At the moment, we see a great interest for application of Anti Sense Oligonucleotides (ASOs) in order to regulate the
expression of genes related to certain diseases. These nucleotides obtained a number
of fascinating properties by means of chemical manipulation of natural DNA and
RNA under conservation of Watson-Crick base-pairing. About 35 years ago for our
research in this field, we selected synthetically (short) phosphate-methylated DNA and RNA. It was concluded that there is an exclusive selection in
hybridization affinity with natural DNA and RNA. These (bio)chemical and
physical-chemical properties are extensively published. ASOs have found their way in public health as is clearly shown in the
treatment of (progressive) neurological diseases. We focus specifically
on the past, present and future of the phosphate-methylated
oligonucleotides, illustrated with different research studies in chemistry and biophysics. A new field of
application of modified DNAs is based on interactive improvements of
sensitivity and specificity of nanowire field effect transistor gene chip by
designing phosphate-methylated DNA as probe.
References
[1]
Van Genderen, M.H.P., Koole, L.H. and Buck, H.M. (1989) Hybridization of Phosphate-Methylated DNA and Natural Oligonucleotides. Implications for Protein-Induced DNA Duplex Stabilization. Recueil des Travaux Chimiques des Pays-Bas, 108, 28-32. https://doi.org/10.1002/recl.19891080106
[2]
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. Journal of the American Chemical Society, 109, 3916-3921.
https://doi.org/10.1021/ja00247a015
[3]
Ramakrishnan, B. (1988) Crystal and Molecular Structure of the Ammonium Salt of the Dinucleoside Monophosphate d(CPG). Journal of Biomolecular Structure and Dynamics, 6, 511-523. https://doi.org/10.1080/07391102.1988.10506504
[4]
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. https://doi.org/10.1126/science.7444458
[5]
Raiber, E.-A., Murat, P., Chirgadze, D.Y., Beraldi, D., Luisi, B.F. and Balasubramanian, S. (2015) 5-Formylcytosine Alters the Structure of the DNA Double Helix. Nature Structural & Molecular Biology, 22, 44-49. https://doi.org/10.1038/nsmb.2936
[6]
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. Implication of Phosphate Shielding for the Isomerization of B-DNA into Z-DNA. Recueil des Travaux Chimiques des Pays-Bas, 108, 421-423.
https://doi.org/10.1002/recl.19891081107
[7]
Batista-Duharte, A., Sendra, L., Herrero, M.J., Téllez-Martínez, D., Carlos, I.Z. and Salvador, F.A. (2020) Progress in the Use of Antisense Oligonucleotides for Vaccine Improvement. Biomolecules, 10, 316. https://doi.org/10.3390/biom10020316
[8]
Goudsmit, J., Geelen, J., Keulen, W., Notermans, D., Kuiken, C., Ramautarsing, C., Smit, L., Koole, L., van Genderen, M., Buck, H., Sninsky, J. and Krone, W. (1990) Characterization of the African HIV-1 Isolate CBL-4 (RUT) by Partial Sequence Analysis and Virus Neutralization with Peptide Antibody and Antisense Phosphate-Methylated DNA. AIDS, 4, 559-564.
https://doi.org/10.1097/00002030-199006000-00010
[9]
Buck, H.M., Koole, L.H., van Genderen, M.H.P., Smit, L., Geelen, J.L.M.C. and Goudsmit, J. (1990) Phosphate-Methylated DNA Aimed at HIV-1 RNA Loops and Integrated DNA Inhibits Viral Infectivity. Science, 248, 208-212.
https://doi.org/10.1126/science.2326635
[10]
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, 125-126.
https://doi.org/10.1126/science.2218505
[11]
Schulze-Gahmen, U. and Hurley, J.H. (2018) Structural Mechanism for HIV-1 TAR Loop Recognition by Tat and the Super Elongation Complex. Proceedings of the National Academy of Sciences of the United States of America, 115, 12973-12978.
https://doi.org/10.1073/pnas.1806438115
[12]
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 at Phosphorus. The Journal of Organic Chemistry, 55, 122-127.
https://doi.org/10.1021/jo00288a025
[13]
Van Genderen, M.H.P., Hilbers, Koole, L.H. and Buck, H.M. (1990) Peptide-Induced Parallel DNA Duplexes for Oligopyrimidines. Stereospecificity in Complexation for Oligo (L-lysine) and Oligo (L-ornithine). Biochemistry, 29, 7838-7845.
https://doi.org/10.1021/bi00486a009
[14]
Van Genderen, M.H.P., van der Heiden, A.P., Koole, L.H., van Genderen, M.H.P., Coenen, A.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 Prallel Right-Handed Duplex for SP r(CPU). Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen, 93, 33-38.
[15]
Buck, H.M. (2017) 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. Journal of Biophysical Chemistry, 7, 9-25.
[16]
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-Fluorenylme-thoxycarbonyl as Transient Base Protecting Group. The Journal of Organic Chemistry, 54, 1657-1664. https://doi.org/10.1021/jo00268a030
[17]
Buck, H.M. (1996) Phosphate-Methylated DNA: A Unique Oligonucleotide as with Other Modified DNAs. Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen, 99, 145-153.
[18]
Buck, H.M. (1997) The Impact of Chirality of Phosphorus in Methylphosphotriester DNA on Duplex Formation and Its Significance for Inducing Methylation-Resistance Genes. Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen, 100, 1-9.
[19]
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 Research, 17, 4769-4782. https://doi.org/10.1093/nar/17.12.4769
[20]
Song, W., Dominska, M., Greenwell, P.W. and Petes, T.D. (2014) Genome-Wide High Resolution Mapping of Chromosome Fragile Sites in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America, 111, E210-E2218. https://doi.org/10.1073/pnas.1406847111
[21]
Cohen, J. and Kaiser, J. (2019) Gates and NIH Join Forces on HIV and Sickle Cell Diseases. Science, 366, 558-559. https://doi.org/10.1126/science.366.6465.558-b
[22]
EP0358657B1 (1993) Poly(deoxyribonucleotides), Pharmaceutical Compositions, Use and Preparation of the Poly(deoxyribonucleotides).
[23]
Corey, D.R. (2017) Nusinersen, an Antisense Oligonucleotide Drug for Spiral Muscular Atrophy. Nature Neuroscience, 20, 479-499. https://doi.org/10.1038/nn.4508
[24]
Kagle, E. and Kawaguchi, K. (1997) Laboratory Detection and Rotational Rest Frequencies of NaSH. ApJ, 491, L129-L132. https://doi.org/10.1086/311069
[25]
Leavitt, B.R. and Tabrizi, S.J. (2020) Antisense Oligonucleotides for Neurodegeneration. Science, 367, 1428-1429. https://doi.org/10.1126/science.aba4624
[26]
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. Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen, 93, 21-28.
[27]
Hu, W.P., Tsai, C.C., Yang, Y.-S., Chan, H.W.-H. and Chen, W.-Y. (2018) Synergetic Improvements of Sensitivity and Specificity of Nanowire Field Effect Transistor Gene Chip by Designing Neutral DNA as Probe. Scientific Reports, 8, Article No. 12598. https://doi.org/10.1038/s41598-018-30996-4
[28]
Wölfe, R., Corman, V.M., Guggemos, W., Seilmaier, M., Zange, S., Müller, M.A., Niemeyer, D., Jones T.C., Vollmar, P., Rothe, C., Hoelscher, M., Bleicker, T., Brünink, S., Schneider, J., Ehmann, R., Zwirglmaier, K., Drosten, C. and Wendtner, C. (2020) Virological Assessment of Hospitalized Patients with COVID-2019. Nature.
https://doi.org/10.1038/s41586-020-2196-x
[29]
Chandel, A., Goyal, A.K., Ghosh, G. and Rath, G. (2019) Recent Advances in Aerosolised Drug Delivery. Biomedicine & Pharmacotherapy, 112, Article ID: 108601.
https://doi.org/10.1016/j.biopha.2019.108601
[30]
Li, T.-L., Wu, M.-W., Lin, W.-C., Lai, C.-H., Chang, Y.-H., Su, L.-J. and Chen, W.-Y. (2019) Designed Phosphate-Methylated Oligonucleotides as PCR Primers for SNP Discrimination. Analytical and Bioanalytical Chemistry, 411, 3871-3880.
https://doi.org/10.1007/s00216-019-01865-4
[31]
Paul, S., Roy, S., Monfregola, L., Shang, S., Shoemaker, R. and Caruthers, M.H. (2015) Oxidative Substitution of Boranephosphonate Diesters as a Route to Post-Synthetically Modified DNA. Journal of the American Chemical Society, 137, 3253-3264. https://doi.org/10.1021/ja511145h
[32]
Kuo, T.-C., Wu, M.-W., Lin, W.-C., Matulis, D., Yang, Y.-S., Li, S.-Y. and Chen, W.-Y. (2020) Reduction of Interstrand Charge Repulsion of DNA Duplexes by Salts and by Neutral Phosphotriesters. Contrary Effects for Harnessing Duplex Formation. Journal of the Taiwan Institute of Chemical Engineers.
https://doi.org/10.1016/j.jtice.2020.02.023
[33]
Tsubaki, K., Hammill, M.L., Varley, A.J., Kitamura, M., Okauchi, T. and Desaulniers, J.-P. (2020) Synthesis and Evaluation of Neutral Phosphate Triester Bacbone Modified SiRNAs. ACS Medicinal Chemistry Letters.
https://doi.org/10.1021/acsmedchemlett.0c00232
[34]
Buck, H.M. (2015) Retracted HIV Study Provides New Information about the Status of the in Vitro Inhibition of DNA Replication by Backbone Methylation. Journal of Biophysical Chemistry, 6, 29-34. https://doi.org/10.4236/jbpc.2015.61003
[35]
Arangundy-Franklin, S., Taylor, A.I., Porebski, B.T., Genna, V., Peak-Chew, S., Vaisman, A., Woodgate, R., Orozco, M. and Holliger, P. (2019) A Synthetic Genetic Polymer with an Uncharged Backbone Chemistry Based on Alkylphosphonate Nucleic Acids. Nature Chemistry, 11, 533-542.
