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

Abstract

We fabricated and tested encoders and decoders based on a multiplex, DNA-based electrochemical biosensor that uses electronic (electrochemical) signals as its readout. These devices use two or more sequence-specific DNA probes, with each being modified with a distinct redox reporter. These probes, when interrogated together, serve as encoders and decoders, converting patterns that are encoded and decoded by the presence or absence of specific DNA sequences into specific electronic outputs. We demonstrated these multifunctional, bio-electrochemical devices, for example, 4-to-2 and 8-to-3 encoders and 1-to-2 and 2-to-3 decoders. Accordingly, these devices bridge the division between DNA-based devices and silicon-based electronics. NPG Asia Materials (2012) 4, e1; doi:10.1038/am.2012.1; published online 18 January 2012Keywords: biosensors; decoder; DNA-based; encoder; multiplex INTRODUCTIONIn recent decades, serious attempts have been made to implement computational approaches, models and paradigms that utilize the information transfer and processing abilities of naturally occurring and modified biomolecules. 1-11 A decade ago, for example, Adleman performed a now-classic experiment in which computations were conducted using DNA molecules, demonstrating that biology can provide new computing substrates. [12][13][14][15] In the decade since Adleman's invention, reports have been made of a wide and diverse range of DNA logic devices. [16][17][18][19][20][21][22] Winfree, Stojanovic, Willner, Katz and their co-workers have, for example, developed optically reported 'AND' , 'OR' and 'SET-RESET' logic gate operations. 7,[23][24][25][26][27][28][29][30][31] Although the above examples serve as promising proofs of principle (see also refs 27-35), it remains necessary to create complex, multicomponent devices on a single biomolecular platform to achieve increased computational complexity and develop realistic DNAbased information processing systems. In this study, we fabricated and tested encoders and decoders based on a multiplex, DNA-based electrochemical biosensor that uses electronic (electrochemical) signals as its readout. These devices uses two or more sequence-specific DNA probes that, when interrogated together, serve as encoders, converting patterns that are encoded and decoded by the presence or absence of specific DNA sequences into specific electronic outputs.

Aptamer-functionalized neural recording electrodes for the direct measurement of cocaine in vivo

“…This reversibility ensures that analyte is not consumed or adsorbed in the process 28 . The customizability of aptamer synthesis allows for the incorporation of functional groups, necessary to undergo covalent attachment, as well as reporter molecules, capable of monitoring target binding 29 . Aptamers are commonly functionalized with electrochemical reporter molecules, such as methylene blue (MB), ferrocene and anthraquinone to allow for the direct detection of analyte binding through electrochemical techniques 29 .…”

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

“…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).…”

Ultrasensitive IgG quantification using DNA nano-pyramids

“…Ferrocene-based redox active species and detection have received more attention for electrochemical biosensing owing to their unique catalytic properties, remarkable electrochemical responses and controllable and easy preparation. [31][32][33] Using this system, we detected as low as 2.8 pg ml À1 of IgG and demonstrated a selective and stable sensing system after a week of storage. Our proof-of-concept study shows that this method has a potential to be developed into a biocompatible, sensitive and selective analytical method based on DPs for clinical diagnostics.…”