Computer Simulation of DNA Condensation by PAMAM Dendrimer

• Published in: Macromolecular theory and simulations Vol. 27; no. 2
• Main Authors: Su, Yunxiang, Quan, Xuebo, Li, Libo, Zhou, Jian
• Format: Journal Article
• Language: English
• Published: Weinheim Wiley Subscription Services, Inc 01.03.2018
• Subjects: coarse graining; Computer simulation; dendrimer; Dendrimers; Deoxyribonucleic acid; dissipative particle dynamics; DNA; DNA condensation; gene delivery; Ionic strength; Molecular chains; pH effects
• ISSN: 1022-1344; 1521-3919
• DOI: 10.1002/mats.201700070

In this study, dissipative particle dynamics is employed to investigate the complexation of poly(amido amine) dendrimer and single‐stranded DNA (ssDNA). A coarse‐grained model for ssDNA is constructed, which reproduces correctly the conformational behavior of the ssDNA molecules. The effects of pH, dendrimer generation, ionic strength, and dendrimer/ssDNA charge ratio on DNA–dendrimer complexes are explored. Simulation results show that ssDNA molecules can be significantly condensed by dendrimers and stable complexes are obtained by regulating the pH value. The ssDNA chain penetration would complicate its release from dendrimer, while this can be tuned by different generations of dendrimer. Salt concentration affects the size and stability of the complexes through ion screening effect. Dendrimer/ssDNA charge ratio can be used to control the size and morphology of the complex. This work can help design dendrimer‐based gene vectors. To better understand the DNA condensation by poly(amido amine) dendrimer, dissipative particle dynamics is used to investigate the effects of pH, dendrimer generation, salt concentration, and dendrimer/ssDNA charge ratio on the structure of DNA–dendrimer complexes. The simulation results demonstrate that the size and morphology of its self‐assembled aggregates can be tuned by the above‐mentioned factors.