Single-Stranded DNA-Carbon Nanotube Hybrid Interactions

It has been shown that, under certain conditions, single-stranded DNA (ssDNA) preferentially wraps in a helical fashion around carbon nanotubes (CNTs), forming a water-dispersible hybrid. Recently, its ability to sort mixtures of CNTs based on chirality has been demonstrated using special short ssDNA sequences.   It is believed the emergence of DNA secondary structures, arising from DNA base-base hydrogen bonding, plays a crucial role in enabling this process. 

Previously, through short molecular simulations, we have identified the possibility of hydrogen bond stabilized oligonucleotide secondary structures, deemed β-sheets and β-barrels, on graphene and carbon nanotubes, respectively.  More recently, through the use of replica exchange molecular dynamics (REMD) simulation, we have conducted a study on the (6,5)-CNT, its respective DNA recognition strand, (TAT)₄, and other related sequences.  Starting with one strand simulated on an infinitely long CNT, certain hybrid characteristics begin to emerge.  In particular, a large majority of DNA-CNT hybrids (97% for (TAT)₄) adopt a right-handed helical configuration, with greater than 98% of all DNA bases adsorbing on the CNT sidewall.  Furthermore, DNA strands are found to fully loop around the CNT and stitch to themselves via hydrogen bonds between bases.  A thermodynamic model is presented to accurately predict types and probabilities of configurations to which single strands of DNA will conform on specific CNTs.