Structural insight into antisense gapmer-RNA oligomer duplexes through molecular dynamics simulations

References

• Aboul-Fadl, T. (2005). Antisense oligonucleotides: The state of the art. Current Medical Chemistry, 12, 2193–2214.
   PubMed Web of Science ®Google Scholar
• Aduri, R., Psciuk, B. T., Saro, P., Taniga, H., Schlegel, H. B., & SantaLucia, J. (2007). AMBER force-field parameters for the naturally occurring modified nucleosides in RNA. Journal of Chemical Theory and Computation. 3, 1464–1475.
   PubMed Web of Science ®Google Scholar
• Akdim, F. El., Harchaoui, K., Stroes, E. S., & Kastelein, J. J. (2007). Antisense apolipoprotein B-100 as novel treatment for hypercholesterolemia: focus on ISIS 301012. Future Lipidology. 2, 387–393.
   Web of Science ®Google Scholar
• Auffinger, P., & Westhof, E. (2000). Water and ion binding around RNA and DNA (C,G) oligomers. Journal of Molecular Biology, 300, 1113–1131.
   PubMed Web of Science ®Google Scholar
• Auffinger, P., & Westhof, E. (2001). Water and ion binding around r(UpA)12 and d(TpA)12 oligomers-comparison with RNA and DNA (CpG)12 duplexes. Journal of Molecular Biology, 305, 1057–1072.
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., Postma, J. V., van Gunsteren, W. F., DiNolam, ARHJ, & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81, 3684–3690.
   Web of Science ®Google Scholar
• Bondensgaard, K., Petersen, M., Singh, S. K., Rajwanshi, V. K., Kumar, R., Wengel, J., & Jacobsen, J. P. (2000). Structural studies of LNA:RNA duplexes by NMR: conformations and implications for RNase H activity. Chemistry, 6, 2687–2695.
   PubMed Web of Science ®Google Scholar
• Campbell, J. M., Bacon, T. A., & Wickstrom, E. (1990). Oligodeoxynucleoside phosphorothioate stability in subcellular extracts, culture media, sera and cerebrospinal fluid. Journal of Biochemical and Biophysical Methods, 20, 259–267.
   PubMedGoogle Scholar
• Case, D. A., Darden, T. A., Cheatham III, T. E., Simmerling, C. L., Wang, J, Duke, R. E., … Kollman, P. A. (2012). AMBER 12, San Francisco; University of California.
   Google Scholar
• Chan, H. P., Lim, S., & Wong, W. S. (2006). Antisense oligonucleotides: From design to therapeutic application. Clinical and. Experimental Pharmacology and. Physiology, 33, 533–540.
   PubMed Web of Science ®Google Scholar
• Cheatham, T. E., & Kollman, P. A. (1997). Molecular dynamics simulations highlight the structural differences among DNA: DNA, RNA: RNA, and DNA: RNA hybrid duplexes. Journal of the American Chemical Society, 119, 4805–4825.
   Web of Science ®Google Scholar
• Chen, X., Dudgeon, N., Shen, L., & Wang, J. H. (2005). Chemical modification of gene silencing oligonucleotides for drug discovery and development. Drug Discovery Today, 10, 587–593.
   PubMed Web of Science ®Google Scholar
• Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K.M., Ferguson, D. M., … Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of American Chemical Society 117, 5179–5197.
   Web of Science ®Google Scholar
• Crooke, R. M., Graham, M. J., Lemonidis, K. M., Whipple, C. P., Koo, S., & Perera, R. J. (2005). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Lipid Research, 46, 872–884.
   PubMed Web of Science ®Google Scholar
• Crooke, S. T. (2007). Antisense drug technology: Principles, strategies and applications, 2nd ed., Boca Raton, FL: CRC Press, p 799.
   Google Scholar
• Crouch, R. J., & Dirksen, M. L. (1982). Ribonuclease H. In S.M. Linn & R.J. Roberts (Eds.), Nucleaes (pp. 211–241). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory,.
   Google Scholar
• Declercq, R., Aerschot, A. V., Read, R J., Herdewijn, P., & Meervelt, L. V. (2002). Crystal structure of double helical hexitol nucleic acids. Journal of American Chemical Society, 124, 928–933.
   PubMed Web of Science ®Google Scholar
• Elayadi, A. N., & Corey, D. R. (2001). Application of PNA and LNA oligomers to chemotherapy. Current Opinion in Investigational Drugs, 2, 1057–1561.
   Google Scholar
• Foloppe, N., & Nilsson, L. (2005). Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides. Journal of Physical Chemistry B, 109, 9119–9131.
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Millam, J. M. (2003). Gaussian 03, revision B. 03. Pittsburgh, PA: Gaussian Inc.
   Google Scholar
• Gaillard, T., & Simonson, T. (2017). Full protein sequence redesign with an MMGBSA energy function. Journal of Chemical Theory and Computation. doi: 10.1021/acs.jctc.7b00202.
   PubMed Web of Science ®Google Scholar
• Galderisi, U., Cascino, A., & Giordano, A. (1999). Antisense oligonucleotides as therapeutic agents. Journal of Cellular Physiology. 181, 251–257.
   PubMed Web of Science ®Google Scholar
• Hair, P., Cameron, F., & McKeage, K. (2013). Mipomersen sodium: first global approval. Drugs, 73, 487–493.
   PubMed Web of Science ®Google Scholar
• Harikrishna, S., & Pradeepkumar, P. I. (2017). Probing the binding interactions between chemically modified siRNAs and human argonaute 2 using microsecond molecular dynamics simulations. Journal of Chemical Information and Modeling, 57(4), 883–896.
   PubMed Web of Science ®Google Scholar
• Hehre, W. J., Ditchfield, R., & Pople, J. A. (1972). Self consistent molecular orbital methods.12. further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecules. Journal of Chemical Physics, 56, 2257–2261.
   Web of Science ®Google Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712–725.
   PubMed Web of Science ®Google Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82.
   PubMed Web of Science ®Google Scholar
• Hubbard, S. J., & Thornton, J. M. (1993). Naccess. Computer Program. London: Department of Biochemistry and Molecular Biology, University College London.
   Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of Molecular Graphics, 14, 33–38.
   PubMed Web of Science ®Google Scholar
• Hyrup, B., & Nielson, P. E, (1996). Peptide nucleic acids (PNA): Syntheis, properties and potential applications. Bioorganic and Medicinal Chemistry, 4, 5–23.
   PubMed Web of Science ®Google Scholar
• Jens, K. (2003). Antisense technologies: Improvement through novel chemical modifications. European Journal of Biochemistry, 270, 1628–1644.
   PubMedGoogle Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926–935.
   Web of Science ®Google Scholar
• Kastelein, J. J., Wedel, M. K., Baker, B. F., Su, J., Bradely, J. D., Yu, R. Z., … Crooke, R. M. (2006). Potent reduction of apolipoprotein B and low-density lipoprotein cholesterol by short-term administration of an antisense inhibitor of apolipoprotein B. Circulation. 114, 1729–1735.
   PubMed Web of Science ®Google Scholar
• Koulgi, S., Achalere, A., Sharma, N., Sonavane, U., & Joshi, R. (2013). QM-MM simulations on p53-DNA complex: a study of hot spot and rescue mutants. Journal of Molecular Modeling, 19(12), 5545–5559.
   PubMed Web of Science ®Google Scholar
• Lavery, R., & Sklenar, H. (1988). The definition of generalized helicoidal parameters and of axis curvature for irregular nucleicacids. Journal of Biomolecular Structure and Dynamics, 6, 63–91.
   PubMed Web of Science ®Google Scholar
• Le Calvez, H., Yu, M., & Fang, F. (2004). Biochemical prevention and treatment of viral infections - a new paradigm in medicine for infectious diseases. Virology Journal, 1, 12–12.
   Web of Science ®Google Scholar
• Lu, X. J., & Olson, W. K. (2008). 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature Protocols, 3, 1213–1227.
   PubMed Web of Science ®Google Scholar
• Manoharan, M. (1999). 2’-carbohydrate modifications in antisense oligonucleotide therapy: Importance of conformation, configuration and conjugation. Biochimica et Bhiophysica Acta (BBA) – Gene Structure and Expression, 1489, 117–130.
   PubMed Web of Science ®Google Scholar
• Monia, B. P., Lesnik, E. A., Gonzalez, C., Lima, W. F., McGee, D., Guinosso, C. J., … Freier, S. M. (1993). Evaluation of 2'-modified oligonucleotides containing 2'-deoxy gaps as antisense inhibitors of gene expression. Journal of Biological Chemistry, 268, 14514–14522.
   PubMed Web of Science ®Google Scholar
• Mukherjee, S., & Bhattacharyya, D. (2004). Effect of Phosphorothioate chirality on the grooves of DNA double helices: a molecular dynamics study. Biopolymers, 73, 69–82.
   PubMed Web of Science ®Google Scholar
• Nielsen, K. E., Rasmussen, J., Kumar, R., Wengel, J., Jacobsen, J. P., & Petersen, M. (2004). NMR studies of fully modified locked nucleic acid (LNA) hybrids: solution structure of an LNA: RNA hybrid and characterization of an LNA: DNA hybrid. Bioconjugate. Chemistry, 15, 449–457.
   PubMed Web of Science ®Google Scholar
• Nielsen, K. E., Singh, S. K., Wengel, J., & Jacobsen, J. P. (2000). Solution structure of an LNA hybridized to DNA: NMR study of the d(CT(L)GCT(L)T(L)CT(L)GC): d(GCAGAAGCAG) duplex containing four locked nucleotides. Bioconjugate Chemistry, 11, 228–238.
   PubMed Web of Science ®Google Scholar
• Norberg, J., & Nilsson, L, (2002). Molecular dynamics applied to nucleic acids. Accounts of Chemical Research, 35, 465–472.
   PubMed Web of Science ®Google Scholar
• Noy, A., Perez, A., Marquez, M., Luque, F. J., & Orozco, M. (2005). Structure, recognition properties, and flexibility of the DNA.RNA hybrid. Journal of American Chemical Society, 127, 4910–4920.
   PubMed Web of Science ®Google Scholar
• Pande, V., & Nilsson, L. (2008). Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Acids Research. 36, 1508–1516.
   PubMed Web of Science ®Google Scholar
• Pensato, S., Saviano, M., & Romanelli, A. (2007). New peptide nucleic acid analogues: Synthesis and applications. Expert Opinion on Biological Therapy 7, 1219–1232.
   PubMed Web of Science ®Google Scholar
• Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T. E., 3rd, Laughton, C. A., & Orozco, M., (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers, Biophysical Journal, 92(11), 3817–3829.
   PubMed Web of Science ®Google Scholar
• Petersen, M., Bondensgaard, K., Wengel, J., & Jacobsen, J. P. (2002). Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids. Journal of American Chemical Society, 124, 5974–5982.
   PubMed Web of Science ®Google Scholar
• Pullman, B., & Pullman, A. (1974). Molecular orbital calculations on the conformation of amino acid residues of proteins. Advanced Protein Chemistry, 16, 12–526.
   Google Scholar
• Pullman, B., & Saran, A. (1976). Quantum-mechanical studies on the conformation of nucleic acids and their constituents. Progress in Nucleic Acid Research and Molecular Biology 18, 215–322.
   PubMedGoogle Scholar
• Ricotta, D. N., & Frishman, W. (2012). Mipomersen: a safe and effective antisense therapy adjunct to statins in patients with hypercholesterolemia. Cardiology in Review, 20, 90–95.
   PubMed Web of Science ®Google Scholar
• Roehr, B. (1998). Fomivirsen approved for CMV retinitis. Journal of International Association of Physicians in AIDS Care , 4(10), 14514.
   Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.
   Web of Science ®Google Scholar
• Saenger, W., Hunter, W. N., & Kennard, O. (1986). DNA conformation is determined by economics in the hydration of phosphate groups. Nature, 324, 385–388.
   PubMed Web of Science ®Google Scholar
• Sen, S., & Nilsson, L. (1998). Molecular dynamics of duplex systems involving PNA: structural and dynamical consequences of the nucleic acid backbone. Journal of American Chemical Society, 120, 619–631.
   Web of Science ®Google Scholar
• Sen, S., & Nilsson, L. (2001). MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics. Journal of American Chemical Society, 123, 7414–7422.
   PubMed Web of Science ®Google Scholar
• Seth, P. P., Siwkowski, A., Allerson, C. R., Vasquez, G., Lee, S., Prakash, T. P., … Swayze, E. E. (2009). Short antisense oligonucleotides with novel 2’-4’ conformationaly restricted nucleoside analogues show improved potency without increased toxicity in animals. Journal of Medicinal Chemistry, 52, 4910–4913.
   Web of Science ®Google Scholar
• Sharma, S., Sonavane, U. B., & Joshi, R. R. (2009). Quantum chemical studies of peptide nucleic acid monomers and role of cyclohexyl modification on backbone flexibility. International Journal of Quantum Chemistry, 109, 890–896.
   Web of Science ®Google Scholar
• Soliva, R., Sherer, E., Luque, F. J., Laughton, C. A., & Orozco, M. (2000). Molecular dynamics simulations of PNA center dot DNA and PNA center dot RNA duplexes in aqueous solution. Journal of American Chemical Society, 122, 1219–6008.
   Web of Science ®Google Scholar
• Stein, C. A., Hansen, J. B., Lai, J., Wu, S., Voskresenskiy, A., Hog, A., … Soifer, H. S. (2010). Efficient gene silencing by delivery of locked nucleic acid antisense oligonucleotides, unassisted by transfection reagents. Nucleic Acids Research, 38, e3–e3.
   PubMed Web of Science ®Google Scholar
• Suresh, G., & Priyakumar, U. D. (2013). Structures, dynamics, and stabilities of fully modified locked nucleic acid (β-d-LNA and α-l-LNA) duplexes in comparison to pure DNA and RNA duplexes. Journal of Physical Chemistry B. 117, 5556–5564.
   PubMed Web of Science ®Google Scholar
• Uppuladinne, M. V., Jani, V., Sonavane, U. B., & Joshi, R. R. (2013). Quantum chemical studies of novel 2'-4' conformationally restricted antisense monomers. International Journal of Quantum Chemistry, 113, 2523–2533
   Web of Science ®Google Scholar
• Veedu, R. N., & Wengel, J. (2009). Locked nucleic acid as a novel class of therapeutic agents. RNA Biology, 6, 321–333.
   PubMed Web of Science ®Google Scholar
• Westhof, E. (1988). Water: an integral part of nucleic acid structure. Annual Review of Biophysics and Biophysical Chemistry, 17, 125–144.
   PubMedGoogle Scholar
• York, D. M., Darden, T. A., & Pedersen, L. G. (1993). The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. The Journal of Chemical Physics, 99, 14–8348.
   Web of Science ®Google Scholar
• Zamecnik, P. C., & Stephenson, M. L. (1978). Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proceedings of. National Academy of Science U.S.A., 75, 280–284.
   PubMed Web of Science ®Google Scholar