Paper Citing NAMD - Abstract
Chien, Michael W.; Johnson, Robert R.; Pillai, Shreekumar R.; Singh, Shree Ram; Johnson, A. T. Charlie, Jr.
Mechanics and Energetics of DNA Hybridization on Single-Walled Carbon Nanotubes Explored Using Adaptive Biasing Force Calculations
JOURNAL OF PHYSICAL CHEMISTRY C, 118:2209-2214, JAN 30 2014
Hybrid nanostructures consisting of single-walled carbon nanotubes (swCNs) coated with single stranded DNA (ssDNA) are of great interest due to their numerous potential applications in nanotechnology, medicine, and homeland security. Recent experiments have demonstrated that DNA-CN hybrids can detect the hybridization of complementary DNA strands, paving the way for applications in DNA sequencing and genetic testing. However, the molecular mechanisms remain poorly understood. Previous molecular dynamics (MD) simulations studying DNA-CN self-assembly have found that adsorbed DNA bases are poorly positioned to hybridize with complementary DNA strands. Here, we apply the adaptive biasing force (ABF) method to all-atom MD models, and find that DNA bases must desorb from the swCN sidewall and suffer significant energy penalties to hybridize with complementary DNA. This agrees with the extremely slow hybridization time scales in fluorescence experiments, as well as observations made using DNA-CN transistor devices. We present the free energy landscape for two model systems and compare the energy required to hybridize a G-C versus an A-T pair. These results reveal significant impediments to rapid DNA hybridization on the swCN surface, and further our understanding of the mechanism by which hybridization gradually occurs-essential knowledge for the advancement of nanotechnology based on DNA-CN.
