An optical DNA logic gate based on strand displacement and magnetic separation, with response to multiple microRNAs in cancer cell lysates

Borderline Boolean states improve the biosensing applications of DNA circuits

Molecular circuits have been used in a wide range of diagnosis applications, from the detection of chemical molecules in solution to the complex processing of cell surface receptors. One of the most important challenges of these systems is the lack of distinguishability between different circuit states when each circuit state represents a specific disease. In this work, we designed a molecular amplification circuit with borderline Boolean states that each state can be distinguished with different color intensity. For this purpose, two DNA complexes and four DNA hairpin structures were designed to detect miR-218 and miR-215 biomarkers. One of the designed DNA complexes has two G-quadruplex structures and the other has only one G-quadruplex structure. In the absence of the inputs, all three G-quadruplex structures are active and produce a high-intensity signal, while in the other three states, including the presence of miR-218, the presence of miR-215, and the presence of both inputs, respectively, one, two, and zero G-quadruplex structures are active. Therefore, the designed system can identify two different biomarkers simultaneously with different signal ratios, which can easily distinguish the different states of the circuit. This strategy is very promising to identify diseases in which any combination of biomarkers leads to a particular disease.

Phosphate-responsive 2D-metal–organic-framework-nanozymes for colorimetric detection of alkaline phosphatase

Phosphate-responsive peroxidase-mimicking two-dimensional-metal–organic-framework nanozymes were employed to develop alkaline phosphatase assays with tunable dynamic ranges and colorimetric logic gates.

Growing prospects of DNA nanomaterials in novel biomedical applications

As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.

A DNA Nanotube-Peptide Biocomplex for mRNA Detection and Its Application in Cancer Diagnosis and Targeted Therapy

A biocomplex of DNA nanotube-peptide, consisting of six concatenated DNA strands, three locked DNA strands, and a cell-penetrating peptide, is reported. The barrel-structured DNA nanotube-peptide was successfully applied as a codrug-delivery system for targeting cancer therapy. The mucin 1 protein (MUC-1) aptamer is part of a DNA nanotube that can specifically recognize MUC-1 protein on the surface of MCF-7 cells. Cyclo (Arg-Gly-Asp-d-Phe-Lys; cRGD), as a cell-penetrating peptide, facilitates recruitment and uptake of targeting drugs by binding to integrin receptors (α_v β₃ ) of the cytomembrane surface. Anticancer drugs doxorubicin (DOX) and paclitaxel (PTX) were loaded into the capsulated DNA nanotube-peptide (CDNP), which was used as codrug cargo models. The as-prepared biocomplex can be utilized not only to deliver drugs, but also to achieve anticancer effects in vivo. Experimental results suggested that the treatment efficacy of the codrug delivery platform (CDNP/DOX/PTX) was better than that of a single-drug delivery platform (CDNP/DOX or CDNP/PTX). This system, which is composed of DNA strands and peptide, has good biocompatibility and biodegradability. Furthermore, the system can readily detect target mRNA in MCF-7 cells in vitro. The detection limits of mRNA are 9.7×10^-8 and 1.8×10^-8  m with CDNP/DOX and CDNP/PTX-FITC (FITC=fluorescein isothiocyanate), respectively, as probes.

Fluorometric determination of microRNA-155 in cancer cells based on carbon dots and MnO2 nanosheets as a donor-acceptor pair

A fluorometric method is presented for sensitive deternination of microRNA. It is making use of carbon dots (C-dots) loaded with a DNA probe as fluorophore and MnO₂ nanosheets as the quenching agent. The blue-green fluorescence of the DNA-loaded C-dots is quenched by the MnO₂ nanosheets, but restored on binding target microRNA-155. The maximum excitation wavelength and the maximum emission wavelength of C-dots are at 360 nm and 455 nm, respectively. Fluorescence correlates linearly with the log of the microRNA-155 concentration in two ranges, viz. from 0.15 to 1.65 aM and from 1.65 to 20 aM. The detection limit is as low as 0.1 aM. The assay can discriminate between fully complementary and single-base mismatch microRNA. The assay displayed high specificity when used to detect MCF-7 breast cancer cells which can be detected in concentrations from 1000 to 45,000 cells·mL^-1, with a 600 cells·mL^-1 detection limit. The method was applied to the analysis of serum samples spiked with microRNA, and satisfactory results were acquired. Graphical abstract Schematic of a fluorometric sensing platform for miRNA-155. The method relies on a FRET process between C-dots and MnO₂ nanosheets. This strategy has a practical application for detection of miRNA in cell lines and biological fluids.

Luminescence determination of microRNAs based on the use of terbium(III) sensitized with an enzyme-activated guanine-rich nucleotide

A method is reported for the fluorometric quantitation of microRNA. It is making use of a luminescent probe deribed from terbium(III) ion whose fluorescence is sensitized with a guanine-rich (G-rich) nucleotide. The probe has a large Stokes' shift and strong and sharp emission bands. The assay relies on the wide substrate specificity of terminal deoxynucleotidyl transferase (TdTase), which catalyzes the formation of long G-rich nucleotides when using microRNA primer as a trigger to start the polymerization. The addition of Tb(III) induces the formation of a G-quadruplex from the G-rich nucleotide, and this strongly enhances the green fluorescence of Tb(III) (peaking at 545 nm upon photoexcitation at 290 nm). Specifically, microRNA-21 was chosen as the analyte. The fluorescence intensity of Tb(III) increases linearly in the 1 pM to 1 nM microRNA concentration range, and the detection limit is as low as 0.11 pM. The method can distinguish between family members of microRNA and performs excellently even when applied to extracts of cancer cells. Graphical abstract A fluorometric technique is reported for the determination of microRNA. It is based on signal enhancement based on the sensitization of terbium(III) via a guanine-rich nucleotide sequence. Klenow Fragment exo^- (KFexo^-) generates DNA sequence at the 3'-OH of microRNA, and terminal deoxynucleotidyl transferase (TdTase) catalyzes the formation of long G-rich nucleotides.

Dual approach for the colorimetric determination of unamplified microRNAs by using citrate capped gold nanoparticles

The authors describe a method for the colorimetric determination of unamplified microRNA. It is based on the use of citrate-capped gold nanoparticles (AuNPs) and, alternatively, a microRNA-probe hybrid or a magnetically extracted microRNA that serve as stabilizers against the salt-induced aggregation of AuNPs. The absorbance ratios A₅₂₅/A₆₂₅ of the reacted AuNP solutions were used to quantify the amount of microRNA. The assay works in the range of 5-25 pmol microRNA. The lower limit of detection (LOD) is 10 pmol. The performance of the method was tested by detection of microRNA-210-3p in totally extracted urinary microRNA from normal, benign, and bladder cancer subjects. The sensitivity and specificity for qualitative detection of urinary microRNA-210-3p using the assay are 74% and 88% respectively, which is consistent with real time PCR based assays. The assay was applied to the determination of specific microRNA by using its specific oligo targeter or following magnetic isolation of the desired microRNA. The method is simple, cost-efficient, has a short turn-around time and requires minimal equipment and personnel. Graphical abstract Schematic of the two detection schemes: In the first approach, matched microRNA hybridizes with its specific probe to stabilize gold nanoparticles (AuNPs) against salt induced aggregation and to leave the red color of the AuNPs unchanged. In the second one, microRNA extracted via magnetic nanoparticles (MNP) stabilizes AuNPs against aggregation.

Universal, colorimetric microRNA detection strategy based on target-catalyzed toehold-mediated strand displacement reaction

In this work, we developed a novel, label-free, and enzyme-free strategy for the colorimetric detection of microRNA (miRNA), which relies on a target-catalyzed toehold-mediated strand displacement (TMSD) reaction. The system employs a detection probe that specifically binds to the target miRNA and sequentially releases a catalyst strand (CS) intended to trigger the subsequent TMSD reaction. Thus, the presence of target miRNA releases the CS that mediates the formation of an active G-quadruplex DNAzyme which is initially caged and inactivated by a blocker strand. In addition, a fuel strand that is supplemented for the recycling of the CS promotes another TMSD reaction, consequently generating a large number of active G-quadruplex DNAzymes. As a result, a distinct colorimetric signal is produced by the ABTS oxidation promoted by the peroxidase mimicking activity of the released G-quadruplex DNAzymes. Based on this novel strategy, we successfully detected miR-141, a promising biomarker for human prostate cancer, with high selectivity. The diagnostic capability of this system was also demonstrated by reliably determining target miR-141 in human serum, showing its great potential towards real clinical applications. Importantly, the proposed approach is composed of separate target recognition and signal transduction modules. Thus, it could be extended to analyze different target miRNAs by simply redesigning the detection probe while keeping the same signal transduction module as a universal signal amplification unit, which was successfully demonstrated by analyzing another target miRNA, let-7d.