Computational modeling of a carbon nanotube-based DNA nanosensor

During the last decade the design of biosensors, based on quantum transport in one-dimensional nanostructures, has developed as an active area of research. Here we investigate the sensing capabilities of a DNA nanosensor, designed as a semiconductor single walled carbon nanotube (SWCNT) connected to two gold electrodes and functionalized with a DNA strand acting as a bio-receptor probe. In particular, we have considered both covalent and non-covalent bonding between the DNA probe and the SWCNT. The optimized atomic structure of the sensor is computed both before and after the receptor attaches itself to the target, which consists of another DNA strand. The sensor's electrical conductance and transmission coefficients are calculated at the equilibrium geometries via the non-equilibrium Green's function scheme combined with the density functional theory in the linear response limit. We demonstrate a sensing efficiency of 70% for the covalently bonded bio-receptor probe, which drops to about 19% for the non-covalently bonded one. These results suggest that a SWCNT may be a promising candidate for a bio-molecular FET sensor.

[1]  G. B. Abadir,et al.  Bias-dependent amino-acid-induced conductance changes in short semi-metallic carbon nanotubes , 2010, Nanotechnology.

[2]  Douglas R. Kauffman,et al.  Electronically monitoring biological interactions with carbon nanotube field-effect transistors. , 2008, Chemical Society reviews.

[3]  H. Dai,et al.  Noncovalent sidewall functionalization of single-walled carbon nanotubes for protein immobilization. , 2001, Journal of the American Chemical Society.

[4]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[5]  Stefano Sanvito,et al.  Algorithm for the construction of self-energies for electronic transport calculations based on singularity elimination and singular value decomposition , 2008 .

[6]  Antonino La Magna,et al.  Role of contact bonding on electronic transport in metal–carbon nanotube–metal systems , 2006, cond-mat/0610076.

[7]  C. Toher,et al.  Effects of self-interaction corrections on the transport properties of phenyl-based molecular junctions , 2007, 0712.1747.

[8]  Jean-Christophe Charlier,et al.  Electronic and transport properties of nanotubes , 2007 .

[9]  Charles M. Lieber,et al.  Nanowire-based biosensors. , 2006, Analytical chemistry.

[10]  P. Hohenberg,et al.  Inhomogeneous Electron Gas , 1964 .

[11]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[12]  D. Sánchez-Portal,et al.  The SIESTA method for ab initio order-N materials simulation , 2001, cond-mat/0111138.

[13]  A. Fazzio,et al.  Designing real nanotube-based gas sensors. , 2008, Physical review letters.

[14]  U. Schwingenschlogl,et al.  Finite-bias electronic transport of molecules in a water solution , 2010 .

[15]  C. J. Lambert,et al.  General Green’s-function formalism for transport calculations with spd Hamiltonians and giant magnetoresistance in Co- and Ni-based magnetic multilayers , 1999 .

[16]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[17]  M. Shim,et al.  Noncovalent functionalization of carbon nanotubes for highly specific electronic biosensors , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Stefano Sanvito,et al.  Towards molecular spintronics , 2005, Nature materials.

[19]  Qian Wang,et al.  An investigation of the mechanisms of electronic sensing of protein adsorption on carbon nanotube devices. , 2004, Journal of the American Chemical Society.

[20]  S. Datta Electronic transport in mesoscopic systems , 1995 .

[21]  Luis A. Agapito,et al.  Nonequilibrium Green's function study of Pd4-cluster-functionalized carbon nanotubes as hydrogen sensors , 2009 .

[22]  B. Alder,et al.  THE GROUND STATE OF THE ELECTRON GAS BY A STOCHASTIC METHOD , 2010 .

[23]  A M Ward,et al.  Prostate specific antigen: biology, biochemistry and available commercial assays , 2001, Annals of clinical biochemistry.

[24]  Filip Braet,et al.  Carbon nanotubes for biological and biomedical applications , 2007 .

[25]  Cees Dekker,et al.  Identifying the mechanism of biosensing with carbon nanotube transistors. , 2008, Nano letters.

[26]  J. Ferrer,et al.  Spin and molecular electronics in atomically generated orbital landscapes , 2006 .

[27]  Michael E Phelps,et al.  Systems Biology and New Technologies Enable Predictive and Preventative Medicine , 2004, Science.

[28]  D. Sánchez-Portal,et al.  Numerical atomic orbitals for linear-scaling calculations , 2001, cond-mat/0104170.

[29]  George Grüner Carbon nanotube transistors for biosensing applications. , 2005 .

[30]  Kourosh Kalantar-zadeh,et al.  Nanotechnology-Enabled Sensors , 2007 .

[31]  Conductance oscillations in zigzag platinum chains. , 2005, Physical review letters.

[32]  Hashem Rafii-Tabar,et al.  Computational physics of carbon nanotubes , 2007 .

[33]  M. Klein,et al.  Computational study of a nanobiosensor: a single-walled carbon nanotube functionalized with the coxsackie-adenovirus receptor. , 2009, The journal of physical chemistry. B.

[34]  A. J. Nijdam,et al.  Nanotechnologies for biomolecular detection and medical diagnostics. , 2006, Current opinion in chemical biology.