Skip to main content
SpringerLink
Log in

RNA Nanostructures in Physiological Solutions: Multiscale Modeling and Applications

  • Conference paper
  • First Online:
Physics of Liquid Matter: Modern Problems

Part of the book series: Springer Proceedings in Physics ((SPPHY,volume 171))

Abstract

In this review chapter we focus on the nucleic acid nanotechnology research and its application in the biomedical field. We also describe some of our most recent results on the modeling of ribonucleic acid (RNA ) nanotubes and their characteristics in physiological solution s. This includes the properties that can be characterised by root mean square deviation (RMSD ), radius of gyration and radial distribution function (RDF ) for the RNA nanocluster s, paying special attention to RNA nanotube s. We describe the distribution of \(^{23} {\text{Na}}^{ + }\) and \(^{35} {\text{Cl}}^{ - }\) ions around the tube as a function of time within a distance of 5 \({\AA}\) from the surface of the tube. The results obtained from our computational studies are compared with available experimental results in the literature. The current developments in the coarse grain modeling of the RNA nanoclusters and other biomolecules are also highlighted.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. A.A. Simpson, Y. Tao, P.G. Leiman, M.O. Badasso, Y. He, P.J. Jardine, N.H. Olson, M.C. Morais, S. Grimes, D.L. Anderson, T.S. Baker, M.G. Rossmann, Nature 408(6813), 745 (2000)

    Article  ADS  Google Scholar 

  2. D. Moll, C. Huber, B. Schlegel, D. Pum, U.B. Sleytr, M. Sra, PNAS 99(23), 14646 (2002)

    Article  ADS  Google Scholar 

  3. H. Cui, T. Muraoka, A.G. Cheetham, S.I. Stupp, Nano Lett. 9(3), 945 (2009)

    Article  ADS  Google Scholar 

  4. D. Liu, M. Wang, Z. Deng, R. Walulu, C. Mao, J. Am. Chem. Soc. 126(8), 2324 (2004)

    Article  Google Scholar 

  5. F.A. Aldaye, H.F. Sleiman, J. Am. Chem. Soc. 129(44), 13376 (2007)

    Article  Google Scholar 

  6. P.W.K. Rothemund, N. Papadakis, E. Winfree, PLoS Biol. 2(12), e424 (2004)

    Article  Google Scholar 

  7. S.H. Park, R. Barish, H. Li, J.H. Reif, G. Finkelstein, H. Yan, T.H. LaBean, Nano Lett. 5(4), 693 (2005)

    Article  ADS  Google Scholar 

  8. T.P.J. Knowles, T.W. Oppenheim, A.K. Buell, D.Y. Chirgadze, M.E. Welland, Nat. Nanotechnol. 5(3), 204 (2010)

    Article  ADS  Google Scholar 

  9. N.C. Seeman, Annu. Rev. Biochem. 79, 65 (2010)

    Article  Google Scholar 

  10. C. Lin, Y. Liu, H. Yan, Biochemistry 48(8), 1663 (2009)

    Article  Google Scholar 

  11. F.A. Aldaye, A.L. Palmer, H.F. Sleiman, Science 321(5897), 1795 (2008)

    Article  ADS  Google Scholar 

  12. K. Tanaka, A. Tengeiji, T. Kato, N. Toyama, M. Shionoya, Science 299(5610), 1212 (2003)

    Article  ADS  Google Scholar 

  13. M. Endo, T. Sugita, Y. Katsuda, K. Hidaka, H. Sugiyama, Chem. Eur. J. 16(18), 5362 (2010)

    Article  Google Scholar 

  14. Y. Ke, S. Lindsay, Y. Chang, Y. Liu, H. Yan, Science 319(5860), 180 (2008)

    Article  ADS  Google Scholar 

  15. B. Yurke, A.J. Turberfield, A.P. Mills, F.C. Simmel, J.L. Neumann, Nature 406(6796), 605 (2000)

    Article  ADS  Google Scholar 

  16. S.M. Douglas, J.J. Chou, W.M. Shih, PNAS 104(16), 6644 (2007)

    Article  ADS  Google Scholar 

  17. M. Endo, N.C. Seeman, T. Majima, Angew. Chem. Int. Ed. 44(37), 6074 (2005)

    Article  Google Scholar 

  18. N. Sugimoto, S.I. Nakano, M. Katoh, A. Matsumura, H. Nakamuta, T. Ohmichi, M. Yoneyama, M. Sasaki, Biochemistry 34(35), 11211 (1995)

    Article  Google Scholar 

  19. A. Kitamura, P.J. Jardine, D.L. Anderson, S. Grimes, H. Matsuo, Nucl. Acids Res. 36(3), 839 (2008)

    Article  Google Scholar 

  20. P. Guo, Nat. Nano. 5(12), 833 (2010)

    Article  Google Scholar 

  21. W.W. Grabow, L. Jaeger, Acc. Chem. Res. 47(6), 1871 (2014)

    Article  Google Scholar 

  22. M.S. Searle, D.H. Williams, Nucl. Acids Res. 21(9), 2051 (1993)

    Article  Google Scholar 

  23. K.A. Afonin, W. Kasprzak, E. Bindewald, P.S. Puppala, A.R. Diehl, K.T. Hall, T.J. Kim, M.T. Zimmermann, R.L. Jernigan, L. Jaeger, B.A. Shapiro, Methods 67(2), 256 (2014)

    Article  Google Scholar 

  24. J. Yang, R. Melnik, Discrete and continuous dynamical systems, supplement pp. 1052–1060 (2007)

    Google Scholar 

  25. X. Yang, R. Melnik, Comput. Biol. Chem. 31, 110 (2007)

    Article  MATH  Google Scholar 

  26. M. Anokhina, S. Bessonov, Z. Miao, E. Westhof, K. Hartmuth, R. Lührmann, EMBO J. 32(21), 2804 (2013)

    Article  Google Scholar 

  27. I. Severcan, C. Geary, E. Verzemnieks, A. Chworos, L. Jaeger, Nano Lett. 9(3), 1270 (2009)

    Article  ADS  Google Scholar 

  28. I. Severcan, C. Geary, A. Chworos, N. Voss, E. Jacovetty, L. Jaeger, Nat. Chem. 2(9), 772 (2010)

    Article  Google Scholar 

  29. E. Osada, Y. Suzuki, K. Hidaka, H. Ohno, H. Sugiyama, M. Endo, H. Saito, ACS Nano 8(8), 8130 (2014)

    Article  Google Scholar 

  30. L. Jaeger, A. Chworos, Curr. Opin. Struct. Biol. 16(4), 531 (2006)

    Article  Google Scholar 

  31. N.B. Leontis, E. Westhof, Science 345(6198), 732 (2014)

    Article  ADS  Google Scholar 

  32. J.I. Tomizawa, Cell 38(3), 861 (1984)

    Google Scholar 

  33. J.I. Tomizawa, Cell 47(1), 89 (1986)

    Article  Google Scholar 

  34. A.J. Lee, D.M. Crothers, Structure 6(8), 993 (1998)

    Article  Google Scholar 

  35. W.W. Grabow, P. Zakrevsky, K.A. Afonin, A. Chworos, B.A. Shapiro, L. Jaeger, Nano Lett. 11(2), 878 (2011)

    Article  ADS  Google Scholar 

  36. Y.G. Yingling, B.A. Shapiro, Nano Lett. 7(8), 2328 (2007)

    Article  ADS  Google Scholar 

  37. R.V.N. Melnik, X. Wei, G. MorenoHagelsieb, J. Biol. Syst. 17(03), 425 (2009)

    Article  MathSciNet  Google Scholar 

  38. K.A. Afonin, E. Bindewald, A.J. Yaghoubian, N. Voss, E. Jacovetty, B.A. Shapiro, L. Jaeger, Nat. Nanotechnol. 5(9), 676 (2010)

    Article  ADS  Google Scholar 

  39. N.B. Leontis, A. Lescoute, E. Westhof, Curr. Opin. Struct. Biol. 16(3), 279 (2006)

    Article  Google Scholar 

  40. D. Shu, Y. Shu, F. Haque, S. Abdelmawla, P. Guo, Nat. Nanotechnol. 6(10), 658 (2011)

    Article  ADS  Google Scholar 

  41. B. Cayrol, C. Nogues, A. Dawid, I. Sagi, P. Silberzan, H. Isambert, J. Am. Chem. Soc. 131(47), 17270 (2009)

    Article  Google Scholar 

  42. C.J. Delebecque, A.B. Lindner, P.A. Silver, F.A. Aldaye, Science 333(6041), 470 (2011)

    Article  ADS  Google Scholar 

  43. E. Bindewald, R. Hayes, Y.G. Yingling, W. Kasprzak, B.A. Shapiro, Nucleic Acid Res. 36(suppl 1), D392 (2008)

    Google Scholar 

  44. A. Fire, S. Xu, M.K. Montgomery, S.A. Kostas, S.E. Driver, C.C. Mello, Nature 391(6669), 806 (1998)

    Article  ADS  Google Scholar 

  45. C. Wagner, C. Ehresmann, B. Ehresmann, C. Brunel, J. Biol. Chem. 279(6), 4560 (2004)

    Article  Google Scholar 

  46. E. Laurenti, I. Barde, S. Verp, S. Offner, A. Wilson, S. Quenneville, M. Wiznerowicz, H.R. MacDonald, D. Trono, A. Trumpp, Stem Cells 28(8), 1390 (2010)

    Article  Google Scholar 

  47. K.Y. Chang, I. Tinoco, PNAS 91(18), 8705 (1994)

    Article  ADS  Google Scholar 

  48. S. Hoeprich, Q. Zhou, S. Guo, D. Shu, G. Qi, Y. Wang, P. Guo, Gene Ther. 10(15), 1258 (2003)

    Article  Google Scholar 

  49. L. Ponchon, G. Beauvais, S. Nonin-Lecomte, F. Dardel, Nat. Protocols 4(6), 947 (2009)

    Article  Google Scholar 

  50. C. Chen, S. Sheng, Z. Shao, P. Guo, J. Biol. Chem. 275(23), 17510 (2000)

    Article  Google Scholar 

  51. S.T. Stern, S.E. McNeil, Toxicol. Sci. 101(1), 4 (2008)

    Article  Google Scholar 

  52. S. Singh, A. Sharma, G.P. Robertson, Cancer Res. 72(22), 5663 (2012)

    Article  Google Scholar 

  53. Y. Shu, M. Cinier, S.R. Fox, N. Ben-Johnathan, P. Guo, Mol. Ther. 19(7), 1304 (2011)

    Article  Google Scholar 

  54. J.B. Lee, J. Hong, D.K. Bonner, Z. Poon, P.T. Hammond, Nat. Mater. 11(4), 316 (2012)

    Article  ADS  Google Scholar 

  55. J.B. Bramsen, J. Kjems, Front Genet. 3, 154 (2012)

    Article  Google Scholar 

  56. R. Kanasty, J.R. Dorkin, A. Vegas, D. Anderson, Nat. Mater. 12(11), 967 (2013)

    Article  ADS  Google Scholar 

  57. X.D. Yang, D.R. Mahapatra, R.V.N. Melnik, in AIP Conference Proceedings, vol. 952 (AIP Publishing, 2007), pp. 229–237

    Google Scholar 

  58. S. Guo, N. Tschammer, S. Mohammed, P. Guo, Hum. Gene Ther. 16(9), 1097 (2005)

    Article  Google Scholar 

  59. A. Khaled, S. Guo, F. Li, P. Guo, Nano Lett. 5(9), 1797 (2005)

    Article  ADS  Google Scholar 

  60. J. Yano, K. Hirabayashi, S.I. Nakagawa, T. Yamaguchi, M. Nogawa, I. Kashimori, H. Naito, H. Kitagawa, K. Ishiyama, T. Ohgi, T. Irimura, Clin. Cancer Res. 10(22), 7721 (2004)

    Article  Google Scholar 

  61. H. Li, W.X. Li, S.W. Ding, Science 296(5571), 1319 (2002)

    Article  ADS  Google Scholar 

  62. C. Zhang, Curr. Opin. Mol. Ther. 11(6), 641 (2009)

    Google Scholar 

  63. M.R. Fabian, N. Sonenberg, W. Filipowicz, Annu. Rev. Biochem. 79(1), 351 (2010)

    Article  Google Scholar 

  64. M. Paliy, R. Melnik, B.A. Shapiro, Phys. Biol. 6(4), 046003 (2009)

    Article  ADS  Google Scholar 

  65. S.R. Badu, R. Melnik, M. Paliy, S. Prabhakar, A. Sebetci, B.A. Shapiro, Eur. Biophys. J. 43(10–11), 555 (2014)

    Article  Google Scholar 

  66. T. Kim, B.A. Shapiro, J. Biomol. Struct. Dyn. 31(5), 495 (2013)

    Article  Google Scholar 

  67. J. Vieregg, W. Cheng, C. Bustamante, I. Tinoco, J. Am. Chem. Soc. 129(48), 14966–14973 (2007)

    Article  Google Scholar 

  68. M. Paliy, R. Melnik, B.A. Shapiro, Phys. Biol. 7(3), 036001 (2010)

    Article  ADS  Google Scholar 

  69. T. Hansson, C. Oostenbrink, W. van Gunsteren, Curr. Opin. Struct. Biol. 12(2), 190 (2002)

    Article  Google Scholar 

  70. W. van Gunsteren, D. Bakowies, R. Brgi, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, A. Glttli, T. Hansson, C. Oostenbrink, C. Peter, J. Pitera, L. Schuler, T. Soares, H. Yu, CHIMIA Int. J. Chem. 55(10), 856 (2001)

    Google Scholar 

  71. X. Wang, Y. Wang, L. Zheng, J. Chen, Curr. Med. Chem. 21(17), 1968 (2014)

    Article  Google Scholar 

  72. I.M. Moustafa, H. Shen, B. Morton, C.M. Colina, C.E. Cameron, J. Mol. Biol. 410(1), 159 (2011)

    Article  Google Scholar 

  73. N.J. Deng, P. Cieplak, Biophys. J. 98(4), 627 (2010)

    Article  Google Scholar 

  74. J.W. Chu, G.S. Ayton, S. Izvekov, G.A. Voth, Mol. Phys. 105(2–3), 167 (2007)

    Article  ADS  Google Scholar 

  75. J.W. Chu, S. Izveko, G.A. Voth, Mol. Simul. 32(3–4), 211 (2006)

    Article  Google Scholar 

  76. G.S. Ayton, W.G. Noid, G.A. Voth, Curr. Opin. Struct. Biol. 17(2), 192 (2007)

    Article  Google Scholar 

  77. J. Zhou, I.F. Thorpe, S. Izvekov, G.A. Voth, Biophys. J. 92(12), 4289 (2007)

    Article  ADS  Google Scholar 

  78. F. Ercolessi, J.B. Adams, Euro. Phys. Lett. 26(8), 583 (1994)

    Article  ADS  Google Scholar 

  79. M.S. Daw, M.I. Baskes, Phys. Rev. B 29, 6443 (1984)

    Article  ADS  Google Scholar 

  80. F. Ercolessi, E. Tosatti, M. Parrinello, Phys. Rev. Lett. 57, 719 (1986)

    Article  ADS  Google Scholar 

  81. G.S. Ayton, J.L. McWhirter, P. McMurtry, G.A. Voth, Biophys. J. 88(6), 3855 (2005)

    Article  Google Scholar 

  82. G.S. Ayton, G.A. Voth, Biophys. J. 87(5), 3299 (2004)

    Article  ADS  Google Scholar 

  83. G.S. Ayton, G.A. Voth, Int. J. Multiscale Comput. Eng. 2(2), 291 (2004)

    Article  Google Scholar 

  84. T.E. Ouldridge, A.A. Louis, J.P.K. Doye (2010)

    Google Scholar 

  85. F. Mathieu, S. Liao, J. Kopatsch, T. Wang, C. Mao, N.C. Seeman, Nano Lett. 5(4), 661 (2005)

    Article  ADS  Google Scholar 

  86. M. Bulacu, N. Goga, W. Zhao, G. Rossi, L. Monticelli, X. Periole, D.P. Tieleman, S.J. Marrink, J. Chem. Theory Comput. 9(8), 3282 (2013)

    Article  Google Scholar 

  87. I. Bahar, A. Rader, Curr. Opin. Struct. Biol. 15(5), 586 (2005)

    Article  Google Scholar 

  88. F. Tama, M. Valle, J. Frank, C.L. Brooks, PNAS 100(16), 9319 (2003)

    Article  ADS  Google Scholar 

  89. V. Tozzini, Curr. Opin. Struct. Biol. 15(2), 144 (2005)

    Article  Google Scholar 

  90. N. Hori, S. Takada, J. Chem. Theory Comput. 8(9), 3384 (2012)

    Article  Google Scholar 

  91. R. Das, D. Baker, PNAS 104(37), 14664 (2007)

    Article  ADS  Google Scholar 

  92. J. Bernauer, X. Huang, A.Y.L. Sim, M. Levitt, RNA 17(6), 1066 (2011)

    Article  Google Scholar 

  93. F. Ding, S. Sharma, P. Chalasani, V.V. Demidov, N.E. Broude, N.V. Dokholyan, RNA 14(6), 1164 (2008)

    Article  Google Scholar 

  94. J. Bida, R. Das, Curr. Opin. Struct. Biol. 22(4), 457 (2012)

    Article  Google Scholar 

  95. Z. Xia, D.P. Gardner, R.R. Gutell, P. Ren, J. Phys. Chem. B 114(42), 13497 (2010)

    Article  Google Scholar 

  96. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kal, K. Schulten, J. Comput. Chem. 26(16), 1781 (2005)

    Article  Google Scholar 

  97. D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wirkiewicz-Kuczera, D. Yin, M. Karplus, J. Phys. Chem. B 102(18), 3586 (1998)

    Article  Google Scholar 

  98. N. Foloppe, A.D. MacKerell Jr, J. Comput. Chem. 21(2), 86 (2000)

    Article  Google Scholar 

  99. A.D. MacKerell, N.K. Banavali, J. Comput. Chem. 21(2), 105 (2000)

    Article  Google Scholar 

  100. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 14(1), 33 (1996)

    Article  Google Scholar 

  101. S.R. Badu, R. Melnik, M. Paliy, S. Prabhakar, A. Sebetci, B.A. Shapiro, in Proceedings of IWBBIO-2014 (International Work-Conference on Bioinformatics and Biomedical Engineering, 2014), pp. 601–607

    Google Scholar 

  102. M. Zuker, Nucl. Acids Res. 31(13), 3406 (2003)

    Article  Google Scholar 

  103. N.R. Markham, M. Zuker, in Bioinformatics, ed. by J.M. Keith, no. 453 in Methods in Molecular Biology (Humana Press, 2008), pp. 3–31

    Google Scholar 

  104. Z. Bai, Appl. Numer. Math. 43(12), 9 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  105. P. Guo, O. Coban, N.M. Snead, J. Trebley, S. Hoeprich, S. Guo, Y. Shu, Adv. Drug Deliv. Rev. 62(6), 650 (2010)

    Article  Google Scholar 

Download references

Acknowledgments

Authors are grateful to the NSERC and CRC Programs for their support and Shared Hierarchical Academic Research Computing Network (SHARCNET: www.sharcnet.ca) for providing the computational facilities. Finally, we would like to thank Dr. P.J. Douglas Roberts for helping with technical SHARCNET computational aspects.

Author information

Authors and Affiliations

  1. MS2 Discovery Interdisciplinary Research Institute, M2NeT Laboratory, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada

    Shyam Badu, Roderick Melnik & Sanjay Prabhakar

Authors
  1. Shyam Badu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Roderick Melnik
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sanjay Prabhakar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Shyam Badu or Roderick Melnik .

Editor information

Editors and Affiliations

  1. Faculty of Physics, Taras Shevchenko National University, Kyiv, Ukraine

    Leonid Bulavin

  2. Head of Department of Physical Chemistry of Disperse Minerals, Biocolloidal Chemistry Institute, Kiev, Ukraine

    Nikolai Lebovka

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this paper

Cite this paper

Badu, S., Melnik, R., Prabhakar, S. (2015). RNA Nanostructures in Physiological Solutions: Multiscale Modeling and Applications. In: Bulavin, L., Lebovka, N. (eds) Physics of Liquid Matter: Modern Problems. Springer Proceedings in Physics, vol 171. Springer, Cham. https://doi.org/10.1007/978-3-319-20875-6_13

Download citation

Publish with us

Policies and ethics

Search

Navigation