Exploiting Polydopamine Nanospheres to DNA Computing: A Simple, Enzyme-Free and G-Quadruplex-Free DNA Parity Generator/Checker for Error Detection during Data Transmission

Abstract

Molecular logic devices with various functions play an indispensable role in molecular data transmission/processing. However, during any kinds of data transmission, a constant and unavoidable circumstance is the appearance of bit errors, which have serious effects on the regular logic computation. Fortunately, these errors can be detected via plugging a parity generator (pG) at the transmitting terminal and a parity checker (pC) at the receiving terminal. Herein, taking advantage of the efficient adsorption/quenching ability of polydopamine nanospheres toward fluorophore-labeled single-stranded DNA, we explored this biocompatible nanomaterial to DNA logic computation and constructed the first simple, enzyme-free, and G-quadruplex-free DNA pG/pC for error detection through data transmission. Besides, graphene oxide (GO) was innovatively introduced as the "corrective element" to perform the output-correction function of pC. All the erroneous outputs were corrected to normal conditions completely, ensuring the regular operation of later logic computing. The total operation of this non-G4 pG/pC system (error checking/output-correction) could be completed within 1 h (about / of previous G4 platform) in a simpler and more efficient way. Notably, the odd pG/pC with analogous functions was also achieved through negative logic conversion to the fabricated even one. Furthermore, the same system could also perform three-input concatenated logic computation (XOR-INHIBIT), enriching the complexity of PDs-based logic computation.

A simple, label-free, electrochemical DNA parity generator/checker for error detection during data transmission based on “aptamer-nanoclaw”-modulated protein steric hindrance

“…Luckily, these bits can be detected via placing a parity generator (pG) at the sending module and a parity checker (pC) at the receiving module. As described in the pG/pC operating principles,24–29 an even pG could generate an additional parity bit (P) and add it to the initial binary bits Dn, changing the number of 1's ( Σ ) in the DnP string to even. For example, if two bits of data (D1 and D2) are to be sent, the 2-bit even pG will endow a binary value to P (the output of pG) in light of the truth table of an XOR gate (see Scheme 1A and Fig.…”

“…The Σ value of the D1D2P string received by the pC remains even, and the pC exhibits a “normal” signal (Scheme 1A, the smiling face) via yielding output C = 0. However, if errors appear during the transmission of the three bits, the Σ value of the received wrong 3-bit string will change to odd (see Table 1), then the pC will give an “alarm” signal (Scheme 1A, the sad face) via producing output C = 1 24–29. All of the above describes the “error detection” procedure of the even pG/pC, and the odd pG/pC qualifies similar functions.…”

“…All of the above describes the “error detection” procedure of the even pG/pC, and the odd pG/pC qualifies similar functions. Although scientists have made great efforts to advance the pG/pCs, most of the current pG/pCs are constructed upon semiconductor substrates,24–29 and only a few molecular pG/pCs have been achieved based on organic molecules or DNAs using optical (fluorescent or colorimetric) signals as outputs 28,29. To the best of our knowledge, no electrochemical DNA pG/pC system has ever been reported and further endeavours are required to realize it.…”

Tyramine Hydrochloride Based Label‐Free System for Operating Various DNA Logic Gates and a DNA Caliper for Base Number Measurements

“…There is no doubt that aD NA system that could not only perform DNA analysis, but also execute complicated logic computation would greatly fulfill the requirements of computing complexity. [11,14,15,34] The above caliperc ould also execute AND-AND logic computation ( Figure 6A). Strands G0 and GB were used as two inputs of the first AND logic gate, the outputs of which were different mixtures of G0 and GB, in which the formation of duplex G0/GB was defined aso utput 1a nd otherm ixtures of the two strands were defined as output 0, respectively.A sm entioned previously,o nly the coexistence of all three strandsc ould form intact G4.…”

Dual-electrochromic bipolar electrode-based universal platform for the construction of various visual advanced logic devices

“…[10][11][12] Although great research achievements have been realized in this area, there is still considerable room for progress. 13,14 One significant limitation is that most of the previously reported advanced logic gates (such as full/half adder/subtractor, 15 encoder/decoder, 7,16 and multiplexer/demultiplexer 17,18 ) were fabricated using luminescent 19,20 or traditional electrochemical platforms, 10,21 whose outputs (luminescence, voltage, current) were often recorded using additional equipment and difficult to visualize by the naked eye. By contrast, colorimetric logic platforms present visual outputs that are rapidly responsive, easy-to-read, and could be observed by the naked eye.…”