Study on the role of polyethylenimine as gene delivery carrier using molecular dynamics simulations

References

• Ledley F. Nonviral gene-therapy: the promise of genes as pharmaceutical products. Human Gene Therapy. 1995;6:1129.
   PubMed Web of Science ®Google Scholar
• Luo D, Saltzman W. Synthetic DNA delivery systems. Nature Biotechnology. 2000;18:33.
   PubMed Web of Science ®Google Scholar
• Mulligan R. The basic science of gene-therapy. Science. 1993;260:926.
   PubMed Web of Science ®Google Scholar
• Lehrman S. Virus treatment questioned after gene therapy death. Nature. 1999;401:517.
   PubMed Web of Science ®Google Scholar
• Boussif O, Lezoualc'h F, Zanta MA, Mergny MD, Scher-man D, Demeneix B, Behr JP. A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine. Proceedings of the National Academy of Sciences USA. 1995;92:7297.
   PubMed Web of Science ®Google Scholar
• Godbey W, Wu K, Mikos A. Poly(ethylenimine) and its role in gene delivery. Journal of Controlled Release. 1999;60:149.
   PubMed Web of Science ®Google Scholar
• Jere D, Jiang HL, Arote R, Kim YK, Choi YJ, Cho MH, Akaike T, Chot CS. Degradable polyethylenimines as DNA and small interfering RNA carriers. Expert Opinion Drug Delivery. 2009;6:827.
   PubMed Web of Science ®Google Scholar
• Cheatham T, Kollman P. Molecular dynamics simulation of nucleic acids. Annual Review of Physical Chemistry. 2000;51:435.
   PubMed Web of Science ®Google Scholar
• Cheatham T, Young M. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers. 2000;56:232.
   PubMed Web of Science ®Google Scholar
• Lu D, Aksimentiev A, Shih A, Cruz-Chu E, Freddolino P, Arkhipov A, Schulten K. The role of molecular modeling in bionanotechnology. Physical Biology. 2006;3:S40.
   PubMed Web of Science ®Google Scholar
• Pouton C, Seymour L. Key issues in non-viral gene delivery. Advanced Drug Delivery Reviews. 2001;46:187.
   PubMed Web of Science ®Google Scholar
• Pack D, Hoffman A, Pun S, Stayton P. Design and development of polymers for gene delivery. Nature Reviews Drug Discovery. 2005;4:581.
   PubMed Web of Science ®Google Scholar
• Kircheis R, Wightman L, Wagner E. Design and gene delivery activity of modified polyethylenimines. Advanced Drug Delivery Reviews. 2001;53:341.
   PubMed Web of Science ®Google Scholar
• Wagner E, Cotten M, Foisner R, Birnstiel M. Transferrin-polycation-DNA complexes: the effect of polycations on the structure of the complex and DNA delivery to cells. Proceedings of the National Academy of Sciences USA. 1991;88:4255.
   PubMed Web of Science ®Google Scholar
• Hansma H, Golan R, Hsieh W, Lollo C, Mullen-Ley P, Kwoh D. DNA condensation for gene therapy as monitored by atomic force microscopy. Nucleic Acids Research. 1998;26:2481.
   PubMed Web of Science ®Google Scholar
• Schaffer D, Fidelman N, Dan N, Lauffenburger D. Vector unpacking as a potential barrier for receptor-mediated polyplex gene delivery. Biotechnology and Bioengineering. 2000;67:598.
   PubMed Web of Science ®Google Scholar
• Wolfert M, Dash P, Nazarova O, Oupicky D, Seymour L, Smart S, Strohalm J, Ulbrich K. Polyelectrolyte vectors for gene delivery: influence of cationic polymer on biophysical properties of complexes formed with DNA. Bioconjugate Chemistry. 1999;10:993.
   PubMed Web of Science ®Google Scholar
• Schaffer D, Lauffenburger D. Optimization of cell surface binding enhances efficiency and specificity of molecular conjugate gene delivery. Journal of Biological Chemistry. 1998;273:28004.
   PubMed Web of Science ®Google Scholar
• Schaffert D, Wagner E. Gene therapy progress and prospects: synthetic polymer-based systems. Gene Therapy. 2008;15:1131.
   PubMed Web of Science ®Google Scholar
• Marsh M. Endocytosis. Oxford: Oxford University Press; 2001.
   Google Scholar
• Behr J. The proton sponge: a trick to enter cells the viruses did not exploit. Chimia. 1997;51:34.
   Web of Science ®Google Scholar
• Erbacher P, Roche A, Monsigny M, Midoux P. The reduction of the positive charges of polylysine by partial gluconoylation increases the transfection efficiency of polylysine/DNA complexes. Biochimica et Biophysica Acta. 1997;1324:27.
   PubMed Web of Science ®Google Scholar
• Godbey W, Wu K, Mikos A. Size matters: molecular weight affects the efficiency of poly(ethylenimine) as a gene delivery vehicle. Journal of Biomedical Materials Research. 1999;45:268.
   PubMed Web of Science ®Google Scholar
• Choosakoonkriang S, Lobo B, Koe G, Koe J, Middaugh C. Biophysical characterization of PEI/DNA complexes. Journal of Pharmaceutical Sciences. 2003;92:1710.
   PubMed Web of Science ®Google Scholar
• Utsuno K, Uludag H. Thermodynamics of polyethylenimine-DNA binding and DNA condensation. Biophysical Journal. 2010;99:201.
   PubMedGoogle Scholar
• Prevette LE, Kodger TE, Reineke TM, Lynch ML. Deciphering the role of hydrogen bonding in enhancing pDNA-polycation interactions. Langmuir. 2007;23:9773.
   PubMedGoogle Scholar
• Alshamsan A, Haddadi A, Incani V, Samuel J, Lavasanifar A, Uludag H. Formulation and delivery of siRNA by oleic acid and stearic acid modified polyethylenimine. Molecular Pharmaceutics. 2009;6:121.
   PubMed Web of Science ®Google Scholar
• Patel M, Anchordoquy T. Contribution of hydrophobicity to thermodynamics of ligand-DNA binding and DNA collapse. Biophysical Journal. 2005;88:2089.
   PubMed Web of Science ®Google Scholar
• Stevens M. Simple simulations of DNA condensation. Biophysical Journal. 2001;80:130.
   PubMed Web of Science ®Google Scholar
• Winkler R, Steinhauser M, Reineker P. Complex formation in systems of oppositely charged polyelectrolytes: a molecular dynamics simulation study. Physical Review E. 66: 2002: 021802-1–7.
   Google Scholar
• Hayashi Y, Ullner M, Linse P. A Monte Carlo study of solutions of oppositely charged polyelectrolytes. Journal of Chemical Physics. 2002;116:6836.
   Web of Science ®Google Scholar
• Hayashi Y, Ullner M, Linse P. Complex formation in solutions of oppositely charged polyelectrolytes at different polyion compositions and salt content. Journal of Physical Chemistry B. 2003;107:8198.
   Google Scholar
• Hayashi Y, Ullner M, Linse P. Oppositely charged polyelectrolytes. Complex formation and effects of chain asymmetry. Journal of Physical Chemistry B. 2004;108:15266.
   Web of Science ®Google Scholar
• Dias R, Pais A, Miguel M, Lindman B. Modeling of DNA compaction by polycations. Journal of Chemical Physics. 2003;119:8150.
   Google Scholar
• Ziebarth J, Wang Y. Coarse-grained molecular dynamics simulations of DNA condensation by block copolymer and formation of core-corona structures. Journal of Physical Chemistry B. 2010;114:6225.
   PubMedGoogle Scholar
• Voulgarakis NK, Rasmussen KO, Welch PM. Dendrimers as synthetic gene vectors: cell membrane attachment. Journal of Chemical Physics. 2009;130.
   Google Scholar
• Ziebarth J, Wang Y. Molecular dynamics simulations of FNA-polycation complex formation. Biophysical Journal. 2009;97:1971.
   PubMedGoogle Scholar
• Ouyang D, Zhang H, Herten D-P, Parekh HS, Smith SC. Structure, dynamics, and energetics of siRNA-cationic vector complexation: a molecular dynamics study. Journal of Physical Chemistry B. 2010;114:9220.
   PubMed Web of Science ®Google Scholar
• Ouyang D, Zhang H, Parekh HS, Smith SC. Structure and dynamics of multiple cationic vectors-siRNA complexation by all-atomic molecular dynamics simulations. Journal of Physical Chemistry B. 2010;114:9231.
   PubMed Web of Science ®Google Scholar
• Mills M, Orr B, Holl MMB, Andricioaei I. Microscopic basis for the mesoscopic extensibility of dendrimer-compacted DNA. Biophysical Journal. 2010;98:834.
   PubMedGoogle Scholar
• Pavan GM, Danani A, Pricl S, Smith DK. Modeling the multivalent recognition between dendritic molecules and DNA: understanding how ligand ‘sacrifice’ and screening can enhance binding. Journal of the American Chemical Society. 2009;131:9686.
   PubMed Web of Science ®Google Scholar
• Pavan GM, Albertazzi L, Danani A. Ability to adapt: different generations of pamam dendrimers show different behaviors in binding siRNA. Journal of Physical Chemistry B. 2010;114:2667.
   PubMed Web of Science ®Google Scholar
• Pavan GM, Kostiainen MA, Danani A. Computational approach for understanding the interactions of uv-degradable dendrons with DNA and siRNA. Journal of Physical Chemistry B. 2010;114:5686.
   PubMedGoogle Scholar
• Pavan GM, Mintzer MA, Simanek EE, Merkel OM, Kissel T, Danani A. Computational insights into the interactions between DNA and siRNA with ‘rigid’ and ‘flexible’ triazine dendrimers. Biomacromolecules. 2010;11:721.
   PubMedGoogle Scholar
• Dai L, Mu Y, Nordenskiold L, van der Maarel JRC. Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules. Physical Review Letters. 2008;100:118301.
   PubMed Web of Science ®Google Scholar
• Suh J, Paik H, Hwang B. Ionization of poly(ethylenimine) and poly(allylamine) at various pHs. Bioorganic Chemistry. 1994;22:318.
   Web of Science ®Google Scholar
• Tang MX, Szoka FC. The influence of polymer structure on the interactions of cationic polymers with DNA and morphology of the resulting complexes. Gene Therapy. 1997;4:823.
   PubMed Web of Science ®Google Scholar
• Sun C, Tang T, Uludag H, Cuervo JE. Molecular dynamics simulations of DNA/PEI complexes: effect of PEI branching and protonation State. Biophysical Journal. 2011;100:2754.
   PubMed Web of Science ®Google Scholar
• MacKerel Jr. A, Brooks III C, Nilsson L, Roux B, Won Y, Karplus M. In: Schleyer PVR et al., editors. The encyclopedia of computational chemistry, Vol. 1. Chichester: Wiley; 1998, pp. 271–277.
   Google Scholar
• Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, MacKerell AD Jr. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry. 2010;31:671.
   PubMed Web of Science ®Google Scholar
• Phillips J, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R, Kale L, Schulten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 2005;26:1781.
   PubMed Web of Science ®Google Scholar
• Jorgensen W. Quantum and statistical mechanical studies of liquids.10. Transferable intermolecular potential functions for water, alcohols, and ethers - application to liquid water. Journal of the American Chemical Society. 1981;103:335.
   Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald – an N-log(N) method for Ewald sums in large systems. Journal of Chemical Physics. 1993;98:10089.
   Web of Science ®Google Scholar
• Srinivasan J, Cheatham T, Cieplak P, Kollman P, Case D. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. Journal of the American Chemical Society. 1998;120:9401.
   Web of Science ®Google Scholar
• Reyes C, Kollman P. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. Journal of Molecular Biology. 2000;297:1145.
   PubMed Web of Science ®Google Scholar
• Gohlke H, Case D. Converging free energy estimates: MMPB(GB) SA studies on the protein–protein complex Ras–Raf. Journal of Computational Chemistry. 2004;25:238.
   PubMed Web of Science ®Google Scholar
• Honig B, Sharp K, Yang A. Macroscopic models of aqueous solutions: biological and chemical applications. Journal of Physical Chemistry. 1993;97:1101.
   Web of Science ®Google Scholar
• Brooks B, Bruccoleri R, Olafson D, States D, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry. 1983;4:187.
   Web of Science ®Google Scholar
• Sitkoff D, Sharp K, Honig B. Accurate calculation of hydration free-energies using macroscopic solvent models. Journal of Physical Chemistry. 1994;98:1978.
   Web of Science ®Google Scholar