Comparing the Properties of Electrochemical-Based DNA Sensors Employing Different Redox Tags

Abstract

Many electrochemical biosensor approaches developed in recent years utilize redox labeled (most commonly methylene blue or ferrocene) oligonucleotide probes site-specifically attached to an interrogating electrode. Sensors in this class have been reported employing a range of probe architectures, including single- and double-stranded DNA, more complex DNA structures, DNA and RNA aptamers and, most recently, DNA-small molecule chimeras. Signaling in this class of sensors is generally predicated on binding-induced changes in the efficiency with which the covalently attached redox label transfers electrons with the interrogating electrode. Here we have investigated how the properties of the redox tag affect the performance of such sensors. Specifically, we compare the differences in signaling and stability of electrochemical DNA sensors (E-DNA sensors) fabricated using either ferrocene or methylene blue as the signaling redox moiety. We find that while both tags support efficient E-DNA signaling, ferrocene produces slightly improved signal gain and target affinity. These small advantages, however, come at a potentially significant price: the ferrocene-based sensors are far less stable than their methylene blue counterparts, particularly with regards to stability to long-term storage, repeated electrochemical interrogations, repeated sensing/regeneration iterations, and employment in complex sample matrices such as blood serum.

DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors

“…Our encoders are based on the E-DNA sensor, a previously described electrochemical sensor 36,37 architecture that consists of an electrodeattached, redox-reporter-modified DNA probe (Figure 1). These E-DNA sensors turn 'off' (that is, their redox reporter produces less faradic current) when the hybridization of the target to the DNA probe forces the redox reporter away from the electrode.…”

DNA probe modified with 3-iron bis(dicarbollide) for electrochemical determination of DNA sequence of Avian Influenza Virus H5N1

“…The majority of developed recently electrochemical DNA or PNA sensors are based on phenomena of hybridization -induced conformational change in oligonucletoide probe with covalently attached redox active label at the top of the probe, either ferrocene (Anne et al, 2003;Anne et al, 2006;Aoki et al, 2007;Aoki et al, 2010;Fan et al, 2003) or methylene blue (Farjami et al, 2011;Ferapontova et al, 2009;Kang et al, 2009, Lai et al, 2006Liu et al, 2010;Lubin et al, 2009;Patterson et al, 2010;Pavlovic et al, 2008;Ricci et al, 2007;Ricci et al, 2010;Yang et al, 2010). In such type of genosensors the rate and efficiency of charge transport is affected by changes of DNA strands flexibility.…”

“…The most frequently used redox active labels is ferrocene (Anne et al, 2006;Aoki et al, 2010;Chatelain et al, 2012;Zhao et al, 2012;Zhuang et al, 2013) as well as methylene blue (Abi et al, 2012;Farjami et al, 2011;Farjami et al, 2012;Ferapontova et al, 2009;Kang et al, 2009;Kang et al, 2012;Lai et al, 2006;Liu et al, 2010;Lubin et al, 2009;Patterson et al, 2010;Pavlovic et al, 2008;Ricci et al, 2010;Yang et al, 2010).…”

Label-Free Electrochemical DNA Detection Based on Electrostatic Interaction between DNA and Ferrocene Dendrimers

“…[3][4][5] Of all DNA detection methods, electrochemical methods have the advantages of low cost, simplicity, rapid response, and impressive compatibility with miniaturization. [6][7][8] In electrochemical methods, hybridization is detected by a signal change that is mostly generated from redox labels such as [Ru(NH 3 ) 6 ] 3+/2+ , 6,7,9,10 [Fe(CN) 6 ] 4-/3-, [11][12][13][14] [Co(phen) 3 ] 3+/2+ , 15 methylene blue, 16 ferrocene, 8,17 and conductive polymers. 2,4 A sandwich-type assay is widely used to detect the target DNA in electrochemical methods, especially in methods that involve the use of semiconductor nanoparticles, 18 enzymes, 19 and vesicles 20 for labeling.…”

“…[21][22][23] Ferrocenes in a dendrimer can amplify a signal whereas ferrocene molecules attached to oligonucleotide probes act as a redox tag because a single dendrimer contains multiple ferrocene molecules. 17 Under a physiological condition where the pH is 7.4, terminal protonated amine groups in a dendrimer have a positive charge due to the dendrimer's high pKa (of approximately 9.5). 24 Therefore, an Fc-Den can bind to the target DNA by using electrostatic attraction under a physiological condition between the negatively charged DNA backbone and the terminated amine groups in the dendrimer.…”