Mechanism and Free Energy of DNA Hybridization on Single-Walled Carbon Nanotubes Using Adaptive Biasing Force Simulations

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DNA-carbon nanotube hybrids (DNA-NT) consist of single stranded DNA self-assembled to the sidewall of single-walled carbon nanotubes. DNA-NT show great promise for applications in nanotechnology, including chemical sensing and sequence-specific DNA detection. Details of the hybridization of DNA from DNA-NT remain controversial and must be rationalized with computational studies that suggest the presence of significant energetic and conformational barriers hindering this process. This motivated the use of adaptive biasing force (ABF) MD simulations to overcome energy barriers and enable exploration of reaction pathways leading to hybridization of DNA strands initially adsorbed on the NT. It was found that significant conformational changes and complete desorption of DNA bases were necessary to allow hybridization of adjacent base pairs. Energy barriers of ~10-20 kBT associated with these processes should lead to slow hybridization under ambient, consistent with observations of long equilibration timescales (~1 day) for DNA hybridization in aqueous solutions of NT. It was also found that GC base pairing has a stronger binding free energy compared to AT base pairing. These results further our understanding of DNA hybridization in the DNA-NT system, which is essential for the advancement of DNA-NT nanotechnology.

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Journal: TechConnect Briefs
Volume: 3, Nanotechnology 2013: Bio Sensors, Instruments, Medical, Environment and Energy (Volume 3)
Published: May 12, 2013
Pages: 119 - 122
Industry sector: Medical & Biotech
Topics: Diagnostics & Bioimaging, Sensors - Chemical, Physical & Bio
ISBN: 978-1-4822-0586-2