DOI: 10.1021/la102671g 19191 Langmuir 2010, 26(24), 19191–19198 Published on Web 11/22/2010 pubs.acs.org/Langmuir © 2010 American Chemical Society Electrochemical Characterization of Thin Film Electrodes Toward Developing a DNA Transistor Stefan Harrer,* Shafaat Ahmed, Ali Afzali-Ardakani, Binquan Luan, Philip S. Waggoner, Xiaoyan Shao, Hongbo Peng, Dario L. Goldfarb, Glenn J. Martyna, Stephen M. Rossnagel, Lili Deligianni, and Gustavo A. Stolovitzky IBM T. J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States Received July 7, 2010. Revised Manuscript Received November 7, 2010 The DNA-Transistor is a device designed to control the translocation of single-stranded DNA through a solid-state nanopore. Functionality of the device is enabled by three electrodes exposed to the DNA-containing electrolyte solution within the pore and the application of a dynamic electrostatic potential well between the electrodes to temporarily trap a DNA molecule. Optimizing the surface chemistry and electrochemical behavior of the device is a necessary (but by no means sufficient) step toward the development of a functional device. In particular, effects to be eliminated are (i) electrochemically induced surface alteration through corrosion or reduction of the electrode surface and (ii) formation of hydrogen or oxygen bubbles inside the pore through water decomposition. Even though our motivation is to solve problems encountered in DNA transistor technology, in this paper we report on generic surface chemistry results. We investigated a variety of electrode-electrolyte-solvent systems with respect to their capability of suppressing water decomposition and maintaining surface integrity. We employed cyclic voltammetry and long-term amperometry as electrochemical test schemes, X-ray photoelectron spectroscopy, atomic force microscopy, and scanning, as well as transmission electron microscopy as analytical tools. Characterized electrode materials include thin films of Ru, Pt, nonstoichiometric TiN, and nonstoichiometric TiN carrying a custom-developed titanium oxide layer, as well as custom-oxidized nonstoichio- metric TiN coated with a monolayer of hexadecylphosphonic acid (HDPA). We used distilled water as well as aqueous solutions of poly(ethylene glycol) (PEG-300) and glycerol as solvents. One millimolar KCl was employed as electrolyte in all solutions. Our results show that the HDPA-coated custom-developed titanium oxide layer effectively passivates the underlying TiN layer, eliminating any surface alterations through corrosion or reduction within a voltage window from -2 V to þ2 V. Furthermore, we demonstrated that, by coating the custom-oxidized TiN samples with HDPA and increasing the concentration of PEG-300 or glycerol in aqueous 1 mM KCl solutions, water decomposition was suppressed within the same voltage window. Water dissociation was not detected when combining custom-oxidized HDPA-coated TiN electrodes with an aqueous 1 mM KCl-glycerol solution at a glycerol concentration of at least 90%. These results are applicable to any system that requires nanoelectrodes placed in aqueous solution at voltages that can activate electrochemical processes. I. Introduction Employing solid nanopores for detection of whole DNA mole- cules has been successfully demonstrated by several groups. 2-4 All these approaches enable DNA detection with a resolution of not less than approximately 10-15 nucleotides. 4 A number of methods for nucleobase identification using nanopores have been proposed recently. 5 One such method is the use of a nanopore in combination with DNA-induced current signals for reading out specific nucleotide sequences as the DNA molecule is pulled through the pore. However, these methods have not been brought to practice in a nanopore yet due to (i) limited fabrication capabilities for a suitable nanopore device, (ii) lack of means to sufficiently slow down DNA translocation inside the pore, and (iii) lack of sufficient control of the DNA molecule while it translocates. 5 We have previously introduced a device capable of base-by-base ratcheting of single- stranded DNA through a solid-state nanopore, which we call DNA-Transistor. 1,7 In this device, DNA-trapping is enabled by generating a potential well inside the nanopore along its longi- tudinal direction temporarily trapping the negatively charged ssDNA in a predefined position. Three electrodes located inside the pore are used to create an electrostatic potential well. DNA is solved in an aqueous electrolyte solution and pulled into the pore by introducing an external constant potential drop between the two reservoirs on each side of the pore. Pore diameters are typically on the order of 3-5 nm. The two core requirements for maintaining our device functionality are that the pore (i) remains unaltered and operational as well as (ii) unobstructed during device operation. Hence, corrosion or reduction effects on electrode surfaces as well as bubble formation through water decomposition inside the pore must be minimized. *Corresponding author. E-mail: sharrer@us.ibm.com. Phone: þ1-914- 945-2535. (1) Polonsky, S.; Rossnagel, S.; Stolovitzky, G. Nanopore in metal-dielectric sandwich for DNA position control. Appl. Phys. Lett. 2007, 91, 153103-1– 153103-3. (2) Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Characteriza- tion of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770–13773. (3) Braha, O.; et al. Designed protein pores as components for biosensors. Chem. Biol. 1997, 4, 497–505. (4) Meller, A.; Nivon, L.; Brandin, L.; Golovchenko, E.; Branton, D. Voltage- driven DNA translocations through a nanopore. Phys. Rev. Lett. 2001, 86, 3435– 3438. (5) Branton, D.; et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 2008, 26, 1146–1153. (6) Bard, A. J.; Parsons, R.; , Jordan, J. Standard potentials in aqueous solution, 1st ed.; CRC Press: Boca Raton, 1985; ISBN 0-8247-7291-1. (7) Peng, H.; Polonsky, S.; Stolovitzky, G.; Luan, B.; Martyna, G.; , Rossnagel, S. Solid-state nanopore with multiple embedded circular addressable electrodes, submitted for publication, April 2010.