Poly(amidoamine)-based dendrimer/siRNA complexation studied by computer simulations: effects of pH and generation on dendrimer structure and siRNA binding.
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Sabrina Pricl | Paola Posocco | Erik Laurini | E. Laurini | S. Pricl | P. Posocco | K. Karatasos | Kostas Karatasos
[1] T. Rana,et al. Delivery of Therapeutic RNAi by Nanovehicles , 2009, Chembiochem : a European journal of chemical biology.
[2] J. Sommer,et al. Simulations of Dendrimers with Flexible Spacer Chains and Explicit Counterions under Low and Neutral pH Conditions , 2010 .
[3] Alexander D. MacKerell,et al. Development and current status of the CHARMM force field for nucleic acids , 2000, Biopolymers.
[4] A. Clarke,et al. Gene manipulation through the use of small interfering RNA (siRNA): from in vitro to in vivo applications. , 2007, Advanced drug delivery reviews.
[5] J. Fréchet,et al. Designing dendrimers for drug delivery. , 1999, Pharmaceutical science & technology today.
[6] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[7] J. Baker,et al. Efficient transfer of genetic material into mammalian cells using Starburst polyamidoamine dendrimers. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[8] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[9] R. Larson,et al. Molecular dynamics studies of the size, shape, and internal structure of 0% and 90% acetylated fifth-generation polyamidoamine dendrimers in water and methanol. , 2006, The journal of physical chemistry. B.
[10] K. Herwig,et al. Intramolecular structural change of PAMAM dendrimers in aqueous solutions revealed by small-angle neutron scattering. , 2010, The journal of physical chemistry. B.
[11] Kristina Fant,et al. DNA condensation by PAMAM dendrimers: self-assembly characteristics and effect on transcription. , 2008, Biochemistry.
[12] K. Karatasos,et al. Statics and dynamics of model dendrimers as studied by molecular dynamics simulations , 2001 .
[13] A. Schätzlein,et al. Dendrimers in gene delivery. , 2005, Advanced drug delivery reviews.
[14] I. Vattulainen,et al. Complexes Comprised of Charged Dendrimers, Linear Polyelectrolytes, and Counterions: Insight through Coarse-Grained Molecular Dynamics Simulations , 2008 .
[15] Maurizio Fermeglia,et al. Binding at the Core. Computational Study of Structural and Ligand Binding Properties of Naphthyridine-Based Dendrimers , 2007 .
[16] Ling Peng,et al. PAMAM Dendrimers Mediate siRNA Delivery to Target Hsp27 and Produce Potent Antiproliferative Effects on Prostate Cancer Cells , 2009, ChemMedChem.
[17] Gregory S Smith,et al. Structural investigation of PAMAM dendrimers in aqueous solutions using small-angle neutron scattering: effect of generation. , 2008, The journal of physical chemistry. B.
[18] F. Szoka,et al. Polyamidoamine cascade polymers mediate efficient transfection of cells in culture. , 1993, Bioconjugate chemistry.
[19] S. Kosmacheva,et al. Transfection efficiencies of PAMAM dendrimers correlate inversely with their hydrophobicity. , 2010, International journal of pharmaceutics.
[20] E. Meijer,et al. Encapsulation of Guest Molecules into a Dendritic Box , 1994, Science.
[21] K. Karatasos,et al. Molecular dynamics simulations of polyamidoamine dendrimers and their complexes with linear poly(ethylene oxide) at different pH conditions: static properties and hydrogen bonding. , 2009, Physical chemistry chemical physics : PCCP.
[22] K. Karatasos,et al. Local Dynamics and Hydrogen Bonding in Hyperbranched Aliphatic Polyesters , 2009 .
[23] Ling Peng,et al. PAMAM dendrimers for efficient siRNA delivery and potent gene silencing. , 2006, Chemical communications.
[24] Yu-qiang Ma,et al. Complexation of a Linear Polyelectrolyte with a Charged Dendrimer: Polyelectrolyte Stiffness Effects , 2010 .
[25] I. Andricioaei,et al. Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding. , 2008, The journal of physical chemistry. B.
[26] A. Wynveen,et al. The effects of pH, salt and bond stiffness on charged dendrimers , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.
[27] Sabrina Pricl,et al. Less is more – multiscale modelling of self-assembling multivalency and its impact on DNA binding and gene delivery , 2010 .
[28] Alexander D. MacKerell,et al. Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS. , 2006, Journal of chemical theory and computation.
[29] R. Zhuo,et al. Improving gene delivery efficiency of bioreducible poly(amidoamine)s via grafting with dendritic poly(amidoamine)s. , 2010, Macromolecular bioscience.
[30] Professor Dr. George A. Jeffrey,et al. Hydrogen Bonding in Biological Structures , 1991, Springer Berlin Heidelberg.
[31] F. Cavalieri,et al. Water and polymer dynamics in chemically cross-linked hydrogels of poly(vinyl alcohol): a molecular dynamics simulation study. , 2007, The journal of physical chemistry. B.
[32] B. Brooks,et al. Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .
[33] J. Baker,et al. The interaction of plasmid DNA with polyamidoamine dendrimers: mechanism of complex formation and analysis of alterations induced in nuclease sensitivity and transcriptional activity of the complexed DNA. , 1997, Biochimica et biophysica acta.
[34] K. Herwig,et al. Electrostatic Swelling and Conformational Variation Observed in High-Generation Polyelectrolyte Dendrimers , 2010 .
[35] Maurizio Fermeglia,et al. Computer-aided simulation of a dendrimer with a protoporphyrinic core as potential, novel hemoprotein mimic. , 2002, Bioorganic & medicinal chemistry.
[36] R. Juliano,et al. Tat-Conjugated PAMAM Dendrimers as Delivery Agents for Antisense and siRNA Oligonucleotides , 2005, Pharmaceutical Research.
[37] M. Fox,et al. Hydrogen bonding interactions between Starburst dendrimers and several molecules of biological interest , 1999 .
[38] R. Haag,et al. Dendritic Polyamines: Simple Access to New Materials with Defined Treelike Structures for Application in Nonviral Gene Delivery , 2004, Chembiochem : a European journal of chemical biology.
[39] E. Marshall. Gene Therapy on Trial , 2000, Science.
[40] T. Park,et al. Functional polymers for targeted delivery of nucleic acid drugs. , 2009, Macromolecular bioscience.
[41] Maurizio Fermeglia,et al. 550 POSTER Designing nanovectors for siRNA delivery: coupled experimental/modeling investigations , 2008 .
[42] Sean C. Smith,et al. Structure and dynamics of multiple cationic vectors-siRNA complexation by all-atomic molecular dynamics simulations. , 2010, The journal of physical chemistry. B.
[43] Alessandro Pedretti,et al. VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming , 2004, J. Comput. Aided Mol. Des..
[44] E. W. Meijer,et al. New Dendrimer–Peptide Host–Guest Complexes: Towards Dendrimers as Peptide Carriers , 2002, Chembiochem : a European journal of chemical biology.
[45] V. Ivanov,et al. Columnar mesophases of the complexes of DNA with low-generation poly(amido amine) dendrimers. , 2009, Biomacromolecules.
[46] S. Betigeri,et al. Surface-modified and internally cationic polyamidoamine dendrimers for efficient siRNA delivery. , 2008, Bioconjugate chemistry.
[47] Maurizio Fermeglia,et al. Polyamidoamine (Yet Not PAMAM) dendrimers as bioinspired materials for drug delivery: structure-activity relationships by molecular simulations. , 2004, Biomacromolecules.
[48] Eichman,et al. The use of PAMAM dendrimers in the efficient transfer of genetic material into cells. , 2000, Pharmaceutical science & technology today.
[49] Maurizio Fermeglia,et al. Scaling properties in the molecular structure of three-dimensional, nanosized phenylene-based dendrimers as studied by atomistic molecular dynamics simulations , 2003 .
[50] Dzmitry G. Shcharbin,et al. Dendrimers in gene transfection , 2009, Biochemistry (Moscow).
[51] Ling Peng,et al. Polycationic dendrimers interact with RNA molecules: polyamine dendrimers inhibit the catalytic activity of Candida ribozymes. , 2005, Chemical communications.
[52] L. Albertazzi,et al. Ability to adapt: different generations of PAMAM dendrimers show different behaviors in binding siRNA. , 2010, The journal of physical chemistry. B.
[53] Stephen P. Fox,et al. Delivery strategies for siRNA-mediated gene silencing. , 2006, Current drug delivery.
[54] I. Andricioaei,et al. Poly(amidoamine) dendrimers on lipid bilayers II: Effects of bilayer phase and dendrimer termination. , 2008, The journal of physical chemistry. B.
[55] J. Sommer,et al. Monte Carlo simulations of charged dendrimer-linear polyelectrolyte complexes and explicit counterions. , 2011, The Journal of chemical physics.
[56] D. Scherman,et al. A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[57] Sabrina Pricl,et al. Quantifying the effect of surface ligands on dendron-DNA interactions: insights into multivalency through a combined experimental and theoretical approach. , 2010, Chemistry.
[58] T Darden,et al. New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. , 1999, Structure.
[59] Richard Lavery,et al. Simulations of nucleic acids and their complexes. , 2002, Accounts of chemical research.
[60] J. Baker,et al. Regulation of in vitro gene expression using antisense oligonucleotides or antisense expression plasmids transfected using starburst PAMAM dendrimers. , 1996, Nucleic acids research.
[61] P. K. Maiti,et al. Complexation of siRNA with Dendrimer: A Molecular Modeling Approach , 2010 .
[62] K. Karatasos,et al. Association of a weakly acidic anti-inflammatory drug (ibuprofen) with a poly(amidoamine) dendrimer as studied by molecular dynamics simulations. , 2009, The journal of physical chemistry. B.
[63] M. D. Brown,et al. Gene delivery with synthetic (non viral) carriers. , 2001, International journal of pharmaceutics.
[64] P. Kollman,et al. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices , 1998 .
[65] George M Whitesides,et al. Polyvalent Interactions in Biological Systems: Implications for Design and Use of Multivalent Ligands and Inhibitors. , 1998, Angewandte Chemie.
[66] R. Ivkov,et al. Size Invariance of Polyelectrolyte Dendrimers , 2000 .
[67] Sean C. Smith,et al. Structure, dynamics, and energetics of siRNA-cationic vector complexation: a molecular dynamics study. , 2010, The journal of physical chemistry. B.
[68] Shuhua Bai,et al. Recent progress in dendrimer-based nanocarriers. , 2006, Critical reviews in therapeutic drug carrier systems.
[69] S. Pricl,et al. PAMAM dendrimers for siRNA delivery: computational and experimental insights. , 2010, Chemistry.
[70] K. Kataoka,et al. Bioinspired applications of functional dendrimers , 2005 .
[71] Andrea Danani,et al. Computational insights into the interactions between DNA and siRNA with "rigid" and "flexible" triazine dendrimers. , 2010, Biomacromolecules.
[72] S. Zimmerman,et al. Supramolecular Chemistry of Dendrimers , 2001 .
[73] J. Sommer,et al. Simulations of Terminally Charged Dendrimers with Flexible Spacer Chains and Explicit Counterions , 2010 .
[74] Christos N. Likos,et al. Conformations of high-generation dendritic polyelectrolytes , 2010 .
[75] Sabrina Pricl,et al. Modeling the multivalent recognition between dendritic molecules and DNA: understanding how ligand "sacrifice" and screening can enhance binding. , 2009, Journal of the American Chemical Society.
[76] J. Hughes,et al. Dendrimer Delivery of Oligonucleotides , 1996 .
[77] T. Tuschl,et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.
[78] Fabio Beltram,et al. Real-time measurement of endosomal acidification by a novel genetically encoded biosensor , 2009, Analytical and bioanalytical chemistry.
[79] Alexander D. MacKerell,et al. All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .
[80] Cheng-Cai Zhang,et al. Importance of size-to-charge ratio in construction of stable and uniform nanoscale RNA/dendrimer complexes. , 2007, Organic & biomolecular chemistry.
[81] I. Majoros,et al. Progress in cancer nanotechnology. , 2010, Progress in molecular biology and translational science.
[82] Y. Won,et al. Polymer-based siRNA delivery: perspectives on the fundamental and phenomenological distinctions from polymer-based DNA delivery. , 2007, Journal of controlled release : official journal of the Controlled Release Society.
[83] J. Baker,et al. DNA complexing with polyamidoamine dendrimers: implications for transfection. , 1999, Bioconjugate chemistry.
[84] Nicholas J. Turro,et al. Effect of Protonation and PAMAM Dendrimer Size on the Complexation and Dynamic Mobility of 2-Naphthol , 2000 .