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The mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model

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References

  • Novina CD, Sharp PA. The RNAi revolution. Nature. 2004;430:161–164.10.1038/430161a
  • Scherer LJ, Rossi JJ. Approaches for the sequence-specific knockdown of mRNA. Nat Biotechnol. 2003;21:1457–1465.10.1038/nbt915
  • Hannon GJ. RNA interference. Nature. 2002;418:244–251.10.1038/418244a
  • Dykxhoorn DM, Novina CD, Sharp PA. Killing the messenger: short rnas that silence gene expression. Nat Rev Mol Cell Biol. 2003;4:457–467.10.1038/nrm1129
  • Bitko V, Musiyenko A, Shulyayeva O, et al. Inhibition of respiratory viruses by nasally administered siRNA. Nat Med. 2005;11:50–55.10.1038/nm1164
  • Schiffelers RM, Ansari A, Xu J, et al. Cancer siRNA therapy by tumor selective delivery with ligand-targeted sterically stabilized nanoparticle. Nucleic Acids Res. 2004;32:e149-e.
  • Whitehead KA, Langer R, Anderson DG. Knocking down barriers: advances in siRNA delivery. Nat Rev Drug Discovery. 2009;8:129–138.10.1038/nrd2742
  • Barquinero J, Eixarch H, Perez-Melgosa M. Retroviral vectors: new applications for an old tool. Gene Ther. 2004;11:S3–S9.10.1038/sj.gt.3302363
  • Grayson ACR, Doody AM, Putnam D. Biophysical and structural characterization of polyethylenimine-mediated sirna delivery in vitro. Pharm Res. 2006;23:1868–1876.10.1007/s11095-006-9009-2
  • Lee SH, Kim SH, Park TG. Intracellular siRNA delivery system using polyelectrolyte complex micelles prepared from VEGF siRNA-PEG conjugate and cationic fusogenic peptide. Biochem Biophys Res Commun. 2007;357:511–516.10.1016/j.bbrc.2007.03.185
  • Katas H, Alpar HO. Development and characterisation of chitosan nanoparticles for siRNA delivery. J Controlled Release. 2006;115:216–225.10.1016/j.jconrel.2006.07.021
  • Corbet C, Ragelle H, Pourcelle V, et al. Delivery of siRNA targeting tumor metabolism using non-covalent PEGylated chitosan nanoparticles: Identification of an optimal combination of ligand structure, linker and grafting method. J Controlled Release. 2016;223:53–63.10.1016/j.jconrel.2015.12.020
  • Kim H-K, Davaa E, Myung C-S, et al. Enhanced siRNA delivery using cationic liposomes with new polyarginine-conjugated PEG-lipid. Int J Pharm. 2010;392:141–147.10.1016/j.ijpharm.2010.03.047
  • Han J, Cai J, Borjihan W, et al. Preparation of novel curdlan nanoparticles for intracellular siRNA delivery. Carbohyd Polym. 2015;117:324–330.10.1016/j.carbpol.2014.09.069
  • Davis ME, Zuckerman JE, Choi CHJ, et al. Evidence of RNAi in humans from systemically administered siRNA via targeted nanoparticles. Nature. 2010;464:1067–1070.10.1038/nature08956
  • Patil ML, Zhang M, Minko T. Multifunctional triblock nanocarrier (PAMAM-PEG-PLL) for the efficient intracellular siRNA delivery and gene silencing. ACS Nano. 2011;5:1877–1887.10.1021/nn102711d
  • Semple SC, Akinc A, Chen J, et al. Rational design of cationic lipids for siRNA delivery. Nat Biotechnol. 2010;28:172–176.10.1038/nbt.1602
  • Liu Z, Winters M, Holodniy M, et al. siRNA delivery into human T cells and primary cells with carbon‐nanotube transporters. Angew Chem Int Ed. 2007;46:2023–2027.10.1002/(ISSN)1521-3773
  • Zeng H, Little HC, Tiambeng TN, et al. Multifunctional dendronized peptide polymer platform for safe and effective siRNA delivery. J Am Chem Soc. 2013;135:4962–4965.10.1021/ja400986u
  • Forbes DC, Peppas NA. Polycationic nanoparticles for siRNA delivery: comparing ARGET ATRP and UV-initiated formulations. ACS Nano. 2014;8:2908–2917.10.1021/nn500101c
  • Dahlman JE, Barnes C, Khan OF, et al. In vivo endothelial siRNA delivery using polymeric nanoparticles with low molecular weight. Nat Nanotechnol. 2014;9:648–655.10.1038/nnano.2014.84
  • Li J, Ouyang Y, Kong X, et al. A multi-scale molecular dynamics simulation of PMAL facilitated delivery of siRNA. RSC Adv. 2015;5:68227–68233.10.1039/C5RA10965E
  • Pombo-García K, Weiss S, Zarschler K, et al. Zwitterionic polymer-coated ultrasmall superparamagnetic iron oxide nanoparticles with low protein interaction and high biocompatibility. ChemNanoMat. 2016;2:959–971.10.1002/cnma.201600233
  • Xu X, Kanduč M, Wu J, et al. Potential of mean force and transient states in polyelectrolyte pair complexation. J Chem Phys. 2016;145:034901.10.1063/1.4958675
  • Merlitz H, Li C, Wu C, et al. Polyelectrolyte brushes in external fields: molecular dynamics simulations and mean-field theory. Soft Matter. 2015;11:5688–5696.10.1039/C5SM01275A
  • Carrillo J-MY, Dobrynin AV. Polyelectrolytes in salt solutions: molecular dynamics simulations. Macromolecules. 2011;44:5798–5816.
  • Meneksedag-Erol D, Tang T, Uludağ H. Molecular modeling of polynucleotide complexes. Biomaterials. 2014;35:7068–7076.10.1016/j.biomaterials.2014.04.103
  • Ouyang D, Zhang H, Parekh HS, et al. Structure and dynamics of multiple cationic vectors− siRNA complexation by all-atomic molecular dynamics simulations. J Phys Chem B. 2010;114:9231–9237.10.1021/jp911913c
  • Sun C, Tang T, Uludag H. A molecular dynamics simulation study on the effect of lipid substitution on polyethylenimine mediated siRNA complexation. Biomaterials. 2013;34:2822–2833.10.1016/j.biomaterials.2013.01.011
  • Karatasos K, Posocco P, Laurini E, et al. Poly(amidoamine)-based dendrimer/siRNA complexation studied by computer simulations: effects of pH and generation on dendrimer structure and siRNA binding. Macromol Biosci. 2012;12:225–240.10.1002/mabi.v12.2
  • Marrink SJ, Risselada HJ, Yefimov S, et al. The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B. 2007;111:7812–7824.10.1021/jp071097f
  • Hess B, Kutzner C, van der Spoel D, et al. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4:435–447.10.1021/ct700301q
  • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33–38.10.1016/0263-7855(96)00018-5
  • Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. J Chem Phys. 2007;126:014101.10.1063/1.2408420
  • Parrinello M, Rahman A. Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys. 1981;52:7182–7190.10.1063/1.328693
  • Bartels C. Analyzing biased Monte Carlo and molecular dynamics simulations. Chem Phys Lett. 2000;331:446–454.10.1016/S0009-2614(00)01215-X
  • Kumar S, Rosenberg JM, Bouzida D, et al. THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem. 1992;13:1011–1021.10.1002/(ISSN)1096-987X
  • Mao S, Neu M, Germershaus O, et al. Influence of polyethylene glycol chain length on the physicochemical and biological properties of poly (ethylene imine)-graft-poly (ethylene glycol) block copolymer/SiRNA polyplexes. Bioconjug Chem. 2006;17:1209–1218.10.1021/bc060129j
  • Liu X, Howard KA, Dong M, et al. The influence of polymeric properties on chitosan/siRNA nanoparticle formulation and gene silencing. Biomaterials. 2007;28:1280–1288.10.1016/j.biomaterials.2006.11.004

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