Coarse-Grained
Simulation Study of Sequence Effects
on DNA Hybridization in a Concentrated Environment
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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