Charge Transfer through Single-Stranded Peptide Nucleic Acid Composed of Thymine Nucleotides Amit Paul, ² Richard M. Watson, ‡ Paul Lund, ‡ Yangjun Xing, § Kathleen Burke, ‡ Yufan He, § Eric Borguet,* ,§ Catalina Achim,* ,‡ and David H. Waldeck* ,² Department of Chemistry, UniVersity of Pittsburgh, Pittsburgh, PennsylVania 15260; Department of Chemistry, Carnegie Mellon UniVersity, Pittsburgh, PennsylVania 15213; and Department of Chemistry, Temple UniVersity, Philadelphia, PennsylVania 19122 ReceiVed: December 14, 2007; In Final Form: February 18, 2008 Self-assembled monolayers (SAMs) of single-stranded peptide nucleic acids (PNAs) containing 3 to 7 thymine (T) nucleotides, a C-terminus cysteine, and an N-terminus ferrocene group were formed on gold electrodes. The existence of two redox environments for the ferrocene was detected by cyclic voltammetry and was attributed to the presence of “lying-down” and “standing-up” PNA molecules. By exploiting the chemical instability of the ferrocenium ion, electrochemical cycling was used to destroy the ferrocene of “lying-down” molecules while keeping the ferrocene in the “standing-up” molecules intact. Electrochemical measurements were used to determine the electron-transfer rate through the “standing-up” PNA molecules. The tunneling decay constant for these SAMs was determined to be about 0.9 Å -1 . Introduction The interest in self-assembled monolayers (SAMs) 1,2 of nucleic acids has increased recently, largely because of their potential applications in molecular electronics, 3 materials sci- ence, 4 molecular recognition, 5 biotechnology, and biosensor development. 6-8 An understanding of the charge transport (CT) through such SAMs is needed to realize their potential in molecular electronics and biosensing. The past decade has seen progress in understanding charge transfer through deoxyribo- nucleic acid (DNA), which is believed to occur through either a superexchange mechanism, 9-19 which dominates at short distances, or a hopping mechanism, 20-25 which dominates at large distances. The weak distance dependence of the charge hopping mechanism and its prevalence in duplex DNA systems have motivated the exploration of charge transfer through DNA and its promise for molecular electronics by a large number of different research groups. Nevertheless, only a few research groups have studied CT in DNA monolayers, probably because of the difficulties in creating well-defined DNA assemblies on a metal surface. 26-28 For example, Hartwich et al. 29 used cyclic voltammetry to characterize charge transfer in mixed monolayers of DNA having a pyrroloquinoline-quinone redox probe attached to DNA through a spacer and linked to an Au(111) surface through an ethane-thiol linker. These studies determined that the CT rate constant for a 12-base-pair (bp) DNA duplex was 1.5 s -1 , while for the same duplex containing two mismatches it was 0.6 s -1 , and that charge transfer could not be detected for single-stranded (ss) DNA at a scan rate of >10 mV s -1 . Liu et al. 30 argued that CT through a monolayer of a 30-bp double-stranded (ds) DNA takes place through the nucleobase stack and does not involve the DNA backbone. They based their argument on the fact that the rate constant for CT of 30 s -1 was not affected by breaks in the sugar-phosphate backbone and was too small to be measured when a mismatch was introduced in the ds DNA. Interestingly, a similar rate constant for CT was measured for a monolayer of a 15-bp ds DNA. 31 CT rate constants for ss oligonucleotides are also quite high. For example, Kraatz and collaborators reported a CT rate constant of 12 s -1 for a 20-base ss DNA monolayer, which was only 10 times lower than the rate constant for a monolayer of the corresponding 20-bp ds DNA. 32,33 The studies on duplex DNA indicate an important role for the base pairs in CT, and those on ss-DNA suggest that the bases may contribute significantly even when they are not involved in base pairing. Peptide nucleic acid (PNA) is an analogue of DNA that has a neutral and achiral backbone based on aminoethylglycine, in contrast to the negatively charged and chiral backbone of DNA (Figure 1a). 34,35 Like DNA, PNA forms duplexes with itself and other nucleic acids by Watson-Crick base pairing. The PNA‚ PNA duplexes adopt a helical structure termed P-type, which has a large pitch with 18 bases/turn, diameter of 28 Å, and 3.2- 3.4 Å rise/base pair. 36-38 Recent work shows that ligand- modified PNA can be used as a scaffold for transition metal ions. 39-41 The inorganic nucleic acid structures formed by this method contain transition metal ions at specific positions and may mediate CT over tens of nanometers, in a manner similar to that in which metal cofactors mediate electron transfer in metalloproteins. The study of charge transfer in such metalized PNA is a long-term goal toward which the experiments described below are targeted. ssPNA has a clear advantage over ssDNA for SAM prepara- tion because it is neutral. 42-44 Martin-Gago and co-workers 42-44 successfully prepared SAMs of ss PNA molecules having a cysteine group at the C-terminus that bound the PNA to the gold surface. They characterized the surface by X-ray photo- emission spectroscopy (XPS), atomic force microscopy (AFM), X-ray absorption near-edge spectroscopy (XANES), and reflec- tion-absorption infrared spectroscopy (RAIRS). They proposed that the formation of PNA SAMs occurs in two main steps; at low coverage, the adsorbed ss PNA molecules lie down on the surface; as the surface coverage increases, the layer of lying * To whom correspondence should be addressed. ² University of Pittsburgh. ‡ Carnegie Mellon University. § Temple University. 7233 J. Phys. Chem. C 2008, 112, 7233-7240 10.1021/jp711764q CCC: $40.75 © 2008 American Chemical Society Published on Web 04/16/2008 Downloaded by TEMPLE UNIV on September 6, 2009 | http://pubs.acs.org Publication Date (Web): April 16, 2008 | doi: 10.1021/jp711764q