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Modeling of RNA nanotubes using molecular dynamics simulation

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Abstract

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.

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References

  • Afonin KA, Bindewald E, Yaghoubian AJ, Voss N, Jacovetty E, Shapiro BA, Jaeger L (2010) In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat Nano 5(9):676–682. doi:10.1038/nnano.2010.160

    Article  CAS  Google Scholar 

  • Afonin KA, Kireeva M, Grabow WW, Kashlev M, Jaeger L, Shapiro BA (2012) Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs. Nano Lett 12(10):5192–5195

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Badu SR, Melnik R, Paliy M, Prabhakar S, Sebetci A, Shapiro BA (2014) High performance computing studies of RNA nanotubes. In: Proceedings of IWBBIO-2014

  • 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):22365–22370

  • Binder K, Horbach J, Kob W, Paul W, Varnik F (2004) Molecular dynamics simulations. J Phys Condens Matter 16(5):S429

    Article  CAS  Google Scholar 

  • Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the langevin piston method. J Chem Phys 103(11):4613–4621

    Article  CAS  Google Scholar 

  • Grabow WW, Zakrevsky P, Afonin KA, Chworos A, Shapiro BA, Jaeger L (2011) Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes. Nano Lett 11(2):878–887

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Guo P, Zhang C, Chen C, Garver K, Trottier M (1998) Inter-RNA interaction of phage 29 pRNA to form a hexameric complex for viral DNA transportation. Mol Cell 2(1):149–155

    Article  PubMed  CAS  Google Scholar 

  • Hansson T, Oostenbrink C, van Gunsteren W (2002) Molecular dynamics simulations. Curr Opin Struct Biol 12(2):190–196

    Article  PubMed  CAS  Google Scholar 

  • Holbrook SR (2005) RNA structure: the long and the short of it. Curr Opin Struct Biol 15(3):302–308

    Article  PubMed  CAS  Google Scholar 

  • Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38

    Article  PubMed  CAS  Google 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):651664

  • Jaeger L, Westhof E, Leontis NB (2001) TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucl Acids Res 29(2):455–463

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Kanasty R, Dorkin JR, Vegas A, Anderson D (2013) Delivery materials for siRNA therapeutics. Nat Mater 12(11):967–977

    Article  PubMed  CAS  Google 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):495–510

  • Lee AJ, Crothers DM (1998) The solution structure of an RNA looploop complex: the ColE1 inverted loop sequence. Structure 6(8):993–1007. doi:10.1016/S0969-2126(98)00101-4

    Article  PubMed  CAS  Google Scholar 

  • Lee JB, Hong J, Bonner DK, Poon Z, Hammond PT (2012) Self-assembled RNA interference microsponges for efficient siRNA delivery N Mater 11(4):316–322

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Leontis NB, Lescoute A, Westhof E (2006) The building blocks and motifs of RNA architecture. Curr Opin Struct Biol 16(3):279–287

    Article  PubMed  CAS  Google 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):3586–3616

  • Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101(5):4177–4189

    Article  CAS  Google 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):046003

  • Paliy M, Melnik R, Shapiro BA (2010) Coarse-graining RNA nanostructures for molecular dynamics simulations. Phys Biol 7(3):036001

  • Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kal L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781–1802

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Shu D, Shu Y, Haque F, Abdelmawla S, Guo P (2011) Thermodynamically stable RNA three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics. Nat Nano 6(10):658–667

    Article  CAS  Google Scholar 

  • Shu Y, Cinier M, Fox SR, Ben-Johnathan N, Guo P (2011) Assembly of therapeutic pRNA-siRNA nanoparticles using bipartite approach. Mol Ther 19(7):1304–1311

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Tomizawa JI (1984) Control of cole 1 plasmid replication: the process of binding of RNA I to the primer transcript. Cell 38(3):861–870

  • Tomizawa JI (1986) Control of ColE1 plasmid replication: binding of RNA I to RNA II and inhibition of primer formation. Cell 47(1):89–97

    Article  PubMed  CAS  Google 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):14966–14973

  • 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):7721–7726

  • Yingling YG, Shapiro BA (2007) Computational design of an RNA hexagonal nanoring and an RNA nanotube. Nano Lett 7(8):2328–2334

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

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.

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Authors and Affiliations

  1. MS2Discovery Interdisciplinary Research Institute, M2Net Lab, Wilfrid Laurier University, 75 University Avenue, Waterloo, ON, N3L 3V6, Canada

    S. R. Badu, R. Melnik & S. Prabhakar

  2. Department of Mechanical and Materials Engineering, Department of Chemistry, Surface Science Western, University of Western Ontario, London, Otario, N6A 5B9, Canada

    M. Paliy

  3. Department of Mechanical Engineering, Mevlana University, 42003, Konya, Turkey

    A. Sebetci

  4. Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD, 20892, USA

    B. A. Shapiro

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  1. S. R. Badu
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  2. R. Melnik
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  3. M. Paliy
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  4. S. Prabhakar
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  5. A. Sebetci
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  6. B. A. Shapiro
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Correspondence to S. R. Badu.

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Badu, S.R., Melnik, R., Paliy, M. et al. Modeling of RNA nanotubes using molecular dynamics simulation. Eur Biophys J 43, 555–564 (2014). https://doi.org/10.1007/s00249-014-0985-6

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  • DOI: https://doi.org/10.1007/s00249-014-0985-6

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