Enzyme-free ultrasensitive fluorescence detection of epithelial cell adhesion molecules based on a toehold-aided DNA recycling amplification strategy

Understanding the relationship between sequences and kinetics of DNA strand displacements

Precisely modulating the kinetics of toehold-mediated DNA strand displacements (TMSD) is essential for its application in DNA nanotechnology. The sequence in the toehold region significantly influences the kinetics of TMSD. However, due to the large sample space resulting from various arrangements of base sequences and the resulted complex secondary structures, such a correlation is not intuitive. Herein, machine learning was employed to reveal the relationship between the kinetics of TMSD and the toehold sequence as well as the correlated secondary structure of invader strands. Key factors that influence the rate constant of TMSD were identified, such as the number of free hydrogen bonding sites in the invader, the number of free bases in the toehold, and the number of hydrogen bonds in intermediates. Moreover, a predictive model was constructed, which successfully achieved semi-quantitative prediction of rate constants of TMSD even with subtle distinctions in toehold sequence.

Aptamer-Based Probes for Cancer Diagnostics and Treatment

Aptamers are single-stranded DNA or RNA oligomers that have the ability to generate unique and diverse tertiary structures that bind to cognate molecules with high specificity. In recent years, aptamer researches have witnessed a huge surge, owing to its unique properties, such as high specificity and binding affinity, low immunogenicity and toxicity, and simplicity of synthesis with negligible batch-to-batch variation. Aptamers may bind to targets, such as various cancer biomarkers, making them applicable for a wide range of cancer diagnosis and treatment. In cancer diagnostic applications, aptamers are used as molecular probes instead of antibodies. They have the potential to detect various cancer-associated biomarkers. For cancer therapeutic purposes, aptamers can serve as therapeutic or delivery agents. The chemical stabilization and modification strategies for aptamers may expand their serum half-life and shelf life. However, aptamer-based probes for cancer diagnosis and therapy still face several challenges for successful clinical translation. A deeper understanding of nucleic acid chemistry, tissue distribution, and pharmacokinetics is required in the development of aptamer-based probes. This review summarizes their application in cancer diagnostics and treatments based on different localization of target biomarkers, as well as current challenges and future prospects.

Correction: A fluorescent biosensor for cardiac biomarker myoglobin detection based on carbon dots and deoxyribonuclease I-aided target recycling signal amplification

Correction for ‘A fluorescent biosensor for cardiac biomarker myoglobin detection based on carbon dots and deoxyribonuclease I-aided target recycling signal amplification’ by Jishun Chen et al., RSC Adv., 2019, 9, 4463–4468, https://doi.org/10.1039/C8RA09459D.

Correction: Ultrasensitive fluorescent aptasensor for CRP detection based on the RNase H assisted DNA recycling signal amplification strategy

[This corrects the article DOI: 10.1039/C9RA01352K.].

Aptamer-based fluorescent sensors for the detection of cancer biomarkers

Aptamers are short single-stranded RNA or DNA molecules that can recognize a series of targets with high affinity and specificity. Known as "chemical antibodies", aptamers have many unique merits, including ease of chemical synthesis, high chemical stability, low molecular weight, lack of immunogenicity, and ease of modification and manipulation compared to their protein counterparts. Using aptamers as the recognition groups, fluorescent aptasensors provide exciting opportunities for sensitive detection and quantification of analytes. Herein, we give an overview on the recent development of aptamer-based fluorescent sensors for the detection of cancer biomarkers. Based on various nanostructured sensor designs, we extended our discussions on sensitivity, specificity and the potential applications of aptamer-based fluorescent sensors in early diagnosis, treatment and prognosis of cancers.

An enzyme-mediated universal fluorescent biosensor template for pathogen detection based on a three-dimensional DNA walker and catalyzed hairpin assembly

An enzyme-mediated universal fluorescent biosensor template for rapid detection of pathogens was developed based on the strategy of a three-dimensional (3D) DNA walker and catalyzed hairpin assembly (CHA) reaction. In the bacterial recognition step, a strand displacement reaction between bacteria and the double-stranded complex caused the release of the walker strand. The walker strand triggered the DNA walker to produce an enzyme fragment, and the DNA walker used gold nanoparticles (AuNPs) as the track to provide an excellent DNA ligand anchoring area. In the CHA step, the enzyme fragment induced the CHA cycle to yield fluorescence signals, which greatly enhanced the conversion ratio of trigger DNA and the sensitivity of the fluorescent biosensor. The effect of the distance and density of the DNA ligand was studied by adjusting the length of poly-adenine (PolyA), and was further explored by its reaction kinetics. By comparing the maximum reaction rate (Vmax), Michaelis constant (Km) and turnover number (Kcat), the optimized PolyA probe was assessed and identified. In this work, the optimized PolyA-DNA probe exhibited an outstanding sensitivity in Salmonella typhimurium (S. ty) detection, which is 11.9 times and 4.6 times higher than those of the SH-DNA and the MCH treated SH-DNA. Meanwhile, a detection limit of 28.1 CFU mL-1 was achieved in Escherichia coli (E. coli) detection. Furthermore, the biosensor achieved good selectivity and high repeatability with recoveries of 91%-115% for real sample detection. Considering these advantages, this template has great potential as a routine tool for pathogen detection and has wide applications in the field of global public health and food safety.

Construction of electrochemical aptasensor of carcinoembryonic antigen based on toehold-aided DNA recycling signal amplification

Carcinoembryonic antigen (CEA), serves as a broad-spectrum tumor marker, and plays an important role in reflecting the existence, therapeutic evaluation, development, monitoring and prognosis of many types of cancer. An electrochemical aptasensor was designed for CEA detection based on toehold-aided DNA recycling. A partially hybridized Probe-4 (i.e. P2/P3/P4) was self-assembled on the surface of a gold electrode serving as the sensing platform. For CEA detection, CEA can bind with aptamer and free probe-1 (P1) can hybridize with P4, triggering toehold-aided DNA recycling. This enables the hybridization of more probe-5 (P5) (labeled with methylene blue (MB)) with P4, causing more methylene blue (MB) to be brought close to the electrode surface. An amplified current signal was thus generated due to more MB in the electrode surface. The proposed design showed good linearity between current response and log CEA concentration ranging from 0.1 to 50 ng·mL^-1, with a detection limit of 20 pg mL^-1. This aptasensor also showed high specificity for CEA detection, and was successfully used in spiked biological samples.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

Signal amplification by strand displacement in a carbon dot based fluorometric assay for ATP

A fluorometric ATP assay is described that makes use of carbon dots and graphene oxide along with toehold-mediated strand displacement reaction. In the absence of target, the fluorescence of carbon dots (with excitation/emission maxima at 360/447 nm) is strong and in the "on" state, because the signal probe hybridizes with the aptamer strand and cannot combine with graphene oxide. In the presence of ATP, it will bind to the aptamer and induce a strand displacement reaction. Consequently, the signal probe is released, the sensing strategy will change into the "off" state with the addition of graphene oxide. This aptasensor exhibits selective and sensitive response to ATP and has a 3.3 nM detection limit. Graphical abstract Schematic of signal amplification by strand displacement in a carbon dot based fluorometric assay for ATP. This strategy exhibits high sensitivity and selectivity with a detection limit as low as 3.3 nM.

Ultrasensitive fluorescent aptasensor for MUC1 detection based on deoxyribonuclease I-aided target recycling signal amplification

A novel sensing strategy for sensitive detection of mucin 1 protein (MUC1) based on deoxyribonuclease I-aided target recycling signal amplification was proposed. In this paper, in the absence of MUC1, the MUC1 aptamer is absorbed on the surface of graphene oxide (GO) via π-stacking interactions. This results in quenching of the fluorescent label and no fluorescence signal is observed. Upon adding MUC1, the probe sequences could be specifically recognized by MUC1, leading to an increase in the fluorescence intensity. The detection limit is as low as 10 pg mL⁻¹, and a linear range from 50 pg mL⁻¹ to 100 ng mL⁻¹. The assay is specific and sensitive, and successfully applied to the determination of MUC1 in spiked human serum, urine and saliva. Importantly, the proposed aptasensing strategy has great potential in detecting various protein and even cancer cells.

A novel sensing strategy for sensitive detection of mucin 1 protein (MUC1) based on deoxyribonuclease I-aided target recycling signal amplification was proposed.