Meso-tetra(4-carboxyphenyl)porphine-Enhanced DNA Methylation Sensing Interface on a Light-Addressable Potentiometric Sensor

Abstract

DNA methylation (DNAm) sensors are an emerging branch in the discipline of sensors. It is believed to be able to promote the next generation of epigenetics-based diagnostic technology. Differing from the traditional biochemical sensors that aimed at individual molecules, the challenge in DNAm sensors is how to determine the amount of 5-methylcytosine (5mC) in a continuous nucleotide sequence. Here, we report a comparative study about meso-tetra(4-carboxyphenyl)porphine (TCPP)-based DNAm sensing interfaces on a light-addressable potentiometric sensor (LAPS), depending on TCPP’s postures that are flat in the π-conjugated TCPP layer on reduced-graphene-oxide-decorated LAPS (#1) and stand-up in the covalently anchored TCPP on glutaraldehyde (GA)-treated LAPS (#2), along with the blank one (only GA-treated LAPS, #3). These DNAm sensing interfaces are also distinct from the traditional biosensing interface on LAPS, that is: it is not functionalized by the sensing indicator (5mC antibody, in this case) but by the target nucleotide sequence. The surface characterization techniques such as Raman spectra, scanning electron microscopy, and X-ray photoelectron spectroscopy are conducted to prove the decorations, as well as the anchored nucleotides. It is found that, though all of them can detect as low as one 5mC in the target sequence, the enhanced DNAm sensitivity is obtained by #2, which is evidenced by the higher output-voltage changing ratio for the 5mC site of #2 than those of #1 and #3. Furthermore, the underlying causes for the improved sensitivity in #2 are proposed, according to the conformational and electronic properties of TCPP molecules. Conclusively, TCPP’s synergetic function, including the molecular configuration and the activate (carboxyl) groups on its peripheral substituents, to improve the DNAm sensing interface on LAPS is investigated and demonstrated. This can shed light on a new approach for DNA methylation detection, with the merits of low cost, independence on bisulfite conversion, and polymerase chain reaction.

Possibility of Combining Carbon Dots and Liquid Exfoliated Graphene as a Carbon-Based Light Addressable Potentiometric Sensor

“…The improved linear sensitivity for identifying the 5mC sites is confirmed by comparing these data with those measured by Si-LAPS. 15 We are convinced that the as-proofed C-LAPS could be an ideal candidate for the next-generation LAPS. The ssDNA strands were purchased from Sangon Biotech Co. Ltd., Shanghai (China).…”

“…The electronic feature of C-LAPS examined using the LAPS detection setup is presented in Figure S6 (blank line), which is similar to that of Si-LAPS. 15 Response to the Immune Reaction. So far, the basic electronic and photoelectronic features about C-LAPS with the structure of CDs/LEG@PDDA/ITO are carefully examined, and the inherent working mechanism surmised from the experimental data demonstrates that the basic principle of the traditional Si-LAPS is replicated here, that is to say that the key element of Si-LAPS is replaced by the heterojunction of CDs and LEG stacking film, as mentioned in the section of Working Mechanism of C-LAPS.…”

“…C-LAPS' response to the immobilized ssDNA is coincident with the response of Si-LAPS to the same ssDNA immobilization tests. 15 Furthermore, the immune reaction between 5mC anchored on ssDNA and its antibody is examined by the ssDNAmodified C-LAPS. The I ph response is presented in Figure 6C,D.…”

Light-Addressable Potentiometric Sensors in Microfluidics

“…Therefore, various biochemical reactions such as the enzymatic reaction, redox reaction, and antigen–antibody specific reaction could potentially be detected by the LAPS. At present, the LAPS has broad application prospects in the fields of pH detection ( Yang et al, 2020 ), ion detection ( Wen et al, 2016 ; Zhang et al, 2018 ), molecular detection ( Li et al, 2020 ; Zhang et al, 2020 ), enzymatic reaction ( Liang et al, 2017 ), cell metabolism ( Dantism et al, 2015 ; Dantism et al, 2017 ; Wu et al, 2017 ; Du et al, 2018 ; Dantism et al, 2019 ), immunoassay, and DNA detection ( Wu et al, 2015 ; Jia et al, 2019 ; Tian et al, 2019 ).…”

Light-Addressable Potentiometric Sensors in Microfluidics

“…Therefore, various biochemical reactions such as enzymatic reaction, redox reaction, antigen-antibody specific reaction, etc., could potentially be detected by LAPS. At present, LAPS has broad application prospects in the fields of pH detection [4] , ion detection [5][6] , molecular detection [7][8] , enzymatic reaction [9] , cell metabolism [10][11][12][13][14] , immunoassay and DNA detection [15][16][17] .…”