Studies of Functional Nucleic Acids Modified Light Addressable Potentiometric Sensors: X-ray Photoelectron Spectroscopy, Biochemical Assay, and Simulation

Abstract

Functional nucleic acids (FNAs) are promising sensing elements, and extensive interests are excited to integrate FNAs with transducers for biochemical assays. However, efforts for FNAs modified light-addressable-potentiometric-sensor (FNA-LAPS) are rarely reported. LAPS is a versatile transducer with electrolyte-insulator-semiconductor (EIS) structure and can respond almost to any surface electronic deviation. Herein, organized studies for FNA-LAPS including experiments, theoretical derivations, and MEDICI (Synopsys) simulations are presented using Pb-DNAzyme GR-5 and Ag-aptamer as proof-of-concepts, which are typical FNAs with distinctive sensing strategies. First, the on-LAPS occurrences of FNAs and their particular sensing actions are evidenced by tracking their X-ray photoelectron spectroscopy (XPS) core spectra of N 1s, P 2p, C 1s, Ag, etc. Then, applications of FNA-LAPS are executed by a homemade and mobile-phone controlled system, the limit-of-detection is 0.01 ppb, sensitivities are 2.86 (Pb) and 1.53 (Ag) mV/log(ppb) ( R = 0.98), respectively. Furthermore, a charge and resistor mechanism (C&R) is proposed to illustrate the measured LAPS responding for FNAs and their sensing behaviors (Pb-mediated cleavage and Ag-mediated folding), based on carefully analyzing basic LAPS' experimental data and MEDICI calculated distributions of build-in potentials, energy-bands, carriers, etc., at the EIS microinterface (semiconductor side). Finally, demonstrations for C&R based FNA-LAPS principle are provided by the use of MEDICI, as a means to bridge experiments and theoretical deductions. In general, a cross-study for FNA-LAPS is proposed including XPS characterization, biochemistry detection, theoretical analysis, and MEDICI simulation, it is believed their powerful combination would provide an ideal workstation for analytical chemistry applications, not only the traditional determinations but also facilitations for investigating FNAs' configurational transformations.

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

“…In Figure 2B, the resolved curves of P 2p core spectra (SP_ i , i = 1, 2, 3) can be classified into two groups, which are close to 134.0 ± 0.1 and 133.0 ± 0.1 eV, and they agree with P atoms in the phosphate backbone of unpaired ssDNA. 31−33 By comparing the N 1s core spectra (Figure 2C) of TCPP-decorated ones (#1 and #2) with #3 (blank), the existence of TCPP can be identified by the peaks at about 397.6 and 399.9 eV, which are contributed by the N atoms in the porphyrin ring. 34 Moreover, the peak fitting analyses of N 1s and C 1s core spectra (Figures S3 and S4) can provide more proofs of the porphyrin ring and carboxyl in TCPP.…”

“…The gradually growing V out with the changing of V REF from left to right (Figure 3A) agrees with LAPS’ theory for the p-type Si substrate. 31 The measured V out is the out-express of the inner electric field ( E I ) from SI to the bulk of p-Si, which can be altered by the interface state at Si and insulator SiO 2 /Si 3 N 4 (SI), as illustrated in Figure 3A-1,A-2. (1) Exhausted state.…”

Reduced Carboxylate Graphene Oxide based Field Effect Transistor as Pb2+ Aptamer Sensor

“…The response of SP-X-FET for the anchored LSA can be explained in two ways: (1) electron carriers can be injected into the graphene layers through its phosphate backbone, the currents (I DS ) should be increased by the anchored LSA [56]; (2) in reference with our previous work about functional nucleic acid modified LAPS [36], LSA molecules are in double strand architecture before reaction with Pb 2+ , they will increase the resistor across EDL (R EDL ). When LSA is in low concentration, the former is dominant, then the currents are increased, as shown by the red curve in Figure 5A; when the LSA concentration is 1000 nmol/L, LSA molecules will be stacked on the first layer LSA, which will increase R EDL and V EDL , then the lowered I DS is measured.…”

“…It can be identified from the data of apta-X-FET (X = rGO-COOH, rGO and pGp), the highest responding for Pb 2+ and the best coincidence with ICP-MES results are displayed by X = rGO-COOH (the red circle symbols) with the limit-of-detection (LOD) of 0.001ppb, the linear fitted line is obtained in the range of 1–10 ppb with the sensitivity of 6.57 %/ppb (R 2 = 0.91). The sensing principle of the apta-X-FETs for Pb 2+ is outlined at here based on the illustrated mechanism in Section 3.4, as well as our previous work about Pb 2+ mediated cleavage effect on LAPS [36]. LSA’s sensing action can change I DS by two ways: (1) after reaction with Pb 2+ , LSA molecule’s substrate chain (mentioned in Section 2.1) is left, it is a flexible single string and tends to lie on the graphene channel, then more electrons are implanted into the channel; (2) the LSA induced R EDL (in Figure S7) after being cut by Pb 2+ becomes negligible, because the remaining LSA part is so tender that it cannot stand on the channel anymore; then, V EDL will be reduced.…”

“…In this aspect, to prevent lead poisoning, Pb 2+ detection techniques are necessary, such as conventional inductively coupled plasma mass spectrometry (ICP-MS), nano-material assisted colorimetric detection [31,32], UV-vis absorption [33] and stripping analysis [34,35]. LSA sensing strategy which is believed to be the Pb 2+ caused cleavage effect at the position of ribonucleotide adenosine (rA) [5,6], has also been demonstrated to be available to functionalize field effect type sensors [11,36]. The parallel ICP-MS examinations, interference experiments for other metal ions (Cu 2+ , Mn 2+ , Mg 2+ , Hg 2+ , etc.…”