The Chemical and Biochemical Properties of Methylphosphotriester DNA

Buck, HM Henk

doi:10.1081/ncn-200040620

Cited by 11 publications

(24 citation statements)

References 43 publications

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“…After the publication of the Retraction, an explanation for the inhibition of the DNA replication of selected regions at the E. coli pab B gene was suggested by the presence of triethyl ammonium-and possibly triethylmethyl ammonium cations (methyl transfer via the methylating agent) as by-products of the synthesis, vide supra [3]. The latter duplex is faclitated by electrostatic interaction between the positively charged triethylmethyl ammonium groups and the negatively charged phosphate groups in combination with the amphipathic character of the former group [3] [5] [19].…”

Section: General Remarks Concerning the Duplication Studymentioning

confidence: 99%

“…The latter duplex is faclitated by electrostatic interaction between the positively charged triethylmethyl ammonium groups and the negatively charged phosphate groups in combination with the amphipathic character of the former group [3] [5] [19]. Through hydrogen bridging and (partial) methyl shielding of the phosphates, the duplex formation should be increased.…”

Section: General Remarks Concerning the Duplication Studymentioning

confidence: 99%

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

Buck¹

2015

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In this publication attention is given to a retracted article in Science at the end of 1990 concerning the HIV-1 inhibition by a modified backbone DNA as the phosphatemethylated DNA. A disproportion in the presented data resulted in a faulty generalization of the (bio)chemical characteristics of the phosphatemethylated DNA (18-and 20-nucleotides). In the confusion and the outside pressure a related study in Nucleic Acids Research on the in vitro dynamics of a regiospecific inhibition of DNA duplication with long (20-and 18-nucleotides) and short (8-nucleotides) phosphatemethylated DNA was completely ignored. A restoration will be given based on a comprehensive view demonstrating the unique molecular and conformational properties of phosphatemethylated DNA in their (bio)chemistry towards natural DNA and RNA (HIV-1 RNA loops).

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Section: General Remarks Concerning the Duplication Studymentioning

confidence: 99%

Section: General Remarks Concerning the Duplication Studymentioning

confidence: 99%

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

Buck¹

2015

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“…The effect of covalent shielding has been shown in Figure 3 with the circular dichroism (CD) spectra of the two left-handed self-complementary phosphatemethylated d(C P G)'s in combination with the two right-handed self-complementary phosphatemethylated d(G P C)'s [8,18].…”

Section: The B-and Z-geometry In Phosphatemethylated Dna a Specific mentioning

confidence: 99%

“…For the duplex phosphatemethylated d(C P G) we found 9˚C and 13˚C for the R P and S P chirality, respectively. The corresponding d(G P C) duplex shows a transition of 27˚C for both configurations [8,18].…”

Section: The B-and Z-geometry In Phosphatemethylated Dna a Specific mentioning

confidence: 99%

“…Our experimental data are solely based on the base interactions and sugar puckering, controlling in a distinct way the orientation of the backbone. Although phosphatemethylated DNA is an excellent candidate for duplex formation with its natural conjugate, it is unsuitable for duplex formation with RNA [4][5][6][7][8]. It has been shown under biological and physicalchemical conditions that replication is blocked whereas protein synthesis remains essentially unaffected.…”

Section: Introductionmentioning

confidence: 99%

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

Buck¹

2013

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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.

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Different models for phosphate anion shielding in DNA duplexes: An elaboration with ab initio and molecular mechanics calculations

Buck¹

2005

Int J of Quantum Chemistry

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ABSTRACT:In an effort to overcome a significant difference between high-level ab initio calculations and X-ray data of DNA duplexes, Fonseca Guerra et al. [9 -11] studied a number of model systems for A-T and G-C basepairs at various levels of nonlocal Density Functional Theory. There was an excellent agreement with the gasphase experimental bond enthalpies for the A-T and G-C basepairs. On the other hand the hydrogen bond lengths between the bases differ from the X-ray results. After introduction of a molecular environment as local water and Na ϩ ions, the agreement between theory and experiment was excellent. However, careful analysis shows that this picture is far from correct. In fact, the model was constructed as a backbonemodified DNA duplex in which the nonbonding oxygens of the phosphate linkages are completely shielded by proton addition. Experimental results with respect to backbonemodified DNAs clearly show that changes in the backbone focused on phosphate shielding result in DNA duplexes with a variety in conformational behavior. In addition to an analysis of the aforementioned contradiction, we also give molecular mechanics calculations which show that the A-T and G-C bond enthalpies are of the same order as the corresponding results of Fonseca Guerra et al. under the condition of complete anionic shielding of the nonbonded oxygens in the phosphate linkages.

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The Chemical and Biochemical Properties of Methylphosphotriester DNA

Abstract: Methylphosphotriester DNA shows a number of interesting bio-organic properties. Its behavior is quite different from selected modified DNAs as the related methylphosphonate oligonucleotides.

Cited by 11 publications

References 43 publications

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

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

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

Different models for phosphate anion shielding in DNA duplexes: An elaboration with ab initio and molecular mechanics calculations

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The Chemical and Biochemical Properties of Methylphosphotriester DNA

Abstract: Methylphosphotriester DNA shows a number of interesting bio-organic properties. Its behavior is quite different from selected modified DNAs as the related methylphosphonate oligonucleotides.

Cited by 11 publications

References 43 publications

Retracted HIV Study Provides New Information about the Status of the &lt;i&gt;in&lt;/i&gt; &lt;i&gt;Vitro&lt;/i&gt; Inhibition of DNA Replication by Backbone Methylation

Retracted HIV Study Provides New Information about the Status of the &lt;i&gt;in&lt;/i&gt; &lt;i&gt;Vitro&lt;/i&gt; Inhibition of DNA Replication by Backbone Methylation

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

Different models for phosphate anion shielding in DNA duplexes: An elaboration with ab initio and molecular mechanics calculations

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

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