Structure of homopolymer DNA-CNT hybrids

Single-stranded DNA-carbon nanotube (CNT) hybrids have been. used successfully for dispersion and structure-based sorting of CNTs. The structure of the hybrid determines its behavior in solution. Using scaling arguments and molecular dynamics simulations, we have studied various factors that contribute to the free energy of hybrid formation, including adhesion between DNA bases and the CNT, entropy of the DNA backbone, and electrostatic interactions between backbone charges. MD simulations show that a significant fraction of bases unstack from the CNT at room temperature, which reduces effective adhesion between the two per base. For homopolymer wrappings, we show that at low ionic strength, the dominant influences on the structure are adhesion between DNA and the CNT and electrostatic repulsion between backbone charges on the DNA. With a simple analytical model, we show that competition between these two can result in an optimal helical wrapping geometry.