Carbon Nanotube Interaction with DNA Gang Lu, ² Paul Maragakis, ‡ and Efthimios Kaxiras* ,²,§ DiVision of Engineering and Applied Sciences, Department of Chemistry and Chemical Biology, and Department of Physics, HarVard UniVersity, Cambridge, Massachusetts 02138 Received February 24, 2005; Revised Manuscript Received April 12, 2005 ABSTRACT We investigate a system consisting of B-DNA and an array of (10,0) carbon nanotubes periodically arranged to fit into the major groove of the DNA. We obtain an accurate electronic structure of the combined system, which reveals that it is semiconducting and that the bands on either end of the gap are derived exclusively from one of the two components. We discuss in detail how this system can be used as either an electronic switch involving transport through both components, or as a device for ultrafast DNA sequencing. The quest for nanoscale structures with practical applications is rapidly passing from the realm of dreams to reality. The combination of nanoscale structures deriving from solids, such as carbon nanotubes or silicon nanowires, with biologi- cally important structures, such as DNA or polypeptides, is particularly intriguing since it opens the door to novel bio- and nanotechnology applications, as recent experimental successes of marrying the two fields attest. 1-6 Here, following the spirit of these experimental works, we propose and study computationally a system consisting of an array of carbon nanotubes (CNT) in intimate contact with DNA. Combining static molecular modeling simulations for the atomic struc- ture, and quantum mechanical simulations for the electronic structure, we show that this system offers promise as a very sensitive nanoscale electronic device and as a means for ultrafast DNA sequencing. We consider a periodic double stranded DNA and a nanotube array positioned so that it fits snugly at the major groove of the DNA, as shown in Figure 1. The feasibility of assempbling this system will be addressed below. We chose the (10,0) single-walled CNT, because its diameter is compatible with the size of the DNA major groove and at the same time it is a semiconducting structure, offering the possibility of interesting switching devices. As a representa- tive DNA molecule, we chose poly(C)‚poly(G) B-DNA with eleven base-pairs per helical turn. 7 The initial configuration of a single helical turn of B-DNA was generated using the Nucleic Acid Builder. 8 The resulting DNA structure was passivated with a series of hydrogen atoms at the phosphate groups to create a neutral structure using the same procedure as in Ref 7. The geometry of the combined DNA and CNT system was modeled using the CHARMM computational package, 9 with a properly adapted graphitic carbon force field 10 for treating CNTs. With this force field, the (10,0) CNT was allowed to relax from the folded graphene structure to achieve the optimal structure by minimizing the total energy. The structure of the DNA was held fixed, while the CNT, which is rather stiff and does not deform significantly, was allowed to dock to the DNA at the major groove. The final structure was repeated periodically along the DNA axis. The left panel of Figure 1 shows the DNA aligned on top of the CNT array; the right panel shows a side view that reveals the match of the geometrical characteristics of the two structures. The DNA and CNT array meet at an angle of 55.5 degrees, resulting in an array with a spacing of 30 Å between successive CNTs. The particular arrangement we * Corresponding author. E-mail: kaxiras@physics.harvard.edu; tel: (617) 495-7977; fax: (627) 496-2545. ² Division of Engineering and Applied Sciences. ‡ Department of Chemistry and Chemical Biology. § Department of Physics. Figure 1. Proposed DNA-CNT system in top and side views, the latter along the CNT axis (created with VMD 20 ). NANO LETTERS 2005 Vol. 5, No. 5 897-900 10.1021/nl050354u CCC: $30.25 © 2005 American Chemical Society Published on Web 04/23/2005