Recent Developments in DNA-Nanotechnology-Powered Biosensors for Zika/Dengue Virus Molecular Diagnostics

Abstract

Zika virus (ZIKV) and dengue virus (DENV) are highly contagious and lethal mosquito-borne viruses. Global warming is steadily increasing the probability of ZIKV and DENV infection, and accurate diagnosis is required to control viral infections worldwide. Recently, research on biosensors for the accurate diagnosis of ZIKV and DENV has been actively conducted. Moreover, biosensor research using DNA nanotechnology is also increasing, and has many advantages compared to the existing diagnostic methods, such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). As a bioreceptor, DNA can easily introduce a functional group at the 5' or 3' end, and can also be used as a folded structure, such as a DNA aptamer and DNAzyme. Instead of using ZIKV and DENV antibodies, a bioreceptor that specifically binds to viral proteins or nucleic acids has been fabricated and introduced using DNA nanotechnology. Technologies for detecting ZIKV and DENV can be broadly divided into electrochemical, electrical, and optical. In this review, advances in DNA-nanotechnology-based ZIKV and DENV detection biosensors are discussed.

Keywords: DENV; DNA nanotechnology; ZIKV; electrical biosensor; electrochemical biosensor; optical biosensor.

Figure 3

DNA−technology−based ZIKV and DENV detection method using electrochemical method. (A) Nyquist diagram showing the three−step impedance behavior of the gold−Polyethylene terephthalate (PET) biosensor: (a) Clean electrode, solid black line; (b) Z_cap (capture sequence) immobilization; (c) Z_amp,(complementary sequence) hybridization full blue circle (Z_cap immobilized at 0.40 μM for 6 h at a Z_amp concentration of 130 nM). (B) Cyclic voltammetry for three steps of gold-PET biosensor: (a) Clean electrode, black curve; (b) Immobilization of the capture sequence (Z_cap), red curve; (c) Hybridization, blue curve (immobilization of 0.40 µM Z_cap for 6 h at 45 °C and a Z_amp concentration of 130 nM). (C) Analytical curve of charge transfer resistance (ΔR_ct = R_ct Hib − R_ct Im). A total of 0.40 μM fixation of the capture sequence (Z_cap) for 5 h. Hybridizations with negative controls using Z_amp at concentrations of 25, 38, 63, 130, 228, 308 and 340 nM (blue circles) and D_amp at concentrations of 63, 130, 228 and 308 nM (orange triangles). Reproduced with permission from [88], published by Elsevier, 2019. (D) Schematic diagram of the electrochemical aptasensor for NS1 detection. (E) Analytical curves comparing biosensor performance for NS1-S1, S4 in undiluted human serum (standard deviations for at least 3 individual electrodes). (F) Changes in charge transfer resistance (ΔR_ct) of undiluted human serum NS1-S4, NS1-S1 and envelope protein at a concentration of 1 ng/mL for other DENV proteins. Reproduced with permission from [89] published by Elsevier, 2021. (G) Schematic diagram of a platform for the detection of two different DNA sequences (ZIKV, DENV) using one electrochemical sensor. (H) Calibration curve of ZIKV sensor response (current density) at a 10 min response time using T-ZIKV of the corresponding concentration with m−ZIKV and f−ZIKV. (I) Calibration curve of DENV sensor response at a 30 min response time using T−DENV of the corresponding concentration with m−DENV−11 and f−DENV−19. (concentration range 1 nM–75 nM). Reproduced with permission from [90], published by Elsevier, 2019.

Figure 5

DNA−technology−based ZIKV and the DENV detection method using electrical method. (A) Conceptual drawing of ZIKV RNA affinity sensor with AC electrokinetics (ACEK) capacitive sensing. Analytes are attracted towards the electrode surface through ACEK effects. Specific binding between the functionalized ZIKV probe and ZIKV RNA causes a change at the interface (Cint), and the binding leads to a change in Cint, which is detected electrically using the same ACEK signal. Other particles, including influenza A virus, human herpesvirus virus 1 (HSV−1), DNA and DENV RNA, are considered non-specific interferences. (B) Responses of non-specific nucleic acid (HSV−1 and DENV) and virus (influenza A), and dose–response of ZIKV RNA spiked in serum/lysing solution. Reproduced with permission from [97], published by European Chemical Societies Publishing, 2017. (C) Dose responses of ZIKV gRNA human serum samples in 1:1:1 and 2:1:1 mixtures of serum, Guanidine thiocyanate (GuSCN), and 2 × saline-sodium citrate (SSC) as hybridization buffers. ZIKV (target) and DENV (interference) gRNA sample concentrations were converted into the equivalent concentration in pure serum. Adapted with permission from [98]. (D) A schematic diagram of the RT−PCR product of DEN−2 hybridized to the PNA−functionalized silicon nanowire (SiNW) sensor. Because PNA is neutral, the resistance change of the SiNW sensor before and after hybridization is attributed to the introduction of the negatively charged DNA (RT−PCR product). (E) Specificity of the SiNW sensor for the RT−PCR product of DEN−2. The purified RT−PCR product was applied to the complementary and the non-complementary PNA-functionalized SiNW sensors, respectively. (F) Resistance change versus concentrations of the RT-PCR product of DEN−2. Varying concentrations of the RT−PCT product from 100 fM to 1 fM were applied to the PNA-functionalized SiNW sensor. Negative RT−PCR product was used as a control. Reproduced with permission from [100], published by Elsevier, 2010.

Figure 7

DNA-technology-based ZIKV and DENV detection method using optical method. (A) Schematic illustration of the conjugation of plasmonic NPs to GSH-CdSeS quantum dots (Qdot646). (B) (a) Effect of fluorescence quenching of plasmonic NPs on fluorescence of Qdot646 particles by type; (b–e) LSPR-mediated fluorescence enhancement of ZIKV RNA using type-specific plasmonic NP-Qdot-MB biosensor probes. Reproduced with permission from [115] published by Elsevier, 2017. (C) Schematic illustration of fluorescent biosensor for ZIKV detection using 3D DNA Walker part and LCHA part. (D) Changes in the FL spectrum of ZIKV according to the concentration of the fabricated biosensor. Reproduced with permission from [122], published by Elsevier, 2022. (E) Schematic illustration of the fabricated DENV detection fluorescence aptasensor. (F) Calibration curve of F_DBA+NS1/F_DBA according to concentration change of DENV NS1 in buffer and 5% human serum. Reproduced with permission from [124], published by Elsevier, 2021.

Figure 1

Application of DNA nanotechnology in (A) DNA hydrogel, (B) biosensors, (C) vaccines and (D) drug delivery.

Figure 2

Schematic diagram of an electrochemical sensor. Changes in CV, EIS, and SWV signals before and after binding.

Figure 4

Schematics of (A) FET-based biosensor showing the change in voltage and current before and after bonding and (B) capacitive biosensor showing the change in capacitance before and after bonding.

Figure 6

Schematic diagram of an optical sensor. Changes in intensity signals before and after binding.