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Redox modifications for electrochemical applications

Oligonucleotides with redox modifications

Methylene blue and Ferrocene redox modifications

In recent years, a variety of new approaches of oligonucleotide-based biosensors have been developed. Many of the oligonucleotides (e.g. aptamers) are marked with one of the two redox modifications - methylene blue (MB) or ferrocene (Fc) - and linked to an electrode. 
In the last few years on the basis of aptamer technology some promising systems already have been developed with bio-sensory potential. In biosensors, so-called E-sensors, oligonucleotide probes are labeled with methylene blue or ferrocene and covalently attached to the surface of electrodes (e.g. gold electrodes).1,2

Methylene blue modification at the 3´- or 5´-end of an oligo

Figure 1: Chemical structure of methylene blue connected to the 5´- or 3´-end of the oligonucleotide
Ferrocene modification at the 3´- or 5´-terminus of an oligo

Figure 2: Chemical structure of ferrocene connected to the 5´- or 3´-end of the oligonucleotide

In the absence of appropriate complementary strand redox-active probes take a certain conformation, where a defined distance between the probe and the electrode surface do exist. The addition of the target molecule results in a conformational change, where the loop structure of the redox-active probe dissolves and the distance between the redox dye and the electrode surface changes. Due to the changed position of the probe, electron transfer between electrode and redox component is affected and can be detected using appropriate measurement methods. Thus, the conformational change of the probe can be visualised by optical and electrochemical methods.

              conformational change of redox-active probe

The redox modifications ferrocene and methylene blue offered by are already well established modifications which allow the direct differentiation of the three-dimensional structures. provides methylene blue and ferrocene as the 3'-or 5'-modification in scale S, M and L up to a length of 50 bases. 

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1. Comparing the Properties of Electrochemical-Based DNA Sensors Employing Different Redox Tags. Kang D, Zuo X, Yang R, Xia F, Plaxc, KW, White R; Anal Chem. (2009), 81(21): 9109–9113.

2. Ferrocene-oligonucleotide conjugates for electrochemical probing of DNA. Ihara T, Maruo Y, Takenaka S, Takagi M; Nucleic Acids Res (1996), 24. 4273.

3. DNA biomolecular-electric encoder and decoder devices constructed by multiplex biosensors. Kang D, White RJ, Xia F, Zuo X, Vallée-Bélisle A, Plaxco KW; NPG Asia Materials (2012), 4, doi:10.1038/am.2012.1. 

4. Uridine-Conjugated Ferrocene DNA Oligonucleotides: Unexpected Cyclization Reaction of the Uridine Base. Yu CJ, Yowanto H, Wan Y, Meade TJ, Chong Y, Strong M, Donilon LH, Kayyem JF, Gozin, M, Blackburn GFJ; Am. Chem. Soc. (2000), 122, 6767-6768.

5. 2´-Ribose-Ferrocene Oligonucleotides for Electronic Detection of Nucleic Acids. Yu CJ, Wang H, Wan Y, Yowanto H, Kim JC, Donilon LH, Tao C, Strong M, Chong YJ; Org. Chem. (2001), 66, 2937-2942.