PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2013 | 1 | 1 |
Tytuł artykułu

Engineered RNA Nanodesigns for Applications in RNA Nanotechnology

Treść / Zawartość
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
Nucleic acids have emerged as an extremely promising platform for nanotechnological applications because of their unique biochemical properties and functions. RNA, in particular, is characterized by relatively high thermal stability, diverse structural flexibility, and its capacity to perform a variety of functions in nature. These properties make RNA a valuable platform for bio-nanotechnology, specifically RNA Nanotechnology, that can create de novo nanostructures with unique functionalities through the design, integration, and re-engineering of powerful mechanisms based on a variety of existing RNA structures and their fundamental biochemical properties. This review highlights the principles that underlie the rational design of RNA nanostructures, describes the main strategies used to construct self-assembling nanoparticles, and discusses the challenges and possibilities facing the application of RNA Nanotechnology in the future.
Wydawca
Rocznik
Tom
1
Numer
1
Opis fizyczny
Daty
otrzymano
2012-12-19
zaakceptowano
2013-04-18
online
2013-05-31
Twórcy
  • Center for Cancer Research Nanobiology
    Program, National Cancer Institute,
    Frederick, MD 21702, USA
  • Center for Cancer Research Nanobiology
    Program, National Cancer Institute,
    Frederick, MD 21702, USA
  • Center for Cancer Research Nanobiology
    Program, National Cancer Institute,
    Frederick, MD 21702, USA , shapirbr@mail.nih.gov
Bibliografia
  • Garibotti, A.V., Liao, S. & Seeman, N.C. A simple DNA-basedtranslation system. Nano letters 7, 480-483 (2007).[PubMed][Crossref]
  • Seeman, N.C. Structural DNA nanotechnology: an overview.Methods in molecular biology 303, 143-166 (2005).
  • Lin, C., Liu, Y. & Yan, H. Designer DNA nanoarchitectures.Biochemistry 48, 1663-1674 (2009).[Crossref][PubMed]
  • Seeman, N.C. Nanomaterials based on DNA. Annual reviewof biochemistry 79, 65-87 (2010).[Crossref]
  • Feldkamp, U. & Niemeyer, C.M. Rational design of DNAnanoarchitectures. Angewandte Chemie 45, 1856-1876 (2006).[Crossref]
  • Lin, C., Liu, Y., Rinker, S. & Yan, H. DNA tile basedself-assembly: building complex nanoarchitectures.Chemphyschem 7, 1641-1647 (2006).[Crossref][PubMed]
  • Chen, J.H. & Seeman, N.C. The electrophoretic properties ofa DNA cube and its substructure catenanes. Electrophoresis12, 607-611 (1991).[Crossref][PubMed]
  • Andersen, F.F. et al. Assembly and structural analysis of acovalently closed nano-scale DNA cage. Nucleic acidsresearch 36, 1113-1119 (2008).[Crossref]
  • Brucale, M. et al. Characterization and modulation of thehierarchical self-assembly of nanostructured DNA tiles intosupramolecular polymers. Organic & biomolecular chemistry4, 3427-3434 (2006).[PubMed]
  • Erben, C.M., Goodman, R.P. & Turberfield, A.J. A selfassembledDNA bipyramid. Journal of the AmericanChemical Society 129, 6992-6993 (2007).
  • Goodman, R.P. et al. Reconfigurable, braced, threedimensionalDNA nanostructures. Nature nanotechnology 3,93-96 (2008).[Crossref]
  • He, Y. et al. Hierarchical self-assembly of DNA into symmetricsupramolecular polyhedra. Nature 452, 198-201 (2008).
  • Licata, N.A. & Tkachenko, A.V. Self-assembling DNA-cagedparticles: nanoblocks for hierarchical self-assembly. Physicalreview 79, 011404 (2009).
  • Shih, W.M., Quispe, J.D. & Joyce, G.F. A 1.7-kilobase singlestrandedDNA that folds into a nanoscale octahedron. Nature427, 618-621 (2004).
  • Zhang, S. & Seeman, N.C. Symmetric Holliday junctioncrossover isomers. Journal of molecular biology 238, 658-668 (1994).
  • Zimmermann, J., Cebulla, M.P., Monninghoff, S. & vonKiedrowski, G. Self-assembly of a DNA dodecahedronfrom 20 trisoligonucleotides with C(3h) linkers. AngewandteChemie 47, 3626-3630 (2008).[Crossref]
  • Chen, J.H. & Seeman, N.C. Synthesis from DNA of amolecule with the connectivity of a cube. Nature 350, 631-633 (1991).
  • Aldaye, F.A., Palmer, A.L. & Sleiman, H.F. Assemblingmaterials with DNA as the guide. Science 321, 1795-1799(2008).
  • Erben, C.M., Goodman, R.P. & Turberfield, A.J. Singlemoleculeprotein encapsulation in a rigid DNA cage.Angewandte Chemie 45, 7414-7417 (2006).[Crossref]
  • Bhatia, D. et al. Icosahedral DNA nanocapsules by modularassembly. Angewandte Chemie (International ed 48, 4134-4137 (2009).[Crossref]
  • Yang, H. et al. Metal-nucleic acid cages. Nature chemistry 1,390-396 (2009).[PubMed][Crossref]
  • Lee, H. et al. Molecularly self-assembled nucleic acidnanoparticles for targeted in vivo siRNA delivery. Naturenanotechnology 7, 389-393 (2012).[Crossref][PubMed]
  • Rothemund, P.W. Folding DNA to create nanoscale shapesand patterns. Nature 440, 297-302 (2006).
  • Andersen, E.S. et al. DNA origami design of dolphin-shapedstructures with flexible tails. ACS nano 2, 1213-1218 (2008).[PubMed][Crossref]
  • Maune, H.T. et al. Self-assembly of carbon nanotubes intotwo-dimensional geometries using DNA origami templates.Nature nanotechnology 5, 61-66 (2010).[PubMed][Crossref]
  • Voigt, N.V. et al. Single-molecule chemical reactions on DNAorigami. Nature nanotechnology 5, 200-203 (2010).[PubMed][Crossref]
  • Pal, S., Deng, Z., Ding, B., Yan, H. & Liu, Y. DNA-origamidirectedself-assembly of discrete silver-nanoparticlearchitectures. Angewandte Chemie 49, 2700-2704 (2010).[Crossref]
  • Kuzuya, A. et al. Programmed nanopatterning of organic/inorganic nanoparticles using nanometer-scale wellsembedded in a DNA origami scaffold. Small 6, 2664-2667(2010).[Crossref]
  • Ke, Y. et al. Scaffolded DNA Origami of a DNA TetrahedronMolecular Container. Nano Lett (2009).[PubMed][Crossref]
  • Andersen, E.S. et al. Self-assembly of a nanoscale DNA boxwith a controllable lid. Nature 459, 73-76 (2009).
  • Zadegan, R.M. et al. Construction of a 4 ZeptolitersSwitchable 3D DNA Box Origami. ACS nano DOI: 10.1021/nn303767b (2012).[Crossref]
  • Douglas, S.M., Bachelet, I. & Church, G.M. A logic-gatednanorobot for targeted transport of molecular payloads.Science 335, 831-834 (2012).
  • Dietz, H., Douglas, S.M. & Shih, W.M. Folding DNA intotwisted and curved nanoscale shapes. Science 325, 725-730 (2009).
  • Liedl, T., Hogberg, B., Tytell, J., Ingber, D.E. & Shih, W.M.Self-assembly of three-dimensional prestressed tensegritystructures from DNA. Nature nanotechnology 5, 520-524(2010).[Crossref][PubMed]
  • Kuzyk, A. et al. DNA-based self-assembly of chiral plasmonicnanostructures with tailored optical response. Nature 483,311-314 (2012).
  • Elghanian, R., Storhoff, J.J., Mucic, R.C., Letsinger,R.L. & Mirkin, C.A. Selective colorimetric detection ofpolynucleotides based on the distance-dependent opticalproperties of gold nanoparticles. Science 277, 1078-1081(1997).
  • Mirkin, C.A., Letsinger, R.L., Mucic, R.C. & Storhoff,J.J. A DNA-based method for rationally assemblingnanoparticles into macroscopic materials. Nature 382,607-609 (1996).
  • Mirkin, C.A. Programming the assembly of two- and threedimensionalarchitectures with DNA and nanoscale inorganicbuilding blocks. Inorganic chemistry 39, 2258-2272 (2000).[Crossref]
  • Lin, C., Liu, Y. & Yan, H. Designer DNA Nanoarchitectures(dagger). Biochemistry (2009).[Crossref]
  • Douglas, S.M. et al. Self-assembly of DNA into nanoscalethree-dimensional shapes. Nature 459, 414-418 (2009).[Crossref][PubMed]
  • Pinheiro, A.V., Han, D., Shih, W.M. & Yan, H. Challenges andopportunities for structural DNA nanotechnology. Naturenanotechnology 6, 763-772 (2011).[Crossref][PubMed]
  • Guo, P. The emerging field of RNA nanotechnology. Naturenanotechnology 5, 833-842 (2010).[PubMed][Crossref]
  • Chworos, A. et al. Building programmable jigsaw puzzleswith RNA. Science (New York, N.Y 306, 2068-2072 (2004).
  • Westhof, E. & Massire, C. Structural biology. Evolution of RNAarchitecture. Science (New York, N.Y 306, 62-63 (2004).
  • Leontis, N.B., Lescoute, A. & Westhof, E. The building blocksand motifs of RNA architecture. Current opinion in structuralbiology 16, 279-287 (2006).[PubMed]
  • Leontis, N.B. & Westhof, E. Analysis of RNA motifs. Currentopinion in structural biology 13, 300-308 (2003).[PubMed]
  • Delebecque, C.J., Lindner, A.B., Silver, P.A. & Aldaye, F.A.Organization of intracellular reactions with rationally designedRNA assemblies. Science 333, 470-474 (2011).
  • Rodrigo, G., Landrain, T.E. & Jaramillo, A. De novo automateddesign of small RNA circuits for engineering syntheticriboregulation in living cells. Proceedings of the NationalAcademy of Sciences of the United States of America 109,15271-15276 (2012).
  • Gallivan, J.P. Toward reprogramming bacteria with smallmolecules and RNA. Current opinion in chemical biology 11,612-619 (2007).[PubMed]
  • Seshachar, B.R. & Dass, C.M. Evidence for the conversionof desoxyribonucleic acid (DNA) to ribonucleic acid (RNA) inEpistylis articulata From. (Ciliata: Peritricha). Experimental cellresearch 5, 248-250 (1953).[Crossref]
  • Dounce, A.L. Nucleic acid template hypotheses. Nature 172,541 (1953).
  • Geiduschek, E.P. & Haselkorn, R. Messenger RNA. Annualreview of biochemistry 38, 647-676 (1969).[Crossref]
  • Crick, F.H. The origin of the genetic code. Journal ofmolecular biology 38, 367-379 (1968).
  • Lacey, J.C., Jr. & Pruitt, K.M. Origin of the genetic code.Nature 223, 799-804 (1969).
  • Kruger, K. et al. Self-splicing RNA: autoexcision andautocyclization of the ribosomal RNA intervening sequenceof Tetrahymena. Cell 31, 147-157 (1982).[Crossref][PubMed]
  • Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. &Altman, S. The RNA moiety of ribonuclease P is the catalyticsubunit of the enzyme. Cell 35, 849-857 (1983).[Crossref]
  • Fire, A. et al. Potent and specific genetic interference bydouble-stranded RNA in Caenorhabditis elegans. Nature391, 806-811 (1998).[PubMed][Crossref]
  • Grabow, W.W. et al. RNA nanotechnology in nanomedicine.Nanomedicine and Drug Delivery 1, 208-221 (2012).
  • Jaeger, L. & Chworos, A. The architectonics of programmableRNA and DNA nanostructures. Current opinion in structuralbiology 16, 531-543 (2006).[PubMed]
  • Bramsen, J.B. & Kjems, J. Development of Therapeutic-Grade Small Interfering RNAs by Chemical Engineering.Frontiers in genetics 3, 154 (2012).[Crossref]
  • Krieg, A.M. Is RNAi dead? Mol Ther 19, 1001-1002 (2011).[Crossref][PubMed]
  • Chen, J. & Xie, J. Progress on RNAi-based molecularmedicines. International journal of nanomedicine 7, 3971-3980 (2012).[PubMed][Crossref]
  • Win, M.N. & Smolke, C.D. A modular and extensible RNAbasedgene-regulatory platform for engineering cellularfunction. Proceedings of the National Academy of Sciencesof the United States of America 104, 14283-14288 (2007).
  • Afonin, K.A., Danilov, E.O., Novikova, I.V. & Leontis,N.B. TokenRNA: a new type of sequence-specific, labelfreefluorescent biosensor for folded RNA molecules.Chembiochem 9, 1902-1905 (2008).[Crossref]
  • Stojanovic, M.N. & Kolpashchikov, D.M. Modular aptamericsensors. Journal of the American Chemical Society 126,9266-9270 (2004).
  • Pfleger, B.F., Pitera, D.J., Smolke, C.D. & Keasling, J.D.Combinatorial engineering of intergenic regions in operonstunes expression of multiple genes. Nature biotechnology 24,1027-1032 (2006).[Crossref][PubMed]
  • Callura, J.M., Dwyer, D.J., Isaacs, F.J., Cantor, C.R. & Collins,J.J. Tracking, tuning, and terminating microbial physiologyusing synthetic riboregulators. Proceedings of the NationalAcademy of Sciences of the United States of America 107,15898-15903 (2010).
  • Lucks, J.B., Qi, L., Mutalik, V.K., Wang, D. & Arkin, A.P. VersatileRNA-sensing transcriptional regulators for engineering geneticnetworks. Proceedings of the National Academy of Sciencesof the United States of America 108, 8617-8622 (2010).
  • Purnick, P.E. & Weiss, R. The second wave of syntheticbiology: from modules to systems. Nature reviews 10, 410-422 (2009).[Crossref]
  • Rinaudo, K. et al. A universal RNAi-based logic evaluator thatoperates in mammalian cells. Nature biotechnology 25, 795-801 (2007).[Crossref][PubMed]
  • Davis, J.H. et al. RNA helical packing in solution: NMRstructure of a 30 kDa GAAA tetraloop-receptor complex.Journal of molecular biology 351, 371-382 (2005).
  • Afonin, K.A. & Leontis, N.B. Generating new specific RNAinteraction interfaces using C-loops. Journal of the AmericanChemical Society 128, 16131-16137 (2006).
  • Yingling, Y.G. & Shapiro, B.A. Computational design of anRNA hexagonal nanoring and an RNA nanotube. Nano letters7, 2328-2334 (2007).[PubMed][Crossref]
  • Geary, C., Baudrey, S. & Jaeger, L. Comprehensive featuresof natural and in vitro selected GNRA tetraloop-bindingreceptors. Nucleic acids research 36, 1138-1152 (2008).[Crossref]
  • Geary, C., Chworos, A. & Jaeger, L. Promoting RNA helicalstacking via A-minor junctions. Nucleic acids research 39,1066-1080 (2011).[Crossref]
  • Shu, Y., Cinier, M., Shu, D. & Guo, P. Assembly ofmultifunctional phi29 pRNA nanoparticles for specific deliveryof siRNA and other therapeutics to targeted cells. Methods54, 204-214 (2011).[Crossref]
  • Afonin, K.A., Lin, Y.P., Calkins, E.R. & Jaeger, L. Attenuationof loop-receptor interactions with pseudoknot formation.Nucleic acids research 40, 2168-2180 (2012).[Crossref]
  • Grabow, W.W., Zhuang, Z., Swank, Z.N., Shea, J.E. &Jaeger, L. The Right Angle (RA) Motif: A Prevalent RibosomalRNA Structural Pattern Found in Group I Introns. Journal ofmolecular biology 424, 54-67 (2012).
  • Tuerk, C. & Gold, L. Systematic evolution of ligands byexponential enrichment: RNA ligands to bacteriophage T4DNA polymerase. Science (New York, N.Y 249, 505-510(1990).
  • Ellington, A.D. & Szostak, J.W. In vitro selection of RNAmolecules that bind specific ligands. Nature 346, 818-822(1990).
  • Afonin, K.A., Cieply, D.J. & Leontis, N.B. Specific RNA selfassemblywith minimal paranemic motifs. Journal of theAmerican Chemical Society 130, 93-102 (2008).
  • Breaker, R.R. Engineered allosteric ribozymes as biosensorcomponents. Current opinion in biotechnology 13, 31-39(2002).[PubMed]
  • Jaschke, A. Artificial ribozymes and deoxyribozymes. Currentopinion in structural biology 11, 321-326 (2001).[PubMed]
  • Nimjee, S.M., Rusconi, C.P. & Sullenger, B.A. Aptamers: anemerging class of therapeutics. Annual review of medicine56, 555-583 (2005).[Crossref]
  • Xiao, Z. & Farokhzad, O.C. Aptamer-functionalizednanoparticles for medical applications: challenges andopportunities. ACS nano 6, 3670-3676 (2012).[Crossref][PubMed]
  • Thiel, K.W. & Giangrande, P.H. Therapeutic applications ofDNA and RNA aptamers. Oligonucleotides 19, 209-222(2009).[PubMed][Crossref]
  • Tucker, B.J. & Breaker, R.R. Riboswitches as versatile genecontrol elements. Current opinion in structural biology 15,342-348 (2005).[PubMed]
  • Breaker, R.R. Prospects for riboswitch discovery andanalysis. Molecular cell 43, 867-879 (2011).[Crossref][PubMed]
  • Pecot, C.V., Calin, G.A., Coleman, R.L., Lopez-Berestein, G. & Sood, A.K. RNA interference in theclinic: challenges and future directions. Nat Rev Cancer11, 59-67 (2011).[PubMed][Crossref]
  • Petrocca, F. & Lieberman, J. Promise and challenge of RNAinterference-based therapy for cancer. J Clin Oncol 29, 747-754 (2011).[Crossref][PubMed]
  • Davis, M.E. et al. Evidence of RNAi in humans fromsystemically administered siRNA via targeted nanoparticles.Nature 464, 1067-1070 (2010).
  • Kim, D.H. et al. Synthetic dsRNA Dicer substrates enhanceRNAi potency and efficacy. Nature biotechnology 23, 222-226 (2005).[Crossref][PubMed]
  • Severcan, I. et al. A polyhedron made of tRNAs. Naturechemistry 2, 772-779 (2010).[PubMed][Crossref]
  • Bates, A.D. et al. Construction and characterization of a goldnanoparticle wire assembled using Mg2+-dependent RNARNAinteractions. Nano letters 6, 445-448 (2006).[Crossref]
  • Khaled, A., Guo, S., Li, F. & Guo, P. Controllable self-assemblyof nanoparticles for specific delivery of multiple therapeuticmolecules to cancer cells using RNA nanotechnology. Nanoletters 5, 1797-1808 (2005).[PubMed][Crossref]
  • Ohno, H. et al. Synthetic RNA-protein complex shaped likean equilateral triangle. Nature nanotechnology 6, 116-120(2011).[Crossref][PubMed]
  • Klein, D.J., Schmeing, T.M., Moore, P.B. & Steitz, T.A. Thekink-turn: a new RNA secondary structure motif. The EMBOjournal 20, 4214-4221 (2001).[PubMed][Crossref]
  • Severcan, I., Geary, C., Verzemnieks, E., Chworos, A. &Jaeger, L. Square-shaped RNA particles from different RNAfolds. Nano letters 9, 1270-1277 (2009).[Crossref][PubMed]
  • Lescoute, A. & Westhof, E. Topology of three-way junctionsin folded RNAs. RNA (New York, N.Y 12, 83-93 (2006).[Crossref]
  • Laing, C., Jung, S., Iqbal, A. & Schlick, T. Tertiary motifsrevealed in analyses of higher-order RNA junctions. Journalof molecular biology 393, 67-82 (2009).
  • Nasalean, L., Baudrey, S., Leontis, N.B. & Jaeger, L.Controlling RNA self-assembly to form filaments. Nucleicacids research 34, 1381-1392 (2006).[Crossref]
  • Afonin, K.A. et al. Co-transcriptional Assembly of ChemicallyModified RNA Nanoparticles Functionalized with siRNAs.Nano letters (2012).[Crossref][PubMed]
  • Grabow, W.W. et al. Self-assembling RNA nanorings basedon RNAI/II inverse kissing complexes. Nano letters 11, 878-887 (2011).[Crossref][PubMed]
  • Afonin, K.A. et al. In vitro assembly of cubic RNA-basedscaffolds designed in silico. Nature nanotechnology 5, 676-682 (2010).[Crossref][PubMed]
  • Dibrov, S.M., McLean, J., Parsons, J. & Hermann, T. SelfassemblingRNA square. Proceedings of the NationalAcademy of Sciences of the United States of America 108,6405-6408 (2011).
  • Afonin, K.A. et al. Self-assembly of functionalized RNAnanoparticles demonstrating potential advancements inautomated nanomedicine. Nat Protoc (2011).[Crossref]
  • Haque, F. et al. Ultrastable synergistic tetravalent RNAnanoparticles for targeting to cancers. Nano today 7, 245-257 (2012).[PubMed][Crossref]
  • Gugliotti, L.A., Feldheim, D.L. & Eaton, B.E. RNA-mediatedmetal-metal bond formation in the synthesis of hexagonalpalladium nanoparticles. Science 304, 850-852 (2004).
  • Petros, R.A. & DeSimone, J.M. Strategies in the design ofnanoparticles for therapeutic applications. Nat Rev DrugDiscov 9, 615-627 (2010).[PubMed][Crossref]
  • Shukla, G.C. et al. A Boost for the Emerging Field of RNANanotechnology. ACS nano 5, 3405-3418 (2011).[Crossref][PubMed]
  • Ferrari, M. Cancer nanotechnology: opportunities andchallenges. Nat Rev Cancer 5, 161-171 (2005).[Crossref][PubMed]
  • Farokhzad, O.C. & Langer, R. Impact of nanotechnology ondrug delivery. ACS nano 3, 16-20 (2009).[Crossref][PubMed]
  • Westhof, E., Masquida, B. & Jaeger, L. RNA tectonics:towards RNA design. Folding & design 1, R78-88 (1996).
  • Hansma, H.G., Oroudjev, E., Baudrey, S. & Jaeger, L.TectoRNA and ‘kissing-loop’ RNA: atomic force microscopyof self-assembling RNA structures. Journal of microscopy212, 273-279 (2003).
  • Jaeger, L., Westhof, E. & Leontis, N.B. TectoRNA: modularassembly units for the construction of RNA nano-objects.Nucleic acids research 29, 455-463 (2001).[Crossref]
  • Shu, D., Huang, L.P., Hoeprich, S. & Guo, P. Constructionof phi29 DNA-packaging RNA monomers, dimers, andtrimers with variable sizes and shapes as potential parts fornanodevices. Journal of nanoscience and nanotechnology 3,295-302 (2003).
  • Guo, S., Tschammer, N., Mohammed, S. & Guo, P.Specific delivery of therapeutic RNAs to cancer cells via thedimerization mechanism of phi29 motor pRNA. Human genetherapy 16, 1097-1109 (2005).[Crossref]
  • Hoeprich, S. & Guo, P. Computer modeling of threedimensionalstructure of DNA-packaging RNA (pRNA)monomer, dimer, and hexamer of Phi29 DNA packagingmotor. The Journal of biological chemistry 277, 20794-20803 (2002).
  • Simpson, A.A. et al. Structure of the bacteriophage phi29DNA packaging motor. Nature 408, 745-750 (2000).
  • Shu, D., Zhang, H., Jin, J. & Guo, P. Counting of six pRNAs ofphi29 DNA-packaging motor with customized single-moleculedual-view system. The EMBO journal 26, 527-537 (2007).[Crossref]
  • Guo, P., Haque, F., Hallahan, B., Reif, R. & Li, H. Uniqueness,advantages, challenges, solutions, and perspectives intherapeutics applying RNA nanotechnology. Nucleic acidtherapeutics 22, 226-245.[PubMed]
  • Cayrol, B. et al. A Nanostructure Made of a BacterialNoncoding RNA. Journal of the American Chemical Society131, 17270–17276 (2009).
  • Bindewald, E., Afonin, K., Jaeger, L. & Shapiro, B.A.Multistrand RNA secondary structure prediction andnanostructure design including pseudoknots. ACS nano 5,9542-9551 (2011).[PubMed][Crossref]
  • Bindewald, E., Grunewald, C., Boyle, B., O’Connor, M. &Shapiro, B.A. Computational strategies for the automateddesign of RNA nanoscale structures from building blocksusing NanoTiler. Journal of molecular graphics & modelling27, 299-308 (2008).
  • Shu, D., Shu, Y., Haque, F., Abdelmawla, S. & Guo, P.Thermodynamically stable RNA three-way junction forconstructing multifunctional nanoparticles for delivery oftherapeutics. Nature nanotechnology 6, 658-667 (2011).[PubMed][Crossref]
  • Bindewald, E., Hayes, R., Yingling, Y.G., Kasprzak, W. &Shapiro, B.A. RNAJunction: a database of RNA junctionsand kissing loops for three-dimensional structural analysisand nanodesign. Nucleic acids research 36, D392-397(2008).[Crossref]
  • Berman, H.M., Gelbin, A. & Westbrook, J. Nucleic acidcrystallography: a view from the nucleic acid database. Progress in biophysics and molecular biology 66, 255-288(1996).[PubMed]
  • Klosterman, P.S., Hendrix, D.K., Tamura, M., Holbrook, S.R.& Brenner, S.E. Three-dimensional motifs from the SCOR,structural classification of RNA database: extruded strands,base triples, tetraloops and U-turns. Nucleic acids research32, 2342-2352 (2004).[Crossref]
  • Tamura, M. et al. SCOR: Structural Classification of RNA,version 2.0. Nucleic acids research 32, D182-184 (2004).[Crossref]
  • Jossinet, F., Ludwig, T.E. & Westhof, E. Assemble: aninteractive graphical tool to analyze and build RNAarchitectures at the 2D and 3D levels. Bioinformatics (Oxford,England) 26, 2057-2059.
  • Martinez, H.M., Maizel, J.V., Jr. & Shapiro, B.A. RNA2D3D:a program for generating, viewing, and comparing3-dimensional models of RNA. Journal of biomolecularstructure & dynamics 25, 669-683 (2008).
  • Xia, Z., Gardner, D.P., Gutell, R.R. & Ren, P. Coarsegrainedmodel for simulation of RNA three-dimensionalstructures. The journal of physical chemistry 114, 13497-13506.
  • Pettersen, E.F. et al. UCSF Chimera--a visualization system forexploratory research and analysis. Journal of computationalchemistry 25, 1605-1612 (2004).
  • Grell, L., Parkin, C., Slatest, L. & Craig, P.A. EZ-Viz, a tool forsimplifying molecular viewing in PyMOL. Biochem Mol BiolEduc 34, 402-407 (2006).[PubMed][Crossref]
  • Kamaly, N., Xiao, Z., Valencia, P.M., Radovic-Moreno,A.F. & Farokhzad, O.C. Targeted polymeric therapeuticnanoparticles: design, development and clinical translation.Chemical Society reviews 41, 2971-3010.[PubMed][Crossref]
  • Bramsen, J.B. et al. Improved silencing properties usingsmall internally segmented interfering RNAs. Nucleic acidsresearch 35, 5886-5897 (2007).[Crossref]
  • Rose, S.D. et al. Functional polarity is introduced by Dicerprocessing of short substrate RNAs. Nucleic acids research33, 4140-4156 (2005).[Crossref]
  • Grimm, D. & Kay, M.A. Combinatorial RNAi: a winningstrategy for the race against evolving targets? Mol Ther 15,878-888 (2007).[PubMed]
  • Liu, Y.P. et al. Combinatorial RNAi against HIV-1 usingextended short hairpin RNAs. Mol Ther 17, 1712-1723(2009).[Crossref]
  • Mulhbacher, J., St-Pierre, P. & Lafontaine, D.A. Therapeuticapplications of ribozymes and riboswitches. Curr OpinPharmacol 10, 551-556 (2010).[PubMed][Crossref]
  • Win, M.N. & Smolke, C.D. Higher-order cellular informationprocessing with synthetic RNA devices. Science 322, 456-460 (2008).
  • McNamara, J.O., 2nd et al. Cell type-specific delivery ofsiRNAs with aptamer-siRNA chimeras. Nature biotechnology24, 1005-1015 (2006).[Crossref]
  • Zhou, J., Li, H., Li, S., Zaia, J. & Rossi, J.J. Novel dualinhibitory function aptamer-siRNA delivery system for HIV-1therapy. Mol Ther 16, 1481-1489 (2008).[Crossref]
  • Dassie, J.P. et al. Systemic administration of optimizedaptamer-siRNA chimeras promotes regression of PSMAexpressingtumors. Nature biotechnology 27, 839-849(2009).[Crossref][PubMed]
  • Topp, S. & Gallivan, J.P. Emerging applications of riboswitchesin chemical biology. ACS Chem Biol 5, 139-148 (2010).[Crossref][PubMed]
  • Gu, F. et al. Precise engineering of targeted nanoparticlesby using self-assembled biointegrated block copolymers.Proceedings of the National Academy of Sciences of theUnited States of America 105, 2586-2591 (2008).
  • Abe, N., Abe, H. & Ito, Y. Dumbbell-shaped nanocircularRNAs for RNA interference. Journal of the American ChemicalSociety 129, 15108-15109 (2007).
  • Afonin, K.A. et al. Activation of different split functionalities onre-association of RNA-DNA hybrids. Nature nanotechnology8, 296-304 (2013).[Crossref][PubMed]
  • Hoerter, J.A., Krishnan, V., Lionberger, T.A. & Walter, N.G.siRNA-like double-stranded RNAs are specifically protectedagainst degradation in human cell extract. PLoS One 6,e20359 (2011).[Crossref]
Typ dokumentu
Bibliografia
Identyfikatory
Identyfikator YADDA
bwmeta1.element.-psjd-doi-10_2478_rnan-2013-0001
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.