

Abstract

This study was directed on the B-into Z-DNA isomerization with alternating CG sequences monitored with artificial DNA model-systems based on methylation of the phosphate backbone. The chemical concept for this transition wherein shielding of the oxygen anions of the backbone phosphates plays an essential role, resulted in the preparation of the phosphatemethylated d(CpG). Even on this primitive level of only two base pair long, the B-Z conformational aspects of this selfcomplementary duplex could be described in solution with nuclear magnetic resonance (NMR) and circular dichroism (CD) measurements. The exclusivity of this choice became clear after synthesizing phosphatemethylated DNA with longer alternating CG fragments. It could be shown that conflicting conformational effects of the CG and GC fragments resulted in an overall B structure of the phosphatemethylated tetramer d(C P G P C P G). From our model considerations, it is clear that the internal stress introduced by the alternating CG sequences will be promoted by a complete shielding of the phosphate backbone. Elimination of this effect may be realized by a site-specific phosphate shielding. The role of the anti-syn isomerization of G in the CG fragments is clarified by methylation of the phosphate group. This anti-syn transition is absent in corresponding methylphosphonates, suggesting an exclusive role for base-backbone coordination via hydrogen bonding. In addition, we propose that the Binto Z-DNA interconversion may offer a mechanistic view for differences in dynamics between cytosine and its epigenetic derivative 5-methylcytosine. This mechanism has been extended to the demethylation of 5-methylcytosine and the exchange of information between the new epigenetic base, 5-hydroxymethylcytosine and the DNA backbone via an intramolecular phosphorylation. The role of 5-hydroxymethylcytosine in Alzheimer disease has been briefly discussed. In our opinion, this study can be considered as a new dynamic concept for epigenetics based on the dynamics of the B-Z transition in natural and phosphatemethylated DNA.

Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers

“…It is necessary to mention that duplex formation with its natural (charge) complement for a selected composition of sequences may have the possibility for an allosteric-like interaction between the phosphate-methylated strand and its natural complement. This property has been exclusively demonstrated for phosphate-methylated DNAs with their natural counterpart [14]. Accepting a fixed A-geometry for the phosphatemethylated RNA, duplex formation will occur with natural RNA as well as with natural DNA.…”

“…In order to calculate the corresponding ∆H's a factor ~1.5 must be introduced (three hydrogen bridges in C-G and two in A-T base-pairs). This ratio can be abstracted from Figure 3 [14].…”

“…For the role of dispersion interactions it is necessary to have at one's disposal a representative model for the solely duplex-and filling-space structures of the aforementioned (modified) DNA and RNA. For the antiparallel phosphate-methylated DNA there is a self-complementary left-handed dimer d(C P G) [4], its (right-handed) tetramer d(C P G P C P G) [14], and the right-handed r(2ꞌ-OMe)C P G [19] available. The individual duplex structures were obtained from CD and NMR data, vide supra.…”

Retracted HIV Study Provides New Information about the Status of the <i>in</i> <i>Vitro</i> Inhibition of DNA Replication by Backbone Methylation

“…It should be assigned that we are dealing with a high selectivity and enhanced duplex formation of phosphatemethylated DNA (a fixed B-conformation) for its complementary natural DNA (A-and B-conformation) which is in sharp contrast with the poor hybridization affinity at the RNA level (A-conformation). The established selectivity and pronounced duplex formation for natural DNA in contrast to RNA has been concluded from model studies for short phosphatemethylated DNA fragments with 2 -5 nucleotides, vide infra [2]- [6].…”

“…After the publication in Science entitled Inhibition of HIV-1 Infectivity by Phosphate-Methylated DNA: Retraction of Moody et al [1] a number of articles have been published in order to reduce the imbalance between the various passages in the Retraction (presented as a Technical Comment) and the "meltdown" of the bio-and physical chemical properties of phosphatemethylated DNA [2]- [6]. The Retraction mainly focused on the small degree of methylation of the 20-nucleotide DNA's.…”