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Number of results
2015 | 2 | 1 |

Article title

Structural identification of the novel
3 way-junction motif


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A novel RNA motif was identified based on its
sequence by computational structure modeling. The RNA
molecule was reported to be a substrate for the structurally
specific endoribonuclease, Dicer, which cleaves doublestranded
RNA and cuts out 20−25 nucleotide fragments.
This enzymatic property was essential for the potential
utilization of the motif in the nanoparticle design of
further biological experiments. Herein, the protocol for the
prediction of the structure of this motif in-silico is presented,
starting from its primary sequence and proceeding
through secondary and tertiary structure predictions.
Applying RNA architectonics, this novel structural motif,
3wj-nRA, was used for rational RNA nanoparticle design.
The molecules, which are based on this three-way junction
fold, may assemble into more complex, triangular shaped
nano-objects. This trimeric nanoparticle containing
3wj-nRA motif can be further utilized for functionalization
and application.







Physical description


18 - 12 - 2015
26 - 7 - 2015
30 - 9 - 2015



  • [1] Lu W, Lieber CM, Nanoelectronics from the bottom up. NatMater, 2007, 6, 841-850.[Crossref][WoS]
  • [2] Pautrat JL, Nanosciences: Evolution or revolution? ComptesRendus Physique, 2011 12, 605-613.[Crossref][WoS]
  • [3] Xie J, Lee S, Chen XY, Nanoparticle-based theranostic agents.Advanced Drug Delivery Reviews, 2010, 62, 1064-1079.[Crossref][WoS]
  • [4] Sakamoto JH, van de Ven AL, Godin B, Blanco E, Serda RE, etal., Enabling individualized therapy through nanotechnology.Pharmacological Research, 2010, 62, 57-89.[WoS][Crossref]
  • [5] Afonin KA, Bindewald E, Yaghoubian AJ, Voss N, Jacovetty E, etal., In vitro assembly of cubic RNA-based scaffolds designed insilico. Nat Nano, 2010, 5, 676-682.[Crossref]
  • [6] Vijayanathan V, Thomas T, Thomas TJ, DNA nanoparticlesand development of DNA delivery vehicles for gene therapy.Biochemistry, 2002, 41, 14085-14094.[Crossref]
  • [7] Bath J, Turberfield AJ, DNA nanomachines. Nat Nano, 2007, 2,275-284.[Crossref]
  • [8] Pinheiro AV, Han D, Shih WM, Yan H, Challenges andopportunities for structural DNA nanotechnology. Nat Nano,2011, 6, 763-772.[Crossref]
  • [9] Afonin KA, Lindsay B, Shapiro BA, Engineered RNANanodesigns for Applications in RNA Nanotechnology. DNA andRNA Nanotechnology, 2013, 1, 1-15.
  • [10] Guo P, The emerging field of RNA nanotechnology. Nat Nano,2010, 5, 833-842.[Crossref]
  • [11] Afonin KA, Viard M, Koyfman AY, Martins AN, Kasprzak WK, etal., Multifunctional RNA Nanoparticles. Nano Letters, 2014, 14,5662-5671.[Crossref][WoS]
  • [12] Shu Y, Pi FM, Sharma A, Rajabi M, Haque F, et al., Stable RNAnanoparticles as potential new generation drugs for cancertherapy. Advanced Drug Delivery Reviews, 2014, 66, 74-89.[Crossref][WoS]
  • [13] Dao BN, Viard M, Martins AN, Kasprzak WK, Shapiro BA, et al.,Triggering RNAi with multifunctional RNA nanoparticles andtheir delivery. DNA and RNA Nanotechnology, 2015, 2, 1-12.
  • [14] Miao ZC, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM,et al., RNA-Puzzles Round II: assessment of RNA structureprediction programs applied to three large RNA structures.RNA, 2015, 21, 1066-1084.[WoS][Crossref]
  • [15] Jaeger L, Westhof E, Leontis NB, TectoRNA: modular assemblyunits for the construction of RNA nano-objects. Nucleic AcidsRes, 2007, 29, 455-463.[Crossref]
  • [16] Chworos A, Severcan I, Koyfman AY, Weinkam P, Oroudjev E, etal., Building programmable jigsaw puzzles with RNA. Science,2004, 306, 2068-2072.
  • [17] Khaled A, Guo SC, Li F, Guo PX, Controllable self-assemblyof nanoparticles for specific delivery of multiple therapeuticmolecules to cancer cells using RNA nanotechnology. NanoLetters, 2005, 5, 1797-1808.[Crossref]
  • [18] Severcan I, Geary C, Verzemnieks E, Chworos A, Jaeger L,Square-shaped RNA particles from different RNA folds. NanoLett, 2009, 9, 1270-1277.[WoS][Crossref]
  • [19] Grabow WW, Zhuang ZY, Swank ZN, Shea JE, Jaeger L, The RightAngle (RA) Motif: A Prevalent Ribosomal RNA Structural PatternFound in Group I Introns. Journal of Molecular Biology, 2012,424, 54-67.[WoS]
  • [20] Jaeger L, Chworos A, The architectonics of programmableRNA and DNA nanostructures. Curr Opin Struct Biol, 2006, 16,531-543.[Crossref]
  • [21] Chworos A (2014) Rational Design of RNA Nanoparticles andNanoarrays. In: Wang B, editor. RNA Nanotechnology: PanStanford Publishing Pte. Ltd. pp. 213-234.[Crossref]
  • [22] Grabow WW, Jaeger L, RNA Self-Assembly and RNANanotechnology. Accounts of Chemical Research, 2014, 47,1871-1880.[Crossref]
  • [23] Afonin KA, Kasprzak WK, Bindewald E, Kireeva M, Viard M,et al., In Silico Design and Enzymatic Synthesis of FunctionalRNA Nanoparticles. Accounts of Chemical Research, 2014, 47,1731-1741.[Crossref][WoS]
  • [24] Bergeron LJ, Perreault JP, Abou Elela S, Short RNA duplexesguide sequence-dependent cleavage by human Dicer. Rna-aPublication of the Rna Society, 2010, 16, 2464-2473.[WoS][Crossref]
  • [25] Zuker M, Mfold web server for nucleic acid folding andhybridization prediction. Nucleic Acids Research, 2003, 31,3406-3415.[Crossref]

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