The Chemical and Biochemical Properties of Methylphosphotriester DNA and RNA in Comparison with Their Corresponding Methylphosphonates. A Dynamic Model Description

REFERENCES

• Buck , H.M. 2004 . The chemical and biochemical properties of methylphosphotriester DNA . Nucleosides Nucleotides Nucleic Acids , 23 : 1833–1847
   Web of Science ®Google Scholar
• Fire , A. , Xu , S. , Montgomery , M. K. , Kostas , S. A. , Driver , S. E. and Mello , C. C. 1998 . Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans . Nature , 391 : 806–811
   Web of Science ®Google Scholar
• Quaedflieg , P.J.L.M. , van der Heiden , A. P. , Koole , L. H. , van Genderen , M. H.P. , Coenen , A.J.J.M. , van der Wal , S. and Buck , H. M. 1990 . Synthesis and conformation of phosphate-methylated r(CpU) and r(ApU). Formation of a parallel right-handed duplex for Sp r(CpU) . Proc. Kon. Ned. Akad. van Wetensch. , 93 : 33–38
   Google Scholar
• Quaedflieg , P.J.L.M. , van der Heiden , A.P. , Koole , L. H. , Coenen , A.J.J.M. , van der Wal , S. and Meijer , E. M. 1991 . Synthesis and conformational analysis of phosphate-methylated RNA dinucleotides . J. Org. Chem. , 56 : 5846–5859
   Web of Science ®Google Scholar
• Quaedflieg , P.J.L.M. , Koole , L. H. , van Genderen , M.H.P. and Buck , H. M. 1989 . A structural study of phosphate-methylated d(CpG)n and d(GpC)n DNA oligomers. Implications of phosphate shielding for the isomerization of B-DNA into Z-DNA . Recl. Trav. Chim. Pays-Bas , 108 : 421–423
   Google Scholar
• Quaedflieg , P.J. L.M. 1993 . “ Synthesis and structural aspects of backbone-modified nucleic acids ” . Thesis; University of Leiden .
   Google Scholar
• Popenda , M. , Milecki , J. and Adamiak , R. W. 2004 . High salt solution structure of a left-handed RNA double helix . Nucleic Acids Res. , 32 : 4044–4054
   Web of Science ®Google Scholar
• Adamiak , D.A. , Rypniewski , W.R. , Milecki , J. and Adamiak , R. 2001 . The 1.19 Å X-ray structure of 2′-O-Me (CGCGCG)2 duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove . Nucleic Acids Res. , 29 : 4144–4153
   Web of Science ®Google Scholar
• Quaedflieg , P.J.L.M. , Broeders , N.L.H.L. , Koole , L. H. , van Genderen , M.H.P. and Buck , H. M. 1990 . Conformation of the phosphate-methylated DNA dinucleotides d(CpC) and d(TpC). Formation of a parallel miniduplex exclusively for the S configuration . J. Org. Chem. , 55 : 122–127
   Web of Science ®Google Scholar
• van Genderen , M.H.P. , Koole , L.H. and Buck , H.M. 1989 . Hybrization of phosphate-methylated DNA and natural oligonucleotides. Implications for protein-induced DNA duplex destabilization . Recl. Trav. Chim. Pays-Bas , 108 : 28–35
   Google Scholar
• Buck , H.M. and Koole , L.H. 1993 . Poly (deoxyribonucleotides), pharmaceutical compositions, use and preparation of the poly (deoxyribonucleotides) . Eur. Pat., München ,
   Google Scholar
• Miller , P.S. , Agris , C.H. , Aurelian , L. , Blake , K. R. , Lin , S.B. , Murakami , A. , Reddy , M.P. , Smith , C. and Ts’o , P. O.P. 1985 . Control of gene expression by oligonucleoside methylphosphonates . Jerus. Symp. Quantum Chem. Biochem. , 18 : 207–219
   Google Scholar
• Wengel , J. , Vester , B. , Lundberg , L.B. , Douthwaite , S. , S⊘rensen , M. D. , Babu , B. R. , Gait , M. J. , Arzumanov , A. A. , Peterson , M. and Nielsen , J. T. 2003 . LNA and α-L-LNA: towards therapeutic applications . Nucleosides Nucleotides Nucleic Acids , 22 : 601–604
   Web of Science ®Google Scholar
• Kumar , T.S. , Madsen , A.S. , Wengel , J. and Hrdlicka , P.J. 2006 . Synthesis and hybridization studies of 2′-amino-α-L-LNA and tetracyclic “locked LNA.” . J. Org. Chem. , 71 : 4188–4201
   Web of Science ®Google Scholar
• Brown , D. , Arzumanov , A.A. , Turner , J.J. , Stetsenko , D.A. , Lever , A.M.L. and Gait , M.J. 2005 . Antiviral activity of steric-block oligonucleotides targeting the HIV-1 trans-activation response and packaging signal stem-loop RNAs . Nucleosides Nucleotides Nucleic Acids , 24 : 393–396
   Web of Science ®Google Scholar
• Buck , H. M. , Koole , L. H. , van Genderen , M.H.P. , Smit , L. , Geelen , J.L.M.C. , Jurriaans , S. and Goudsmit , J. 1990 . Phosphate-methylated DNA aimed at HIV-1 RNA loops and integrated DNA inhibits viral infectivity . Science , 248 : 208–212
   Web of Science ®Google Scholar
• Moody , H.M. , Quaedflieg , P.J.L.M. , Koole , L.H. , van Genderen , M.H.P. , Buck , H.M. , Smit , L. , Jurriaans , S. , Geelen , J.L.M.C. and Goudsmit , J . 1990 . Inhibition of HIV-1 infectivity by phosphate-methylated DNA . Retraction Science , 250 : 125
   PubMed Web of Science ®Google Scholar
• Moody , H. M. , van Genderen , M. H.P. , Koole , L. H. , Kocken , H. J.M. , Meijer , E. M. and Buck , H. M. 1989 . Regiospecific inhibition of DNA duplication by antisense phosphate-methylated oligodeoxynucleotides . Nucleic Acids Res. , 17 : 4769–4782
   Web of Science ®Google Scholar
• Tsujikawa , L. , Weinfield , M. and Reha-Krantz , L. J. 2003 . Differences in replication of a DNA template containing an ethyl phosphotriester by T4 DNA polymerase and Escherichia coli DNA polymerase I . Nucleic Acids Res. , 31 : 4965–4972
   Web of Science ®Google Scholar
• 1991 . “ Human Retrovirus Laboratory, Academic Medical Centre ” . In Department of Virology, Amsterdam The Netherlands
   Google Scholar
• Kuijpers , W. H.A. , Huskens , J. , Koole , L. H. and van Boeckel , C. A.A. 1990 . Synthesis of well-defined phosphate-methylated DNA fragments: the application of potassium carbonate in methanol as deprotecting reagent . Nucleic Acids Res. , 18 : 5197–5205
   Web of Science ®Google Scholar
• Alul , R. H. , Singman , C. N. , Zhang , G. and Letsinger , R. L. 1991 . Oxalyl-CPG: a labile support for synthesis of sensitive oligonucleotide derivatives . Nucleic Acids Res. , 19 : 1527–1532
   Web of Science ®Google Scholar
• Buck , H. M. 2003 . The biochemical significance of parallel DNA duplexes . Nucleosides Nucleotides Nucleic Acids , 22 : 1549 – 1552 .
   PubMed Web of Science ®Google Scholar
• Marquez , V.E. , Ezzitouni , A. , Russ , P. , Siddiqui , M.A. , Ford , H. Jr. , Feldman , R.J. , Mitsuya , H. , Cliffort , G. and Barchi , J.J. Jr. 1998 . HIV-1 reverse transcriptase can discriminate between two conformationally locked carbocyclic AZT triphosphate analogues . J. Am. Chem. Soc. , 120 : 2780–2789
   Web of Science ®Google Scholar
• Wu , T. , Froeyen , M. , Kempeneers , V. , Pannecouque , C. , Wang , J. , Busson , R. , De Clercq , E. and Herdewijn , P. 2005 . Herdewijn P. Deoxythreosyl phosphonate nucleosides as selective anti-HIV agents . J. Am. Chem. Soc. , 127 : 5056–5065
   Web of Science ®Google Scholar
• Koole , L. H. , Buck , H. M. , Nyilas , A. and Chattopadhyaya , J. 1987 . Structural properties of modified deoxyadenosine structures in solution. Impact of the gauche and anomeric effects on the furanose conformation . Can. J. Chem. , 65 : 2089–2094
   Web of Science ®Google Scholar
• Castelijns , M.M.C.F. , Schipper , P. , van Aken , D. and Buck , H.M. 1981 . Dynamic equilibria between pentavalent protonated oxyphosphoranes and their isomeric tetravalent enol phosphonium ions via inter- and intramolecular proton transfer . J. Org. Chem. , 46 : 47–53
   Web of Science ®Google Scholar
• Loewenstein , A. and Szöke , A. 1962 . The activation energies of proton transfer reactions in water . J. Am. Chem. Soc. , 84 : 1151–1154
   Web of Science ®Google Scholar
• Kovrigin , E. L. and Loria , J. P. 2006 . Characterization of the transition state of functional enzyme dynamics . J. Am. Chem. Soc. , 128 : 7724–7725
   Web of Science ®Google Scholar
• Lin , F. L. , Hoyt , H. M. , van Halbeek , H. , Bergman , R.G. and Bertozzi , C. R. 2005 . Mechanistic investigation of the Staudinger ligation . J. Am. Chem. Soc. , 127 : 2686
   PubMed Web of Science ®Google Scholar
• Kuijpers , W.H.A. , Huskens , J. and van Boeckel , C.A.A. 1990 . The 2-(acetoxymethyl) benzoyl (AMB) group as a new base-protecting group, designed for the protection of (phosphate) modified oligonucleotides . Tetrahedron Letters , 31 : 6729–6732
   Web of Science ®Google Scholar
• Kuijpers , W. H.A. , Kuyl-Yeheskiely , E. , van Boom , J. H. and van Boeckel , C. A.A. 1993 . The application of the AMB protective group in the solid-phase synthesis of methylphosphonate DNA analogues . Nucleic Acids Res. , 21 : 3493–3500
   Web of Science ®Google Scholar
• Meyers , L. C. , Verdine , G. L. and Wagner , G. 1993 . Solution structure of the DNA methylphosphotriester repair domain of Escherichia coli Ada . Biochemistry , 32 : 14089–14094
   Web of Science ®Google Scholar
• Buck , H. M. The impact of chirality of phosphorus in methylphosphotriester DNA on duplex formation and its significance for inducing methylation-resistance genes . Proc. Kon. Ned. Akad. van Wetensch, 1997, 100, 1–9 ,
   Google Scholar
• He , C. , Wei , H. and Verdine , G. L. 2003 . Converting the sacrificial DNA repair protein N-Ada into a catalytic methylphosphotriester repair enzyme . J. Am. Chem. Soc. , 125 : 1450–1451
   Web of Science ®Google Scholar
• van Genderen , M.H.P. , van Hommerig , S.A.M. and Buck , H.M. 1990 . Loop formation in a DNA duplex by hybridization with a phosphate-methylated DNA oligomer. Implications for the use of the hybridization-arrest technique in Alzheimer's disease . Proc. Kon. Ned. Akad. van Wetensch. , 93 : 21–28
   Google Scholar
• Richmond , T. J. , Davey , R. and Davey , C. 2003 . The structure of DNA in the nucleosome core . Nature , 423 : 145–150
   Web of Science ®Google Scholar
• Wang , A.H.-J. , Quigley , G. J. , Kolpak , F. J. , van der Marel , G. , van Boom , J. H. and Rich , A. 1981 . Left-handed double helical DNA: Variations in the backbone conformation . Science , 211 : 171–176
   Web of Science ®Google Scholar
• Buck , H. M. 2005 . Different models for phosphate anion shielding in DNA duplexes: An elaboration with ab initio and molecular mechanics calculations . Int. J. Quantum Chem. , 103 : 308–313
   Web of Science ®Google Scholar
• Ray , S.G. , Cohen , H. , Naaman , R. and Rabin , Y. 2005 . Where is the sodium in self-assembled monolayers of single-stranded DNA? . J. Am. Chem. Soc. , 127 : 17138–17139
   Web of Science ®Google Scholar
• Shi , Y. , Lan , F. , Matson , C. , Mulligan , P. , Whetstine , J.R. , Cole , P.A. , Casero , R.A. and Shi , Y. 2004 . Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 . Cell , 119 : 941–953
   Web of Science ®Google Scholar
• Ferres-Marco , D. , Gutierrez-Garcia , I. , Vallejo , D. M. , Bolivar , J. , Gutierrez-Aviňe , F. J. and Dominguez , M. 2006 . Epigenetic silencers and Notch collaborate to promote malignant tumours by Rb silencing . Nature , 439 : 430–436
   Web of Science ®Google Scholar
• Tsukada , Y. , Fang , J. , Erdjument-Bromage , H. , Warren , M. E. , Borchers , C. H. , Tempst , P. and Zhang , Y. 2006 . Histone demethylation by a family of JmjC domain-containing proteins . Nature , 439 : 811–816
   Web of Science ®Google Scholar
• Viré , E. , Brenner , C. , Deplus , R. , Blanchon , L. , Fraga , M. , Didelot , C. , Morey , L. , van Eynde , A. , Bernard , D. , Vanderwinden , J.-M. , Bollen , M. , Esteller , M. , Di Croce , L. , de Launoit , Y. and Fuks , F. 2006 . The Polycomb group protein EZH2 directly controls DNA methylation . Nature , 439 : 871–874
   Web of Science ®Google Scholar
• van Lier , J.J.C. , Smits , M.T. and Buck , H.M. 1983 . B-Z Transition in methylated DNA. A quantum-chemical study . Eur. J. Biochem. , 132 : 55–62
   PubMedGoogle Scholar
• Sugiyama , H. , Kawai , K. , Matsunaga , A. , Fujimoto , K. , Saito , I. , Robinson , H. and Wang , H.-J. 1996 . Synthesis, structure and thermodynamic properties of 8-methyl-guanine-containing oligonucleotides: Z-DNA under physiological salt conditions . Nucleic Acids Res. , 24 : 1272–1279
   Web of Science ®Google Scholar
• Koole , L. H. , van Genderen , M. H.P. and Buck , H. M. 1987 . A parallel right-handed duplex of the hexamer d(TpTpTpTpTpT) with phosphate triester linkages . J. Am. Chem. Soc. , 109 : 3916–3921
   Web of Science ®Google Scholar
• Diaz , N. and Field , M.J. 2004 . Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations . J. Am. Chem. Soc. , 126 : 529–542
   Web of Science ®Google Scholar
• Cheng , Y. , Zhang , Y. and McCammon , J. A. 2005 . How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study . J. Am. Chem. Soc. , 127 : 1553 – 1562 .
   PubMed Web of Science ®Google Scholar
• Matteucci , M. D. and Caruthers , M. H. 1981 . Synthesis of deoxynucleotides on a polymer support . J. Am. Chem. Soc. , 103 : 3186–3191
   Web of Science ®Google Scholar
• McBride , L. J. , Kierzek , R. , Beaucage , S. L. and Caruthers , M. H. 1986 . Amidine protecting groups for oligonucleotide synthesis . J. Am. Chem. Soc. , 108 : 2040–2048
   Web of Science ®Google Scholar
• Koole , L. H. , Moody , H. M. , Broeders , N.L.H.L. , Quaedflieg , P.J.L.M. , Kuijpers , W. H.A. , van Genderen , M. H.P. , Coenen , A.J.J.M. , van der Wal , S. and Buck , H. M. 1989 . Synthesis of phosphate-methylated DNA fragments using 9-fluorenylmethoxy-carbonyl as transient base protecting group . J. Org. Chem. , 54 : 1657–1664
   Web of Science ®Google Scholar
• Sierzchala , A. B. , Dellinger , D. J. , Betley , J. R. , Wyrzykiewicz , T. K. , Yamada , C. M. and Caruthers , M. H. 2003 . Solid-phase oligodeoxynucleotide synthesis: a two-step cycle using peroxy anion deprotection . J. Am. Chem. Soc. , 125 : 13427–13441
   Web of Science ®Google Scholar