Nucleic Acid Chains Research Articles

Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies.

Pulsed electron-electron double resonance (PELDOR) spectroscopy is a powerful method for determining nucleic acid (NA) structure and conformational dynamics. PELDOR with molecular dynamics (MD) simulations opens up unique possibilities for defining the conformational ensembles of flexible, three-dimensional, self-assembled complexes of NA. Understanding the diversity and structure of these complexes is vital for uncovering matrix and regulative biological processes in the human body and artificially influencing them for therapeutic purposes. To explore the reliability of PELDOR and MD simulations, we site-specifically attached nitroxide spin labels to oligonucleotides, which form self-assembled complexes between NA chains and exhibit significant conformational flexibility. The DNA complexes assembled from a pair of oligonucleotides with different linker sizes showed excellent agreement between the distance distributions obtained from PELDOR and calculated from MD simulations, both for the mean inter-spin distance and the distance distribution width. These results prove that PELDOR with MD simulations has significant potential for studying the structure and dynamics of conformational flexible complexes of NA.

Highly sensitive and label-free immunoassay of chloramphenicol based on poly-adenine-mediated spherical nucleic acid and hybridization chain reaction amplification

In this paper, a label-free fluorescent immunoassay for chloramphenicol was established based on a DNA-assisted signal amplification strategy. The poly-adenine mediated spherical nucleic acid was firstly employed as the substrate of antibody to construct the immunonanoprobes. Enzyme-free signal amplification techniques, hybridization chain reaction and strand displacement reaction, were utilized to develop the dual amplification strategy. The output signal was expressed through the use of G-quadruplex to achieve label free fluorescence changes. Under optimized conditions, the detection limit of this method was reduced to 0.0044 ng/L. The method exhibited a high accuracy to the detection of chloramphenicol in milk samples with a recovery rate from 94.5% to 118.1%. However, the limitations of this method probably lied in the overlong detection time and the possible interference from other compounds present in food samples. The developed label-free fluorescent immunoassay could provide an innovative view for the reliable and ultrasensitive detection of chloramphenicol, which is conducive to the food safety.

Hierarchical Assembly of Single-Stranded RNA.

Single-stranded RNA (ssRNA) plays a major role in the flow of genetic information-most notably, in the form of messenger RNA (mRNA)-and in the regulation of biological processes. The highly dynamic nature of chains of unpaired nucleobases challenges structural characterizations of ssRNA by experiments or molecular dynamics (MD) simulations alike. Here, we use hierarchical chain growth (HCG) to construct ensembles of ssRNA chains. HCG assembles the structures of protein and nucleic acid chains from fragment libraries created by MD simulations. Applied to homo- and heteropolymeric ssRNAs of different lengths, we find that HCG produces structural ensembles that overall are in good agreement with diverse experiments, including nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET). The agreement can be further improved by ensemble refinement using Bayesian inference of ensembles (BioEn). HCG can also be used to assemble RNA structures that combine base-paired and base-unpaired regions, as illustrated for the 5' untranslated region (UTR) of SARS-CoV-2 RNA.

A laser-induced graphene-based electrochemical immunosensor for nucleic acid methylation detection.

The detection of methylation in DNA and RNA is essential for the diagnosis and treatment of a wide range of diseases. A one-step fabricated laser-induced graphene (LIG) electrode has received increasing attention due to its good electrical conductivity, large specific surface area, ease of miniaturization, low cost and flexibility. Herein, a potential biosensor for N6-methyladenosine (m6A-RNA) and 5-methylcystosine-single strand DNA (5mC-ssDNA) detection was designed. The aim of this paper is to address the problem of detecting the m6A-RNA and 5mC-ssDNA content in cells. By stepwise modification of gold nanoparticles (AuNPs), sulfhydryl-modified nucleic acid chains, biotin-modified antibodies, and streptavidin-modified horseradish peroxidase (SA-HRP) at the LIG electrode, the peak current responses exhibited an increase proportional to the concentration of m6A-RNA and 5mC-ssDNA in the hydrogen peroxide-hydroquinone (H2O2-HQ) system. This method demonstrated a low detection limit of 2.81 pM for m6A-RNA and 9.53 pM for 5mC-ssDNA, with a linear detection range of 0.01 nM to 10 nM for both targets. The regression equation was determined as ΔI = 4.83 log c + 12.32 (R2 = 0.9980) for m6A-RNA and ΔI = 9.82 log c + 22.09 (R2 = 0.9903) for 5mC-ssDNA. Our method has good selectivity toward different detection targets of nucleic acid chains, stability for long-term storage and consecutive scanning (RSD of 9.42% and 2.08%, respectively) and reproducibility of 5 electrodes (RSD of 6.85%). This method utilizes gold-sulfur bonding to immobilize the detection target, which improves the conductivity of the LIG electrode and introduces an amplified portion of the signal by taking advantage of antigen-antibody specific binding. Thus, dual detection of m6A-RNA and 5mC-ssDNA was realized. Importantly, this approach is successfully applied for the detection of targets in spiked samples extracted from HeLa cells, suggesting its potential for clinical applications and providing a new perspective for the development of point-of care testing (POCT) techniques.

Separation and purification of short-, medium-, and long-stranded RNAs by RP-HPLC using different mobile phases and C18 columns with various pore sizes.

Nucleic acids, which have been employed in medicines for various diseases, are attracting attention as a new pharmaceutical model. Depending on the target substances, nucleic acid medicines with various nucleic acid chain lengths (several tens of nucleotides [nt] to several thousands of nt) exist. The purification of synthesized nucleic acids is crucial as various impurities remain in the crude product after synthesis. Presently, reversed-phase high-performance liquid chromatography (RP-HPLC) represents an effective purification method for nucleic acids. However, the information regarding the HPLC conditions for separating and purifying nucleic acids of various chain lengths is insufficient. Thus, this technical note describes the separation and purification of short-, medium-, and long-stranded nucleic acids (several tens of nt to thousands of nt) by RP-HPLC with various mobile phases and octadecyl-based columns with various pore sizes, such as normal (9-12 nm), wide (30 nm), and super wide (>30 nm) pores.

Lateral flow strip assay of a gene segment in the COVID-19 virus with combined dual readout mode and preliminary multisite hybrid chain reaction amplification.

The past and present scenario of COVID-19 has revealed the necessity of simple point-of-care tests. When combined with the great advantages of amplification, lateral flow assay nucleic acid analysis represents a more sensitive molecular diagnostic technique compared to universal protein analysis. Room temperature operation, an enzyme-free nature, and in situ elongation make hybrid chain reaction amplification (HCR) a good candidate for amplified combined lateral flow assays (LFAs). Since dual modes of detection can not only satisfy different application scenarios, but also reduce the false-negative rate, in this paper, visual and fluorescent detection based on labelling with colloidal gold nanoparticles and fluorescence labelling were incorporated into a HCR integrated with a LFA. The detection assay was finished in 30 minutes. The linear relationship between the signal and the concentration of the characteristic segment in the COVID-19 ORF gene was demonstrated. The obtained detection limits of as low as 10 fM (6.02 × 103 copies per mL) and 1 fM (6.02 × 102 copies per mL), respectively, were comparable with those in the literature. The multi-site HCR amplification integrated with LFA of a 1053 bp nucleic acid chain was also preliminarily studied, and tri-site amplification was found to exhibit higher signal intensity than single-site amplification. This study provides a promising strategy for simple, sensitive, and wide-ranging detection of pathogenic bacteria.

Multifunctional DNA scaffold mediated gap plasmon resonance: Application to sensitive PD-L1 sensor

The introduction of noble metal nanoparticles with good LSPR characteristics can greatly improve the sensitivity of SPR through resonance coupling effect. The plasma resonance response and optical properties of film coupling nanoparticle systems largely depends on the ingenious design of gap structures. Nucleic acid nanostructures have good stability, flexibility, and high biocompatibility, making them ideal materials for gap construction. 2D MOF (Cu-Tcpp) has a large conjugated surface similar to graphene, which can provide a stable substrate for the directional fixation of nucleic acid nanostructures. However, research on gap coupling plasmon based on nucleic acid nanostructures and 2D MOF is still rarely reported. By integrating the advantages of Cu-Tcpp assembled film and DNA tetrahedron immobilization, a nano gap with porous scaffold structure between the gold film and gold nanorod was build. The rigidity of DNA tetrahedron can precisely control the gap size, and its unique programmability allows us to give the coupling structure greater flexibility through the design of nucleic acid chain. The experimental results and FDTD simulation show that the film coupling nanoparticle systems constructed with DNA tetrahedrons greatly enhance the electric field strength near the chip surface and effectively improve the sensitivity of SPR. This research shows the huge potential of nucleic acid nanomaterials in the construction of SPR chip surface microstructures.

Ultrasensitive ratiometric electrochemical aptasensor based on novel MnCo@C as nonenzyme catalysis for the detection of patulin

With the accumulation of patulin (PAT) in the human body, harm to health could easily be ignored, we urgently required an ultrasensitive platform for the rapid detection. Due to the porosity of NH2-MIL-101, more methylene blue (MB) were adsorbed to form a signal reference by changing the cover of the nucleic acid chain. Combined with a novel innovative manganese/cobalt nanobeam@carbon (MnCo@C) enzyme-free nanoprobe (Nanopro) which has remarkable catalytic performance to develop a novel ratiometric aptamersensor for detection of PAT. The ratio was changed by varying the electrochemical signal of benzoquinone (BQ) (IBQ) and the number of NH2-MIL-101 @MB exposed (IMB). The linear range of the sensor for PAT is 1.00 × 10−4-1.00 × 101 pg·mL−1, and the limit of detection is as low as 0.040 fg·mL−1 (S/N = 3). This aptasensor was successfully applied to detect PAT in Crataegus pinnatifida Bge and Semen Coicis, which exhibited satisfactory RSD (1.21–4.70% and 3.18–5.00%, respectively) and recovery (90.6–106.3% and 90.2–103.1%, respectively).

PDBminer to Find and Annotate Protein Structures for Computational Analysis.

Computational methods relying on protein structure strongly depend on the structure selected for investigation. Typical sources of protein structures include experimental structures available at the Protein Data Bank (PDB) and high-quality in silico model structures, such as those available at the AlphaFold Protein Structure Database. Either option has significant advantages and drawbacks, and exploring the wealth of available structures to identify the most suitable ones for specific applications can be a daunting task. We provide an open-source software package, PDBminer, with the purpose of making structure identification and selection easier, faster, and less error prone. PDBminer searches the AlphaFold Database and the PDB for available structures of interest and provides an up-to-date, quality-ranked table of structures applicable for further use. PDBminer provides an overview of the available protein structures to one or more input proteins, parallelizing the runs if multiple cores are specified. The output table reports the coverage of the protein structures aligned to the UniProt sequence, overcoming numbering differences in PDB structures and providing information regarding model quality, protein complexes, ligands, and nucleic acid chain binding. The PDBminer2coverage and PDBminer2network tools assist in visualizing the results. PDBminer can be applied to overcome the tedious task of choosing a PDB structure without losing the wealth of additional information available in the PDB. Here, we showcase the main functionalities of the package on the p53 tumor suppressor protein. The package is available at http://github.com/ELELAB/PDBminer.

Construction of a fluorescence sensing platform based on RISC and CRISPR/Cas12a for the assay of Ago2 enzyme activity

PurposeArgonaute 2 (Ago2) is a protein with nucleic acid endonuclease activity and is ubiquitous in eukaryotic cells. Ago2 is a core member of RNA interference and is involved in important gene regulation in the body and the development of multiple tumors by affecting oncogenic or oncogenic gene expression. Ago2 is a potential tumor biomarker. Therefore, the assay of Ago2 activity can help monitor the disease progression and prognosis and contribute to the study of the mechanism of disease development. MethodsAgo2-based nucleic acid endonuclease activity cleaves the target hairpin nucleic acid chain and progressively stimulates the hybridization chain reaction (HCR) in the sensing strategy, causing signal amplification to form specific dsDNA, which then triggers the powerful non-selective single nucleic acid chain cleavage activity of the CRISPR/cas12a system and releases the fluorescence signal in the reporter probe. ResultsThe sensitive assay of Ago2 enzyme activity was achieved using the biofunctional properties of RNA-induced silencing complex (RISC) and CRISPR/Cas12a. Under the optimized conditions, the fluorescence signal intensity of the assay was positively correlated with the activity concentration of Ago2, with an excellent linear response range of 0.02–20 nM and a limit of detection (LOD) of 10 pM. When applied to the assay of Ago2 in cell lysates, the experimental recovery was 93.33%-107.08%, and the sensing platform was able to detect the Ago2 content in the presence of interference specifically. ConclusionTherefore, the fluorescence sensing platform successfully constructed in this paper is suitable for the assay of endogenous Ago2 activity in complex samples, and the assay method has the advantages of high specificity, sensitive detection, easy operation and low instrumentation requirements, which is expected to be applied to the actual sample assay in clinical settings. Meanwhile, it provides an assay direction for the biofunctional analysis of nucleases and a feasible direction for applying RISC and Crispr/Cas12a in sensing analysis.

Terahertz waves regulate the mechanical unfolding of tau pre-mRNA hairpins

Intermolecular interactions, including hydrogen bonds, dominate the pairing and unpairing of nucleic acid chains in the transfer process of genetic information. The energy of THz waves just matches with the weak interactions, so THz waves may interact with biomolecules. Here, the dynamic effects of THz electromagnetic (EM) waves on the mechanical unfolding process of RNA hairpins (WT-30nt and its mutants, rHP, SARS-CoV-2, and SRV-1 SF206) are investigated using steered molecular dynamics (SMD) simulations. The results show that THz waves can either promote the unfolding of the double helix of the RNA hairpin during the initial unfolding phase (4-21.8 THz) or significantly enhance (23.8 and 25.5 THz) or weaken (37.4 and 41.2 THz) its structural stability during unfolding. Our findings have important implications for applying THz waves to regulate dynamic deconvolution processes, such as gene replication, transcription, and translation.

Noncanonical Condensation of Nucleic Acid Chains by Hydrophobic Gold Nanocrystals.

Nucleic acid condensates are essential for various biological processes and have numerous applications in nucleic acid nanotechnology, gene therapy, and mRNA vaccines. However, unlike the in vivo condensation that is dependent on motor proteins, the in vitro condensation efficiency remains to be improved. Here, we proposed a hydrophobic interaction-driven mechanism for condensing long nucleic acid chains using atomically precise hydrophobic gold nanoclusters (Au NCs). We found that hydrophobic Au NCs could condense long single-stranded DNA or RNA to form composites of spherical nanostructures, which further assembled into bead-shaped suprastructures in the presence of excessive Au NCs. Thus, suprastructures displayed gel-like behaviors, and Au NCs could diffuse freely inside the condensates, which resemble the collective motions of condensin complexes inside chromosomes. The dynamic hydrophobic interactions between Au NCs and bases allow for the reversible release of nucleic acids in the presence of mild triggering agents. Our method represents a significant advancement toward the development of more efficient and versatile nucleic acid condensation techniques.

Chain hybridization‐based CRISPR‐lateral flow assay enables accurate gene visual detection

Visualized gene detection based on the CRISPR‐Cas12/CRISPR‐Cas13 technology and lateral flow assay device (CRISPR‐LFA) has shown great potential in point‐of‐care testing sector. Current CRISPR‐LFA methodology mainly utilizes conventional immuno-based LFA test strips, which could visualize whether the reporter probe is trans-cleaved by Cas protein, indicating the target positive detection. However, conventional CRISPR‐LFA usually produces false-positive results in target negative assay. Herein, a nucleic acid Chain Hybridization‐based Lateral Flow Assay platform, named CHLFA, has been developed to achieve the CRISPR‐CHLFA concept. Different from the conventional CRISPR‐LFA, the proposed CRISPR‐CHLFA system was established based on the nucleic acid hybridization between the GNP‐probe embedded in test strips and ssDNA (or ssRNA) reporter from CRISPR (LbaCas12a or LbuCas13a) reaction, which eliminated the requirement of immunoreaction in conventional immuno-based LFA. The assay realized the detection of 1–10 copy of target gene per reaction within 50 min. The CRISPR-CHLFA system achieved highly accurate visual detection of target negative samples, thus overcoming the false-positive problem that often produced in assays using conventional CRISPR‐LFA. The CRISPR‐CHLFA platform was further adopted for the visual detection of marker gene from SASR‐CoV-2 Omicron variant and Mycobacterium tuberculosis (MTB), respectively, and 100% accuracy for the analysis of clinical specimens (45 SASR‐CoV-2 specimens and 20 MTB specimens) was obtained. The proposed CRISPR-CHLFA system could provide an alternative platform for the development of POCT biosensors and can be widely adopted in accurate and visualized gene detection.

SERS-fluorescence dual-mode nanoprobe for the detection and imaging of Bax mRNA during apoptosis.

Adual-mode nanoprobe was constructed to detect Bax messenger RNA (mRNA), consisting of gold nanotriangles (AuNTs), a Cy5-modified recognition sequence, and a thiol-modified DNA sequence. Bax mRNA is one of the key pro-apoptotic factors in the apoptosis pathway. Raman enhancement and fluorescence quenching of the signal group Cy5 were performed using AuNTs as substrates. The thiol-modified nucleic acid chain is partially complementary to the Cy5-modified nucleic acid chain to form a double strand and is linked to the AuNTs by the Au-S bond. When Bax mRNA is present, the Cy5-modified strand specifically binds to it to form a more stable duplex, making Cy5 far away from AuNTs, and SERS signal is weakened while fluorescence signal is enhanced. The nanoprobe can be used for the quantitative detection of Bax mRNA in vitro. Combined with the high sensitivity of SERS and the visualization of fluorescence, this method has good specificity and can be used for in situ imaging and dynamic monitoring of Bax mRNA during deoxynivalenol (DON) toxin-induced apoptosis of HepG2 cells. DON plays a pathogenic role mainly by inducing cell apoptosis. Theresults confirmed that the proposed dual-mode nanoprobe has good versatility in various human cell lines.

Significance of miRNAs on the thyroid cancer progression and resistance to treatment with special attention to the role of cross-talk between signaling pathways.

Thyroid cancer (TC) is the most prevalent endocrine malignant tumor. It has many types, the Papillary thyroid cancer (PTC)(most common and follicular thyroid carcinoma (FTC). Several risk factors have been associated with TC radiation exposure, autoimmunity, and genetics. Microribonucleic acids (miRNAs) are the most important genetic determinants of TC. They are small chains of nucleic acids that are able to inhibit the expression of several target genes. They could target several genes involved in TC proliferation, angiogenesis, apoptosis, development, and even resistance to therapy. Besides, they could influence the stemness of TC. Moreover, they could regulate several signaling pathways such as WNT/β-catenin, PI3K/AKT/mTOR axis, JAK/STAT, TGF- β, EGFR, and P53. Besides signaling pathways, miRNAs are also involved in the resistance of TC to major treatments such as surgery, thyroid hormone-inhibiting therapy, radioactive iodine, and adjuvant radiation. The stability and sensitivity of several miRNAs might be exploited as an approach for the usage of miRNAs as diagnostic and/or prognostic tools in TC.

Ultra-precise single-molecule nanopore tool to watch enzymes at work.

We developed a nanopore tool to measure how enzymes move along nucleic acid chains. In this technique, which evolved from our effort in developing nanopore sequencing, the ion current through an engineered protein nanopore is used to measure the motion of the DNA or RNA. With its unprecedented spatiotemporal resolution this new single-molecule tool resolves sub-millisecond and sub-nucleotide-long enzyme steps while providing the exact nucleotide sequence context within the enzyme. In addition, the tool has high throughput and is relatively simple to set up. We find surprisingly strong sequence-dependence in the kinetics of many types of helicases such as in Hel308, PcrA, RecQ, or the SARS-CoV-2 helicase nsp13. Furthermore, we have recorded data with DNA- and RNA-polymerases and reverse transcriptases. With each enzyme we discover behavior that had not been observable with any other single-molecule technique.

The challenge of peptide nucleic acid synthesis.

Peptide nucleic acids (PNAs) are an important class of DNA/RNA mimics that can hybridize complementary chains of nucleic acids with high affinity and specificity. Because of this property and their metabolic stability, PNAs have broad potential applications in different fields. Consisting of a neutral polyamide backbone, PNAs are prepared following the method used for peptide synthesis. In this regard, they are prepared by the sequential coupling of the protected monomers on a solid support using a similar approach to solid-phase peptide synthesis (SPPS). However, PNA synthesis is a little more challenging due to issues of the difficulty on the preparation of monomers and their solubility. Furthermore, the PNA elongation is jeopardized by intra/inter chain aggregation and side reactions. These hurdles can be overcome using different protecting group strategies on the PNA monomer, which also dictate the approach followed to prepare the oligomers. Herein, the main synthetic strategies driven by the protecting group scheme are discussed. However, there is still ample scope for further enhancement of the overall process.

Nucleic Acid Hybridization Enhanced Luminescence for Rapid and Sensitive RNA and DNA Based Diagnostics.

Long-lived emissive nucleic acid probes are widely used in biochemical analysis due to their programmable structures, high signal-to-background ratio, and high sensitivity. Homogeneous detection based on long-lived emissive nucleic acid probes is often achieved through Förster resonance energy transfer (FRET), which suffers from the limitation of a narrow effective distance range. Herein, a new strategy of accessing nucleic acid hybridization-responsive luminescent probes is presented. The photoluminescence (PL) of a Lumi4-Tb complex internally modified with DNA is switched on by nucleic acid hybridization, after which the PL is increased up to 20 times. PL lifetime analysis revealed a possible mechanism of luminescence enhancement. Due to the flexibility of single-stranded nucleic acid chains, the bases and phosphate groups can coordinate with the Tb(III), which reduces the stability of the Tb complex and results in weak PL. After hybridization, the rigid double helix structure suppresses the coordination between Tb(III) and the bases or phosphate groups, causing luminescence enhancement. As the DNA sequence can be freely designed, an array of probes for different DNA or RNA targets can be created with the same Tb complex. Moreover, the novel probe design can afford pM detection limits of DNA or RNA without any nucleic acid amplification and exhibits great potential for nucleic acid detection in clinical diagnosis.

A stabilized weak measurement sensor for aptamer detection

In this study, an aptamer biosensor based on weak value amplification is proposed for the first time. The feasibility, selectivity, robustness, and high detection accuracy of aptamer sensors are verified by the adenosine triphosphate (ATP) detection experiment. The weak measurement system shows high sensitivity to phase changes, corresponding to refractive index changes, attributed to the changes in the spatial configuration of the aptamer nucleic acid chain after specifically capturing the target molecule. As the main energy source in the body, ATP plays an important role in many biological processes, and its detection is of great significance to study cell metabolism, biochemical pathways, and early-stage disease diagnosis. This work provides a new labeling-free detection scheme for aptamer sensors and offers a high-precision and specific detection of small biological molecules based on weak measurement biosensors. The proposed method is of great significance to the development of aptamer sensors and weak value amplification technology.

MOPSS: Toward high-fidelity oligonucleotides for clinical applications.

MOPSS: Toward high-fidelity oligonucleotides for clinical applications.