title: Coarse-grained simulation study of sequence effects on DNA hybridization in a concentrated environment.
abstract: A novel coarse-grained model is developed to elucidate thermodynamics and kinetic mechanisms of DNA self-assembly. It accounts for sequence and solvent conditions to capture key experimental results such as sequence-dependent thermal property and salt-dependent persistence length of ssDNA and dsDNA. Moreover, constant-temperature simulations on two single strands of a homogeneous sequence show two main mechanisms of hybridization: a slow slithering mechanism and a one-order faster zippering mechanism. Furthermore, large-scale simulations at a high DNA strand concentration demonstrate that DNA self-assembly is a robust and enthalpically driven process in which the formation of double helices is deciphered to occur via multiple self-assembly pathways including the strand displacement mechanism. However, sequence plays an important role in shifting the majority of one pathway over the others and controlling size distribution of self-assembled aggregates. This study yields a complex picture on the role of sequence on programmable self-assembly and demonstrates a promising simulation tool that is suitable for studies in DNA nanotechnology.
authors.affiliation: Department of Chemical Engineering and Materials Science, University of California-Irvine , Irvine, California 92697-2575, United States.
authors.forename: Cade B
authors.initials: CB
authors.lastname: Markegard
authors.forename: Iris W
authors.initials: IW
authors.lastname: Fu
authors.forename: K Anki
authors.initials: KA
authors.lastname: Reddy
authors.forename: Hung D
authors.initials: HD
authors.lastname: Nguyen
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D044367:Phase Transition; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded; D004247:DNA