Modeling of RNA nanotubes using molecular dynamics simulation
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In this study, we construct novel RNA nanoclusters, RNA nanotubes made of several nanorings up to the size of 20 nm, utilizing the molecular dynamics simulation, and study their structural properties [i.e., the root mean square deviation, the radius of gyration and the radial distribution function (RDF)] in physiological solutions that can be used for drug delivery into the human body. The patterns of energy and temperature variations of the systems are also discussed. Furthermore, we study the concentration of ions around the tube as a function of time at a particular temperature. We have found that when the temperature increases, the number of ions increases within a certain distance of the tube. We report that the number of ions within this distance around the tubes decreases in quenched runs. This indicates that some ions evaporate with decrease in temperature, as has been observed in the case of the nanoring. RDF plots also demonstrate a similar trend with temperature, as was found in the case of RNA nanorings.
KeywordsRNA nanocluster Nanotube Drug delivery Cancer therapy Bionanotechnology
Authors are grateful to the NSERC and CRC Program for their support and Shared Hierarchical Academic Research Computing Network (SHARCNET: www.sharcnet.ca) for providing the computational facilities. RM and AS acknowledge TUBITAK support. Finally, we would like to thank Dr. P. J. Douglas Roberts for helping with technical SHARCNET computational aspects.
- Badu SR, Melnik R, Paliy M, Prabhakar S, Sebetci A, Shapiro BA (2014) High performance computing studies of RNA nanotubes. In: Proceedings of IWBBIO-2014Google Scholar
- Bailey S, Wichitwechkarn J, Johnson D, Reilly BE, Anderson DL, Bodley JW (1990) Phylogenetic analysis and secondary structure of the bacillus subtilis bacteriophage RNA required for DNA packaging. J Biol Chem 265(36):22365–22370Google Scholar
- Ishikawa J, Furuta H, Ikawa Y (2013) RNA tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. Wiley Interdisciplinary Reviews: RNA 4(6):651664Google Scholar
- Kim T, Shapiro BA (2013) The role of salt concentration and magnesium binding in HIV-1 subtype-a and subtype-b kissing loop monomer structures 31(5):495–510Google Scholar
- MacKerell BD, Bellott D, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wirkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102(18):3586–3616Google Scholar
- Paliy M, Melnik R, Shapiro BA (2009) Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization. Phys Biol 6(4):046003Google Scholar
- Paliy M, Melnik R, Shapiro BA (2010) Coarse-graining RNA nanostructures for molecular dynamics simulations. Phys Biol 7(3):036001Google Scholar
- Tomizawa JI (1984) Control of cole 1 plasmid replication: the process of binding of RNA I to the primer transcript. Cell 38(3):861–870Google Scholar
- Vieregg J, Cheng W, Bustamante C, Tinoco I (2007) Measurement of the effect of monovalent cations on RNA hairpin stability. J Am Chem Soc 129(48):14966–14973Google Scholar
- Yano J, Hirabayashi K, Nakagawa SI, Yamaguchi T, Nogawa M, Kashimori I, Naito H, Kitagawa H, Ishiyama K, Ohgi T, Irimura T (2004) Antitumor activity of small interfering RNA/cationic liposome complex in mouse models of cancer. Clin Cancer Res 10(22):7721–7726Google Scholar