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European Biophysics Journal

, Volume 43, Issue 10–11, pp 555–564 | Cite as

Modeling of RNA nanotubes using molecular dynamics simulation

  • S. R. BaduEmail author
  • R. Melnik
  • M. Paliy
  • S. Prabhakar
  • A. Sebetci
  • B. A. Shapiro
ORIGINAL PAPER

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.

Keywords

RNA nanocluster Nanotube Drug delivery Cancer therapy Bionanotechnology 

Notes

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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Copyright information

© European Biophysical Societies' Association 2014

Authors and Affiliations

  • S. R. Badu
    • 1
    Email author
  • R. Melnik
    • 1
  • M. Paliy
    • 2
  • S. Prabhakar
    • 1
  • A. Sebetci
    • 3
  • B. A. Shapiro
    • 4
  1. 1.MS2Discovery Interdisciplinary Research Institute, M2Net LabWilfrid Laurier UniversityWaterlooCanada
  2. 2.Department of Mechanical and Materials Engineering, Department of Chemistry, Surface Science WesternUniversity of Western OntarioLondonCanada
  3. 3.Department of Mechanical EngineeringMevlana UniversityKonyaTurkey
  4. 4.Center for Cancer Research Nanobiology ProgramNational Cancer InstituteFrederickUSA

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