Probing the Structure of DNA−Carbon Nanotube Hybrids with Molecular Dynamics

• Published in: Nano letters 2008-01, Vol.8 (1), p.69-75
• Main Authors: Johnson, Robert R, Johnson, A. T. Charlie, Klein, Michael L
• Format: Article
• Language: English
• Subjects: Condensed matter: structure, mechanical and thermal properties; Cross-disciplinary physics: materials science; rheology; DNA, Single-Stranded - chemistry; Exact sciences and technology; General equipment and techniques; Instruments, apparatus, components and techniques common to several branches of physics and astronomy; Low-dimensional structures (superlattices, quantum well structures, multilayers): structure, and nonelectronic properties; Materials science; Methods of nanofabrication; Molecular Probes; Nanoscale materials and structures: fabrication and characterization; Nanotubes; Nanotubes, Carbon; Physics; Self-assembly; Sensors (chemical, optical, electrical, movement, gas, etc.); remote sensing; Surfaces and interfaces; thin films and whiskers (structure and nonelectronic properties)
• ISSN: 1530-6984; 1530-6992
• DOI: 10.1021/nl071909j

DNA−carbon nanotube hybrids (DNA−CN) are novel nanoscale materials that consist of single-wall carbon nanotubes (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent experiments on DNA−CN have shown that this material offers a remarkable set of technologically useful properties such as facilitation of SWCN sorting, chemical sensing, and detection of DNA hybridization. Despite the importance of DNA−CN, a detailed understanding of its microscopic structure and physical properties is lacking. To address this, we have performed classical all-atom molecular dynamics (MD) simulations exploring the self-assembly mechanisms, structure, and energetic properties of this nanomaterial. MD reveals that SWCN induces ssDNA to undergo a spontaneous conformational change that enables the hybrid to self-assemble via the π−π stacking interaction between ssDNA bases and SWCN sidewall. ssDNA is observed to spontaneously wrap about SWCN into compact right- or left-handed helices within a few nanoseconds. Helical wrapping is driven by electrostatic and torsional interactions within the sugar−phosphate backbone that result in ssDNA wrapping from the 3‘ end to the 5‘ end.