Complementary Base Research Articles

All-carbon sandwich-type self-powered biosensor for ultrasensitive detection of femtomolar miRNA-141

The latest research shows that the expression level of microRNA-141 can predict the number of prostate cancer cells in the human body and has become an important biomarker. In this paper, an all-carbon sandwich self-powered biosensor based on graphene and carbon cloth is constructed for the highly sensitive detection of the prostate tumor marker miRNA-141. First, gold nanoparticles modified carbon cloth is applied for substrate electrode, and bilirubin oxidase is then immobilized on it to prepare the biocathode of the biofuel cell. Then, aptamer 1 is immobilized on gold nanoparticles-modified carbon cloth as the electrode substrate. The bioconjugate is prepared by immobilizing the aptamer 2-glucose oxidase complex on gold nanoparticles/graphene. In the biofuel cell-based self-powered sensing system, when the target microRNA-141 is present, it undergoes complementary base pairing with aptamer 1 and aptamer 2, and the bioconjugates are immobilized on the anode to form the sandwich structure. The enzyme on the anode undergoes an oxidation reaction to catalyze the reduction of oxygen, and the electrochemical respond of the system increases significantly. The results show that the concentration of microRNA-141 is proportional to the open-circuit voltage value ranging from 0.0001 to 1000 pmol/L with a detection limit of 50 amol/L (S/N = 3). The method has high sensitivity and excellent selectivity and can be applied to sensitively detect tumor marker microRNA-141 in biological matrix.

Improving Precise Genome Editing Using Donor DNA/gRNA Hybrid Duplex Generated by Complementary Bases.

In precise genome editing, site-specific DNA double-strand breaks (DSBs) induced by the CRISPR/Cas9 system are repaired via homology-directed repair (HDR) using exogenous donor DNA templates. However, the low efficiency of HDR-mediated genome editing is a barrier to widespread use. In this study, we created a donor DNA/guide RNA (gRNA) hybrid duplex (DGybrid) that was composed of sequence-extended gRNA and single-stranded oligodeoxynucleotide (ssODN) combined with complementary bases without chemical modifications to increase the concentration of donor DNA at the cleavage site. The efficiency of genome editing using DGybrid was evaluated in Saccharomyces cerevisiae. The results show a 1.8-fold (from 35% to 62%) improvement in HDR-mediated editing efficiency compared to genome editing in which gRNA and donor DNA were introduced separately. In addition, analysis of the nucleic acid introduction efficiency using flow cytometry indicated that both RNA and ssODNs are efficiently incorporated into cells together by using the DNA/RNA hybrid. Our technique would be preferred as a universal and concise tool for improving the efficiency of HDR-mediated genome editing.

A long noncoding RNA HILinc1 enhances pear thermotolerance by stabilizing PbHILT1 transcripts through complementary base pairing

As global warming intensifies, heat stress has become a major environmental constraint threatening crop production and quality worldwide. Here, we characterize Heat-induced long intergenic noncoding RNA 1 (HILinc1), a cytoplasm-enriched lincRNA that plays a key role in thermotolerance regulation of pear (Pyrus spp.). HILinc1 Target 1 (PbHILT1) which is the target transcript of HILinc1, was stabilized via complementary base pairing to upregulate its expression. PbHILT1 could bind to Heat shock transcription factor A1b (PbHSFA1b) to enhance its transcriptional activity, leading to the upregulation of a major downstream transcriptional regulator, Multiprotein bridging factor 1c (PbMBF1c), during heat response. Transient overexpressing of either HILinc1 or PbHILT1 increases thermotolerance in pear, while transient silencing of HILinc1 or PbHILT1 makes pear plants more heat sensitive. These findings provide evidences for a new regulatory mechanism by which HILinc1 facilitates PbHSFA1b activity and enhances pear thermotolerance through stabilizing PbHILT1 transcripts.

Enhancement of biological denitrification by the addition of novel sRNA Pda200 under antibiotic pressure

Paracoccus denitrificans can adapt to complex environmental changes and sRNAs play crucial roles during this process. This work aim to identify antibiotic-induced sRNA that regulated denitrification and explored its potential for functional enhancement of this process. Target prediction indicated complementary base pairing between the denitrifying gene nosZ and the sRNA Pda200. Anaerobic culture of P. denitrificans ATCC 19367 in the presence of florfenicol (FF) resulted in significant decreases in nosZ and Pda200 gene expression (p < 0.01). Two additional denitrifiers isolated from contaminated sediment were co-cultured with ATCC 19367 to generate a consortium. And an inducible Pda200 expression strain was also added. The results revealed that Pda200 significantly enhanced napA, napB and norB expression in different types of denitrifiers under FF condition (p < 0.05 ∼ 0.001). This study identified the sRNA Pda200 as a novel positive regulator of denitrification, which may realize the efficient treatment of antibiotic-contaminated wastewater by microbial agents.

Identification of a miRSNP Regulatory Axis in Abdominal Aortic Aneurysm by a Network and Pathway-Based Integrative Analysis.

Abdominal aortic aneurysm (AAA) refers to local abnormal expansion of the abdominal aorta and mostly occurs in elderly men. MicroRNA (miRNA) is single-stranded RNA consisting of 18–25 nucleotides. It plays a key role in posttranscriptional gene expression and in the regulation of human functions and disease development. miRNA exerts its function mainly through the binding of complementary base pairs to the 3′ regulatory region of mRNA transcripts. Therefore, miRNA-related single-nucleotide polymorphisms (miRSNPs) can affect miRNA expression and processing kinetics. miRSNPs can be classified based on their location: miRSNPs within miRNA-producing genes and miRSNPs within miRNA target genes. Increasing evidence indicates that miRSNPs play an important role in the pathogenic kinetics of cardiovascular diseases. The aim of this study was to identify potential miRNAs and integrate them into a miRSNP-based disease-related pathway network, the results of which are of great significance to the interpretation of the potential mechanisms and functions of miRSNPs in the pathogenesis of diseases.

Inhibition of miR-652-3p Regulates Lipid Metabolism and Inflammatory Cytokine Secretion of Macrophages to Alleviate Atherosclerosis by Improving TP53 Expression.

Purpose The aim was to elucidate the regulatory function of miR-652-3p on lipid metabolism and inflammatory cytokine secretion of macrophages in atherosclerosis. Methods miR-652-3p level in atherosclerosis patients, ox-LDL-treated macrophages, and their controls were monitored by Q-PCR. After ox-LDL treatment and miR-652-3p mimic, si-TP53 and their controls transfection, ELISA, and Q-PCR assays were used to detect IL-1ß, IL-6, and TNF-α levels. oil red O staining was processed to verify cholesterol accumulation. CE/TC and lipid metabolism were also detected. The protein levels of ABCA1, ABCG1, PPARα, CRT1, ADRP, and ALBP were detected by western blot assay. Based on the TargetScan database, the TP53 3′UTR region had complementary bases with miR-652-3p, which was also verified by dual-luciferase reporter gene assay. Finally, the regulation of miR-652-3p and TP53 was confirmed by rescue assay in atherosclerosis. Results miR-652-3p is highly expressed in atherosclerosis, miR-652-3p inhibitor decreased IL-1β, IL-6, and TNF-α expression after ox-LDL treatment. Knockdown of miR-652-3p reduces foam formation in ox-LDL-treated macrophages. miR-652-3p inhibitor ameliorates cholesterol accumulation and lipid metabolism disorder. miR-652-3p negatively regulated TP53 in atherosclerosis. Si-TP53 rescued the effect of miR-652 inhibitor in atherosclerosis. Conclusion miR-652-3p regulates the lipid metabolism of macrophages to alleviate atherosclerosis by inhibiting TP53 expression. It might be a potential target for atherosclerosis treatment.

Hydrazone chemistry-mediated CRISPR/Cas12a system for bacterial analysis.

In this study, a hydrazone chemistry-mediated clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a) system has been proposed for the fist time and constructed. In our system, hydrazone chemistry is designed and employed to accelerate the formation of a whole activation strand by taking advantage of the proximity effect induced by complementary base pairing, thus activating the CRISPR/Cas12a system quickly and efficiently. Moreover, the introduction of hydrazone chemistry can improve the specificity of the CRISPR/Cas12a system, allowing it to effectively distinguish single-base mismatches. The established system has been further applied to analyze Pseudomonas aeruginosa by specific recognition of the probe strand with a characteristic fragment in 16S rDNA to release the hydrazine group-modified activation strand. The method shows a wide linear range from 3.8 × 102 colony-forming units (CFU)/ml to 3.8 × 106 CFU/ml, with the lowest detection limit of 24 CFU/ml. Therefore, the introduction of hydrazone chemistry may also broaden the application of the CRISPR/Cas12a system.

Self-assembly and label-free fluorescent aptasensor based on deoxyribonucleic acid intercalated dyes for detecting lactoferrin in milk powder.

Lactoferrin (Lf), an iron-binding glycoprotein, regulates the immune system. It has broad-spectrum antimicrobial activity and is critical for child physical growth and development. As a common additive in the dairy industry, it is crucial to quantify LF content. This study established a self-assembly and universal fluorescence aptasensor for detecting LF in milk powder based on structure-selective dyes of PicoGreen intercalated in the label-free aptamer. Herein, the aptamer functions as both a specific recognition element against targets and a fluorescent signal reporter integrated with structure-selective dyes. First, the aptamer folds into a three-dimensional spatial structure based on complementary base pairings and intermolecular weak non-covalent interactions. Then, the dye is intercalated into the minor groove structures of the aptamer and triggers its potential fluorescent property. When the target exists, the aptamer binds to it preferentially, and its space structure unfolds. This causes the freeing of the subsequent dye and decreases the corresponding fluorescence. Hence, the reflected fluorescence signals could directly determine the target concentrations. Under the optimum conditions, a good linear relationship (R2, 0.980) was obtained in the Lf range from 20 to 500 nM with a detection limit of 3 nM (2.4 mg/kg) and good specificity, as well as a reliable recovery of 95.8–105.1% in milk powder. In addition, the universality was also confirmed with a good performance by quickly changing the aptamers against other targets (chlorpyrifos, acetamiprid, bovine thyroglobulin, and human transferrin) or utilizing another fluorescence dye. Therefore, this self-assembly aptasensor provides a universal and concise strategy for effective detection.

Exploration and Practice of School-enterprise Collaborative Education

In recent years, school-enterprise collaborative education has become the subject of research in higher vocational colleges. The article explores the significance of school-enterprise collaborative education and the construction of school-enterprise collaborative education mechanism. At the same time, through years of practice, it has proposed the establishment of a "gradual" talent training class system, a "one hospital one case" curriculum system, a "production and teaching sharing" joint team, a school-enterprise complementary practice base, and an off-campus craftsman spirit practice base, practical teaching 6S professional standardization and breeding system and other enterprise college talent training system.

A Cofactor-Based Mechanism for the Origin of the Genetic Code

The origin of the genetic code is probably the central problem of the studies on the origin of life. The key question to answer is the molecular mechanism that allows the association of the amino acids with their triplet codons. We proposed that the codon-anticodon duplex located in the acceptor stem of primitive tRNAs would facilitate the chemical reactions required to synthesize cognate amino acids from simple amino acids (glycine, valine, and aspartic acid) linked to the 3′ acceptor end. In our view, various nucleotide-A-derived cofactors (with reactive chemical groups) may be attached to the codon-anticodon duplex, which allows group-transferring reactions from cofactors to simple amino acids, thereby producing the final amino acid. The nucleotide-A-derived cofactors could be incorporated into the RNA duplex (helix) by docking Adenosine (cofactor) into the minor groove via an interaction similar to the A-minor motif, forming a base triple between Adenosine and one complementary base pair of the duplex. Furthermore, we propose that this codon-anticodon duplex could initially catalyze a self-aminoacylation reaction with a simple amino acid. Therefore, the sequence of bases in the codon-anticodon duplex would determine the reactions that occurred during the formation of new amino acids for selective binding of nucleotide-A-derived cofactors.

Applying the complementary knowledge bases of System Dynamics and Indigenous knowledge in public health research in Aotearoa, New Zealand

Systems Thinking is increasingly applied to address complex societal and public health issues in Aotearoa, New Zealand and has been proposed as a good fit with traditional wisdom and Mātauranga Māori (Indigenous knowledge) from Aotearoa, New Zealand. In this article, we delve into the theoretical underpinnings of Systems Thinking approaches used in Community-Based System Dynamics research and find parallels with Indigenous narratives and knowledge. The synergy created by combining these two knowledge systems and practices is proposed as an effective way to approach public health issues that emerge from complex adaptive systems, particularly in communities with large numbers of Indigenous peoples. Examples are given from an initiative to engage community to improve food security and nutrition in regional Aotearoa, New Zealand.

CRISPR-OTE: Prediction of CRISPR On-Target Efficiency Based on Multi-Dimensional Feature Fusion

ObjectiveClustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a powerful genome editing technology. Guide RNA (gRNA) plays an essential guiding role in the CRISPR system by complementary base pairing with target DNA. Since the CRISPR targeting mechanism problem has not yet been fully resolved, it remains a challenge to predict gRNA on-target efficiency. Current gRNA design tools often lack efficient information extraction and cannot learn the target efficiency patterns thoroughly. Material and methodsIn this study, CRISPR-OTE is proposed to consider both multi-dimensional sequence information and important complementary prior knowledge based on a simple but effective framework. CRISPR-OTE consists of the local-contextual information branch and the prior knowledge branch. The local-contextual information branch extracts multi-dimensional sequence features from the DNA primary sequence by a parallel framework of Convolutional Neural Networks (CNN) and bidirectional Long Short-Term Memory networks (biLSTM). The prior knowledge branch selects the optimal subset of physicochemical features to provide the neural network with complementary knowledge, such as complex secondary structures. A simple feature fusion strategy is also adopted to fully utilize multi-modal data from the two branches. ResultsThe experimental results show that the optimal subset of physicochemical features (RNA secondary structure and melting temperature of 34nt target) can effectively improve the prediction performance. Additionally, combining multi-dimensional sequence features and multi-modal features can extract information more comprehensively. Through transfer learning, CRISPR-OTE trained on the CRISPR-Cpf1 system can also be successfully applied to the CRISPR-Cas9 system. ConclusionThe performance of CRISPR-OTE is superior to other methods in different CRISPR systems and species. Therefore, CRISPR-OTE is a simple on-target efficiency prediction framework with better accuracy and generalization performance.

Could international human rights obligations motivate countries to implement tobacco cessation support?

The World Health Organization (WHO) Framework Convention on Tobacco Control (FCTC) seeks to realize the right to health through national tobacco control policies. However, few states have met their obligations under Article 14 of the FCTC to develop evidence-based policies to support tobacco cessation. This article examines how human rights obligations could provide a legal and moral basis for states to implement greater support for individualsto overcome their addiction to tobacco. The United Nations (UN) has a well-established legal framework for promoting human rights, looking to the right to health to realize health autonomy. Where addiction undermines autonomy, it is widely acknowledged that addiction presents a significant barrier to cessation for individuals who use tobacco, undermining the right to health. The UN human rights system could, therefore, provide a complementary basis for monitoring state obligations under Article 14 of the FCTC, identifying challenges to FCTC implementation and motivating states to support tobacco cessation. The United Nations' human rights system offers a mechanism that could be used to monitor Framework Convention on Tobacco Control implementation in national policy, facilitating accountability for the progressive realization of cessation support.

Hydrogen Peroxide-triggered Chemical Strategy for Controlling CRISPR systems.

The function of the CRISPR system can be conditionally controlled through rationally guided RNA engineering such that the target sequences can be precisely selected and manipulated. In particular, gRNA, as an important component of the CRISPR system, provides a unique tool for multifunctional control of the system based on the structure of the RNA itself. Therefore, we introduced here a protective group on the 2'-OH position of RNA to inhibit RNA-guided nucleic acid cleavage. Next, the modified gRNA can restore its original function under the chemical stimulation of hydrogen peroxide to realize the control of the CRISPR system. The experiment result demonstrated that the operating mechanism of this strategy may be based on chemical modifications that reduce the number of complementary base pairs between RNAs and targets, and the RNA-protein interaction. This further enriches the toolbox of conditional control of CRISPR function and has broad potential for gene editing in living cells and disease treatment using endogenous hydrogen peroxide.

Automatic generation of complementary auxiliary basis sets for explicitly correlated methods.

Explicitly correlated calculations, aside from the orbital basis set, typically require three auxiliary basis sets: Coulomb‐exchange fitting (JK), resolution of the identity MP2 (RI‐MP2), and complementary auxiliary basis set (CABS). If unavailable for the orbital basis set and chemical elements of interest, the first two can be auto‐generated on the fly using existing algorithms, but not the third. In this paper, we present a quite simple algorithm named autoCABS; a Python implementation under a free software license is offered at Github. For the cc‐pVnZ‐F12 (n = D,T,Q,5), the W4‐08 thermochemical benchmark, and the HFREQ2014 set of harmonic frequencies, we demonstrate that autoCABS‐generated CABS basis sets are comparable in quality to purpose‐optimized OptRI basis sets from the literature, and that the quality difference becomes entirely negligible as n increases.

Stable nitronyl nitroxide monoradical MATMP as novel monomer of reversible addition fragmentation chain transfer (RAFT) polymerization for ultrasensitive DNA detection

In this work, it came up a hydrophilic and stable nitronyl nitroxide monoradical 4-methacryloyloxy-2,2,6,6-tetramethylpiperidine 1-oxyl freeradical (MATMP) as new monomer of polymerization for DNA detection. The detection limit was over 1,000,000 times lower than 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) derivatives as electrochemical labels alone. Within this approach, a single biomolecule can be converted into the strong electrochemical signal, therefore lung cancer DNA can be detected at low concentration. For the first step, the HS-PNA probe was fixed on the surface of the Au electrode. After the target DNA was captured by complementary base pairing, 4-cyano-4-(phenylcarbonothioylthio) pentanoic acid (CPAD), chain transfer agent of RAFT polymerization, was bonded to target DNA as reaction via coordination bond of Zr4+. Electroactive polymers had grown by means of surface initiated thermally RAFT polymerization with MATMP as monomer. MATMP polymer significantly improves the electrochemical signal. This method can detect DNA from 0.01 fM to 10 pM, and detection limit is 1.51 aM. The sensitivity of this method is greater than that in most other reported signal amplification strategies of DNA biosensor, which indicates that it is appropriate for single nucleotide polymorphism analysis and will broaden prospects for biological molecules detection application.

A G-quadruplex/hemin structure-undamaged method to inhibit peroxidase-mimic DNAzyme activity for biosensing development

Damaging the structure of the G-quadruplex (G4) to prevent the formation of the G4/hemin complex is presently the only available method to inhibit the activity of the peroxidase-mimic DNAzyme. In this study, a unique intramolecular inhibitory effect of the adjacent base-pair (InE(N:N)), by installing a rationally adjacent base-pair of the G4 core sequence, is proposed for the inhibition of the DNAzyme activity, which eliminates the need to damage the entire G4 structure. Various base pairs show different abilities to inhibit DNAzyme activity. The adjacent adenine: thymine pair possesses the best inhibitory efficiency (17 times). Through detailed investigations of the InE(N:N), it was revealed that the adjacent adenine: thymine pair downregulated the formation of compound I in the catalytic process, thus inhibiting the G4 DNAzyme activity. The mechanism of inhibition indicated that the carbonyl group on the hexatomic ring of the complementary base played an important role. To further reflect the advantages of the proposed strategy, two InE(N:N)-based biosensors were developed for DNA analysis and Uracil-DNA glycosylase (UDG) detection. Compared with existing DNAzyme-based methods, the application of InE(N: N) facilitates the real-time assay and simplifies the design difficulty. Therefore, InE(N:N) provides new insights into the regulation of the DNAzyme activity and offers an efficient approach for the future application of DNAzyme.

Single Particle Inductively Coupled Plasma Mass Spectrometry-Based Homogeneous Detection of HBV DNA with Rolling Circle Amplification-Induced Gold Nanoparticle Agglomeration.

A highly sensitive and simple method based on rolling circle amplification (RCA) and single particle inductively coupled plasma mass spectrometry (spICP-MS) was proposed for the homogeneous detection of hepatitis B virus (HBV) deoxyribonucleic acid (DNA). In the presence of target DNA, long ssDNA possessing a large number of repeating sequence units was generated by RCA. DNA-labeled AuNP probes assembled into long chains based on complementary base pairing, further aggregating into large particles. Small Au NPs hardly produced pulse signals in spICP-MS; obvious pulse signals appeared in spICP-MS after the agglomeration of Au NPs caused by the addition of RCA products and spermidine. On the basis of this, the homogeneous detection of target DNA was realized by spICP-MS with high sensitivity. Under optimal conditions, the proposed method exhibited a good linear relationship between the frequency of the pulse signal of Au in spICP-MS and the concentration of target HBV DNA in the range of 10-2000 fmol L-1 (R = 0.997), the limit of detection was 5.1 fmol L-1, and the relative standard deviation was 3.7-6.8%. Recoveries of 94.2-108% were obtained for target DNA in spiked serum samples, demonstrating a good matrix tolerance ability for the method.

A ratiometric fluorescent aptamer homogeneous biosensor based on hairpin structure aptamer for AFB1 detection.

On the basis of aptamer (Apt) with hairpin structure and fluorescence resonance energy transfer (FRET), a ratio fluorescent aptamer homogeneous sensor was prepared for the determination of Aflatoxin B1 (AFB1). Initially, the Apt labeled simultaneously with Cy5, BHQ2, and cDNA labeled with Cy3 were formed a double-stranded DNA through complementary base pairing. The fluorescence signal of Cy3 and Cy5 were restored and quenched respectively. Thus, the ratio change of FCy3 to FCy5 was used to realized the detection of AFB1 with wider detection range and lower limit of detection (LOD). The response of the optimized protocol for AFB1 detection was wider linear range from 0.05 ng/mL to 100 ng/mL and the LOD was 12.6 pg/mL. The sensor designed in this strategy has the advantages of simple preparation and fast signal response. It has been used for the detection of AFB1 in labeled corn and wine, and has good potential for application in real samples.

A novel aptamer-based small RNA delivery platform and its application to cancer therapy

Major challenges such as nuclease degradation, rapid renal clearance, non-specific delivery, poor cellular uptake and inflammatory response have limited the clinical application of small RNA-mediated gene silencing. To overcome these challenges, we designed a novel targeting small RNA delivery platform comprising of three oligonucleotides: (1) a guide RNA sequence, (2) part of a passenger sequence linked to a DNA aptamer via a PEG linker, and (3) another passenger sequence conjugated to cholesterol, which assemble through complementary base pair annealing. Remarkably, in the presence of magnesium, this molecule self-assembled into a nanoparticle with a hydrophobic cholesterol core, hydrophilic RNA oligonucleotide shell and PEG-linked DNA aptamer flare. The nanoparticles conferred protection to the RNA oligonucleotides against nuclease degradation, which increased bioavailability, and reduced systemic inflammatory responses. The aptamer allowed targeted delivery of RNA therapeutics through cell-specific surface markers, and once inside the cell, the nanoparticles induced lysosomal leakage that released the RNA oligonucleotides into the cytosol to achieve gene silencing. We created a c-Kit-targeting miR-26a delivery particle that specifically accumulated in c-Kit+ breast cancer, significantly increased T cell recruitment, and inhibited tumor growth. Regression of large established tumors were achieved when the nanoparticle was used in combination with anti-CTLA-4 monoclonal antibody.