Double-stranded DNA Research Articles

Evaluation of Vaccinia Virus Infection in Mice Using Two-Reporter Recombinant Virus.

The family Poxviridae comprises multiple viruses with large double-stranded (ds) DNA genomes that can infect numerous vertebrate and invertebrate hosts, including humans. The development of genetic engineering methods for Vaccinia virus (VACV), the prototypic member in the family, have allowed the manipulation of the genomes of poxviruses for the generation of recombinant (r)VACV expressing easily traceable luciferase and/or fluorescent reporter genes. These recombinant viruses have significantly contributed to progress in the field of poxvirus research and accelerated the development of novel prophylactic vaccines and therapeutic antiviral treatments. Recently, we described two reporter rVACV expressing luciferase (Nluc) and fluorescent (GFP or Scarlet) proteins to easily track viral infections in different systems, overcoming the limitations associated with the use of rVACV expressing a single luciferase or fluorescent reporter gene. Here, we describe the experimental procedures to carry out in vitro, in vivo and ex vivo studies using these novel bireporter-expressing rVACV, which also represent an excellent option to study the biology of VACV, including the use of these reporter viruses for testing new antivirals and vaccines, using cultured cells and/or well-characterized animal models of infection.

Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts.

A single guide RNA (sgRNA) directs Cas9 nuclease for gene-specific scission of double-stranded DNA. High Cas9 activity is essential for efficient gene editing to generate gene deletions and gene replacements by homologous recombination. However, cleavage efficiency is below 50% for more than half of randomly selected sgRNA sequences in human cell culture screens or model organisms. We used in vitro assays to determine intrinsic molecular parameters for maximal sgRNA activity including correct folding of sgRNAs and Cas9 structural information. From the comparison of over 10 data sets, we find major constraints in sgRNA design originating from defective secondary structure of the sgRNA, sequence context of the seed region, GC context, and detrimental motifs, but we also find considerable variation among different prediction tools when applied to different data sets. To aid selection of efficient sgRNAs, we developed web-based PlatinumCRISPr, an sgRNA design tool to evaluate base-pairing and sequence composition parameters for optimal design of highly efficient sgRNAs for Cas9 genome editing. We applied this tool to select sgRNAs to efficiently generate gene deletions in Drosophila Ythdc1 and Ythdf, that bind to N 6 methylated adenosines (m6A) in mRNA. However, we discovered that generating small deletions with sgRNAs and Cas9 leads to ectopic reinsertion of the deleted DNA fragment elsewhere in the genome. These insertions can be removed by standard genetic recombination and chromosome exchange. These new insights into sgRNA design and the mechanisms of CRISPR-Cas9 genome editing advance the efficient use of this technique for safer applications in humans.

Modular Access to C2'-Aryl/Alkenyl Nucleosides with Electrochemical Stereoselective Cross-Coupling.

Chemically modified oligonucleotides have garnered significant attention in medicinal chemistry, chemical biology, and synthetic biology due to their enhanced stability in vivo compared to naturally occurring oligonucleotides. However, current methods for synthesizing modified nucleosides, particularly at the C2'-position, are limited in terms of efficiency, modularity, and selectivity. Herein, we report a new approach for the synthesis of highly functionalized C2'-a-aryl/alkenyl nucleosides via an electrochemical nickel-catalyzed cross-coupling of 2'-bromo nucleosides with a variety of (hetero)aryl and alkenyl iodides. This method affords a diverse array of C2'- a-aryl/ alkenyl nucleosides with excellent stereoselectivities, broad substrate scope, and good functional group compatibility. We further synthesized oligonucleotides incorporating C2'-aryl-modified thymidine moieties and demonstrated that their annealed double-stranded DNAs exhibit decreased melting temperatures (Tm). Additionally, oligonucleotides with C2'-aryl modifications at the 3' end showed enhanced resistance to 3'-exonuclease degradation and C2'-aryl modifications did not impede the cellular uptake process, highlighting the potential of these modified oligonucleotides for therapeutic applications.

Structural insights to the RRM-domain of the glycine-rich RNA-binding protein from Sorghum bicolor and its role in cold stress tolerance in E. coli

Sorghum bicolor Glycine-rich RNA-binding protein (SbGRBP), exhibit the ability to bind both single-stranded and double-stranded DNA. The expression of SbGRBP is regulated by heat stress, with the protein localizing to the nucleus and cytosol. The present study delves into the structure and ssDNA binding ability of its truncated version (SbGRBP1–119) which lacks glycine rich domain (GR). This protein has the ability to bind ssDNA Using Nuclear Magnetic Resonance (NMR) spectroscopy, we have revealed the secondary structure of SbGRBP1–119, highlighting the typical configuration of GRBPs with four β-sheets and two α-helices. Notably, we found two additional α-helices at the N-terminal region that seem to interact with ssDNA, a novel observation for GRBPs. Key residues crucial for ssDNA binding were identified, suggesting a specific interaction with the oligonucleotide sequence 5’-TTCTGG-3′. Preliminary assays hinted that SbGRBP1–119 might bolster E. coli resilience to cold stress, indicating a potential chaperone-like role under stress conditions. This study sheds light on the structural basis of SbGRBP1–119's interaction with nucleic acids, deepening our understanding about the role of GRBPs' in RNA metabolism and regulation.

Discovery of KPT-6566 as STAG1/2 Inhibitor sensitizing PARP and NHEJ Inhibitors to suppress tumor cells growth in vitro

Stromal antigen 1 and 2 (STAG1 and STAG2) are two mutually exclusive components of the cohesin complex that is crucial for centromeric and telomeric cohesion. Beyond its structural role, STAG2 also plays a pivotal role in homologous recombination (HR) repair and has emerged as a promising therapeutic target in cancer treatment. Here, we employed a fluorescence polarization (FP)-based high-throughput screening and identified KPT-6566 as a dual inhibitor of STAG1 and STAG2. Biochemical and biophysical analyses demonstrated that KPT-6566 directly binds to STAG1 and STAG2, disrupting their interactions with SCC1 and double-stranded DNA. A metaphase chromosome spread assay showed that KPT-6566 causes premature chromosome separation and induces chromosome damages in HeLa cells. Furthermore, KPT-6566 also impairs DNA damage repair, leading to the accumulation of double-strand breaks and cell apoptosis. Finally, KPT-6566 can sensitize HeLa and HepG2 cells to PARP inhibitor Olaparib and the NHEJ inhibitor UMI-77, exhibiting a synergistic effect in suppressing cell proliferation. Our findings highlight the potential of STAG1/2 as promising therapeutic targets in cancer treatment, particularly when they are targeted in combination with other DNA damage response inhibitors.

Versatile fluorescence biosensors based on CRISPR/Cas12a for determination of site-specific DNA methylation from blood and tissues

The identification of DNA methylation at specific sites is crucial for the early detection of cancer since DNA methylation is intimately associated to the occurrence and development of cancer. Herein, two types of sensors that can detect site-specific DNA methylation were developed to meet practical requirements using methylation sensitive restriction endonuclease and CRISPR/Cas12a. To accomplish rapid detection of target, an AciI-mediated CRISPR/Cas12a assay was developed by coupling AciI to recognize DNA methylation with Cas12a to identify site-specific DNA. Since protospacer adjacent motif (PAM)-dependent endonuclease activity and trans-cleavage activity of Cas12a, it is possible to detect site-specific DNA methylation within 2 h with high specificity and acceptable sensitivity. To satisfy the needs of trace target detection, we developed an GlaI-strand displacement amplification (SDA) assisted CRISPR/Cas12a system. The system converts double-stranded methylated DNA to abundant single-stranded by GlaI and SDA. Then, the combination of SDA and CRISPR/Cas12a enable cascades amplification of signal. The approach can therefore be used to detect methylation at different specified sites, even those without PAM, and can increase sensitivity with a detection limit down to 8.19 fM. Importantly, the assay can distinguish between colorectal cancer and precancerous tissue, as well as identify colorectal patients and healthy people. This study provides a new avenue for the development of new biosensors for methylation analysis, and the two methods devised have the potential to meet the multiple requirements of site-specific methylation testing in various clinical settings.

Dual signal Amplification-Mediated Aptamer-Based electrochemical biosensor for sensitive detection of exosomes

Exosomes, a class of extracellular vesicles carrying the biological information of their parent cells, have emerged as one of the most promising biomarkers for the early screening and prognostic monitoring of cancer. However, the effective capture and sensitive detection of cancer cell-derived exosomes pose significant challenges due to the inevitable interference from internal environment and the limited exosome abundance in clinical samples. Herein, we proposed an aptamer-based electrochemical biosensor combining with Au nanoprobe-mediated dual signal amplification for sensitive detection of tumor-related exosomes. Benefiting from the specific recognition of CD63 aptamer (CD63 Apt), the target exosomes were efficiently captured on the gold electrode, followed by trapping the iDNA-modified Au nanoprobe, which could induce the generation of hybridization chain reaction (HCR). The long double-stranded DNA produced by HCR procedure provided numerous insertion sites to RuHex, achieving the high sensitivity for exosome detection. Under the optimal experimental conditions, this aptamer-based electrochemical biosensor for MCF-7 cancer cell-derived exosome detection exhibited a good linear range within 5 orders of magnitude (from 1.29 × 104 to 1.29 × 108 particle/mL) with a low limit of detection (LOD) to 1.65 × 103 particle/mL. Furthermore, this biosensor possessed good stability and anti-interference ability. Therefore, this analysis platform is considered as a promising candidate for the exosome-based diagnosis and prognosis of cancer in clinical applications.

The disordered negatively charged C-terminus of the large HECT E3 ubiquitin ligase HERC2 provides structural and thermal stability to the HECT C-lobe.

Homologous to the C-terminus of E6AP (HECT) and RCC1-like domain (RLD)-containing protein 2 (HERC2) is a large, 528 kDa E3 ubiquitin ligase that is associated with cancer, oculocutaneous albanism type 2, Prader-Willi syndrome, and other neurological diseases. HERC2 has been found to contribute to double-stranded DNA break repairs, tumor suppression, maintaining centrosome architecture, and ubiquitylation. The C-terminal portion of the HECT domain (C-lobe) of HERC2 is responsible for transferring ubiquitin to a substrate but the precise function of the other eight domains in HERC2 are unknown. Interestingly, HERC2 contains a unique and negatively charged C-terminal tail adjoined to the C-lobe that is predicted to act as a linker to promote interactions between HERC2 and its binding partners. This study aims to better understand the function and relevance of HERC2 in disease by investigating the structural aspects of the HERC2 C-lobe and HERC2 C-terminal tail using AlphaFold followed by molecular dynamics (MD) simulations, multidimensional nuclear magnetic resonance (NMR), and circular dichroism (CD). Secondary structure content analysis from MD simulations and the fully resonance assigned 1H-15N HSQC spectra of the HERC2 C-lobe and the isolated C-terminal tail confirm that the C-lobe is well-folded but the C-terminal tail is disordered. CD melting curves indicate that the flexible C-terminal tail provides improved stability to the C-lobe. Additionally, MD simulations have identified that the interaction between residues D4829 and R4728 is prevalent among the non-bonded contacts between the tail and the C-lobe. Overall, our results demonstrate that the negatively charged C-terminal tail is disordered, provides stability to the C-lobe, and may act as a flexible scaffold for protein-protein interactions.

Dual-modal improved biosensing platform for sugarcane smut pathogen based on biological enzyme-Mg2+ DNAzyme coupled with DNA transporter cascading hybridization chain reaction

Sugarcane smut is a major disease affecting the yield and quality of sugarcane, and its early detection is crucial for the healthy development of sugarcane industry. In this work, a dual-modal biosensing platform is designed based on Au-V-MOF and 3D DNA walker for highly sensitive and precise detection of the sugarcane smut pathogen. This detection system utilizes the catalytic properties of biocatalysts and the precise cleavage of DNAzymes, along with 3D DNA walker nanotechnology and a designed “walking track”, to achieve amplified detection signals and accurate target recognition. The detection platform utilizes catalytic hairpin assembly for target recycling. Output strand T1 interacts with DNAzyme via a 3D transporter, cleaving S1 in Mg2+ presence. This triggers cascading hybridization chain reaction to form long double-stranded DNA structures that absorb substantial methylene blue (MB). This amplifies the electrical signal and causes a proportional color change due to the redox reaction of MB, which enables electrochemical and colorimetric detection of the target. The method shows a linear response range from 0.0001 to 10,000 pM with a detection limit of 56.76 aM (S/N = 3). It features high sensitivity, specificity, and accuracy, which offers significant potential for early warning and precise detection of sugarcane smut.

Conformational Plasticity of SpyCas9 Induced by AcrIIA4 and AcrIIA2: Insights from Molecular Dynamics Simulation

CRISPR-Cas9 systems constitute bacterial adaptive immune systems that protect against phage infections. Bacteriophages encode anti-CRISPR proteins (Acrs) that mitigate the bacterial immune response. However, the structural basis for their inhibitory actions from a molecular perspective remains elusive. In this study, through microsecond atomistic molecular dynamics simulations, we demonstrated the remarkable flexibility of Streptococcus pyogenes Cas9 (SpyCas9) and its conformational adaptability during interactions with AcrIIA4 and AcrIIA2. Specifically, we demonstrated that the binding of AcrIIA4 and AcrIIA2 to SpyCas9 induces a conformational rearrangement that causes spatial separation between the nuclease and cleavage sites, thus making the endonuclease inactive. This separation disrupts the transmission of signals between the protospacer adjacent motif recognition and nuclease domains, thereby impeding the efficient processing of double-stranded DNA. The simulation also reveals that AcrIIA4 and AcrIIA2 cause different structural variations of SpyCas9. Our research illuminates the precise mechanisms underlying the suppression of SpyCas9 by AcrIIA4 and AcrIIA2, thus presenting new possibilities for controlling genome editing with higher accuracy.

Double-stranded DNA invasion by anti-gene oligonucleotide clamps

Double-stranded DNA invasion by anti-gene oligonucleotide clamps

The protein composition of human adenovirus replication compartments.

Human adenoviruses are double-stranded DNA viruses that replicate in the cell nucleus and induce the formation of replication compartments (RCs) that are critical in viral replication and control of virus-host interactions. RCs are specialized virus-induced subnuclear microenvironments where not only viral genome replication and expression are orchestrated but also host proteins that restrict viral replication are co-opted and subverted. The protein composition of these RCs remains largely unexplored. In this study, we isolated adenovirus RC-enriched fractions from infected cells at different times post-infection and employed a tandem mass tag-based quantitative mass spectrometry approach to identify proteins associated with RCs (data available via ProteomeXchange identifier PXD051745). These findings reveal an elaborate network of host and viral proteins potentially relevant for RC formation and function. To validate the RC-protein components identified by mass spectrometry, we employed immunofluorescence and immunoblotting techniques. Proteins previously described to colocalize in RCs in infected cells were identified in the isolated subnuclear fractions. In addition, we validated newly identified proteins associated with RCs, including the high mobility group box 1 (HMGB1), the SET nuclear proto-oncogene, the structure-specific recognition protein 1 (SSRP1), the CCCTC-binding protein (CTCF), and sirtuin 6 (SIRT6). We identified HMGB1 as a protein that binds to the viral DNA binding protein (DBP). Using shRNA knockdowns and inhibitors, we demonstrated that HMGB1 acts as a proviral factor, promoting efficient viral DNA synthesis and progeny production. Our data further suggest potential candidate targets for therapeutic intervention and provide mechanistic insights into the molecular basis of virus-host interactions.IMPORTANCEHuman adenoviruses serve as models for studying respiratory viruses and have provided critical insights into viral genome replication and gene expression, as well as the control of virus-host interactions. These processes are coordinated within virus-induced subnuclear microenvironments known as RCs. We conducted quantitative proteome analyses of RC-enriched subnuclear fractions at different times post-infection with human adenovirus species C type 5, revealing a multifaceted network of proteins that participate in the regulation of gene expression, DNA damage response, RNA metabolism, innate immunity, and other cellular antiviral defense mechanisms. Furthermore, we validated the localization of several host proteins to viral RCs using immunofluorescence microscopy and immunoblotting and identified cellular HMGB1 as a proviral factor late during infection. These findings represent the first analysis of the proteomes of isolated RCs and not only enhance our understanding of nuclear organization during infection but also shed light on the complex interplay between viral and host factors within RCs.

ECL and visual dual-mode detection of miRNA-21 based on HRP/Au NPs composite probe and CRISPR/Cas12a strategy

Signal-amplification sensing strategies for rapid and accurate detection of tumor marker miRNA is of great practical significance for cancer prevention and treatment. Catalytic hairpin assembly (CHA) nucleic acid amplification reaction and CRISPR/Cas12a strategies have exhibited huge prospect due to their flexible design and efficient signal amplification. We constructed an electrochemiluminescence (ECL) biosensor based on horseradish peroxidase/gold nanoparticles (HRP/Au NPs) nanocomposite probe and CRISPR/Cas12a (LbCpf1), and completed a dual-mode detection of miRNA-21. When the target RNA is present in the system, the CHA) cycle was initiated, and the double-stranded DNA containing a specific protospacer adjacent motif (PAM) base sequence was generated to successfully activate the trans-cut activity of CRISPR/Cas12a. After the prepared HRP/Au NPs nanocomposite probe was cleaved by CRISPR/Cas12a, the supernatant containing HRP was collected through magnetic separation and subsequently introduced to the cathode of the bipolar electrode facilitating anodic ECL luminescence response. In addition, the supernatant was added to the TMB chromogenic solution for chromogenic reaction. Thus, ECL detection and visual detection of miRNA-21 were realized. Dual-mode detection improves the accuracy of the sensor, and the utilization of bipolar electrodes on indium tin oxide (ITO) coated glass could also provide some useful references for further development of point-of-care detecting devices for early cancer prevention and diagnosis.

Examination of antinuclear antibody staining patterns and titers in patients with childhood-onset systemic lupus erythematosus.

Antinuclear antibodies (ANA) staining patterns can provide useful information in systemic lupus erythematosus (SLE). In our study, we examined the frequency of ANA staining patterns in disease-related features in childhood-onset SLE patients. ANA and its staining patterns were assessed in childhood-onset SLE patients. Two hundred twenty-three patients were included (F/M = 3/1). Their median age at diagnosis was 14.3 (11.9-16.1) years. The anti-cell (AC)-4/5 (fine or large speckled) pattern was the most common nuclear ANA pattern (75.8%), while the AC-19 (dense fine speckled) pattern was the most frequently detected cytoplasmic ANA pattern (13.1%). The AC-4/5 (fine or large speckled) patterns were notably seen in fever, acute and chronic cutaneous lupus, arthritis, serositis, hematologic involvement, renal involvement, neuropsychiatric involvement, gastrointestinal involvement, and cardiopulmonary involvement (all p < .001). Conversely, the AC-1 (homogeneous) pattern was significantly detected in oral/nasal ulcers and non-scarring alopecia (both p < .001). Regarding the laboratory features, the AC-4/5 (fine or large speckled) patterns exhibited a predominant seen in autoimmune hemolytic anemia, leukopenia, thrombocytopenia, elevated ESR and CRP, hypocomplementemia, direct Coombs, anti-Smith (Sm), anti-SSA and SS-B, anti-ribonucleoprotein (RNP), anti-histone, anti-ribosomal P, lupus anticoagulant, anti-cardiolipin immunoglobulin (Ig)M/IgG, and anti-β2-glycoprotein IgM/IgG positivities (all p < .001). In contrast, the AC-1 (homogeneous) pattern was detected in anti-double-stranded (ds) DNA and anti-histone positivity (both p < .001). Our study showed that AC-4/5 and AC-1 patterns of ANA are frequently detected in many clinical and serological features of childhood-onset SLE patients. However, further studies are needed in larger populations to verify these results.

Genomic analysis and characterization of a new Salmonella phage vB_Sen_ST2 infecting Salmonella enterica serovars Typhi and Typhimurium

In this study, we have characterized and sequenced the whole genome of a new member of the Kuttervirus genus, Salmonella phage vB_Sen_ST2. This phage selectively targets Salmonella enterica serovars Typhi and Typhimurium, which are major etiologic agents of salmonellosis worldwide. Its genome consists of a linear, double-stranded DNA of 156,028 bp, with a G+C content of 44.93%. Based on our results, Salmonella phage vB_Sen_ST2 presents suitable features to be considered as a potential control agent against Salmonella enterica serovars that are responsible for salmonellosis.

Bacterial WYL domain transcriptional repressors sense single-stranded DNA to control gene expression.

Bacteria encode a wide array of immune systems to protect themselves against ubiquitous bacteriophages and foreign DNA elements. While these systems' molecular mechanisms are becoming increasingly well known, their regulation remains poorly understood. Here, we show that an immune system-associated transcriptional repressor of the wHTH-WYL-WCX family, CapW, directly binds single-stranded DNA to sense DNA damage and activate expression of its associated immune system. We show that CapW mediates increased expression of a reporter gene in response to DNA damage in a host cell. CapW directly binds single-stranded DNA by-products of DNA repair through its WYL domain, causing a conformational change that releases the protein from double-stranded DNA. In an Escherichiacoli CBASS system with an integrated capW gene, we find that CapW-mediated transcriptional activation is important for this system's ability to prevent induction of a λ prophage. Overall, our data reveal the molecular mechanisms of WYL-domain transcriptional repressors, and provide an example of how bacteria can balance the protective benefits of carrying anti-phage immune systems against the inherent risk of these systems' aberrant activation.

Development and use of two Xenopus laevis spleen stromal cell lines to study the role of splenic stromal cells in anuran immune processes

The spleen is an important immune organ in adult Xenopus laevis, supporting the differentiation of B cells and acting as the main peripheral lymphoid organ. Key to these processes are the supporting non-hematopoietic cells, or stromal cells, within the spleen tissue. Despite the importance of the spleen to frog immunity, few frog cell lines originating from spleen tissue have been reported. In this study, we report on the establishment and characterization of two cell lines originating from X. laevis spleen tissue, Xela S5F and Xela S5E. Morphological observations and gene expression profiling suggest that Xela S5F is fibroblast-like and Xela S5E is epithelial-like. Both cell lines express transcripts corresponding to a variety of hematopoietic growth factors, suggesting their potential utility as a feeder cell line to support ex vivo myelopoietic cell differentiation. Xela S5F and Xela S5E produce transcripts for a diversity of pattern recognition receptors including toll-like receptors, scavenger receptors, and cytosolic nucleic acid sensors, suggesting anuran spleen stromal cells may be important cellular sensors of pathogens filtered through the spleen. This idea is supported by the increase in transcript levels for antiviral and proinflammatory genes in both cell lines in response to treatment with the commercially available toll-like receptor ligands, flagellin and poly(I:C). However, despite the ability to sense extracellular synthetic analogues of viral nucleic acids [i.e. poly(I:C)] and susceptibility and permissibility of both cell lines to frog virus 3 (FV3), a large double-stranded DNA virus that infects amphibians, neither cell line upregulates key antiviral or proinflammatory transcripts when challenged with FV3. The establishment of Xela S5F and S5E cell lines expands the current X. laevis invitrome and provides new in vitro cell model systems to investigate the role of splenic stromal cells in anuran immune functions.

DNA damage-induced AIM2 pyroptosis in high glucose-induced proximal tubular epithelial cell

Pyroptosis is one of the ways to cause proximal tubular epithelial cell death in diabetic nephropathy (DN), but the exact mechanism remains unclear. Absent in melanoma 2 (AIM2), a sensor for double-stranded DNA, creates an inflammasome that triggers the cleavage of gasdermin D (GSDMD), leading to a type of inflammatory cell death called pyroptosis. This study investigated the role of AIM2 in pyroptosis within proximal tubular epithelial cells in DN. We observed significantly elevated AIM2 expression in renal tubules from DN patients and db/db mice, as well as in high glucose (HG)-induced Human Kidney-2 (HK2) cells. Besides, increased AIM2 expression was accompanied by activation of the pyroptosis pathway (cleaved-caspase-1, GSDMD-FL, GSDMD-NT) in the renal cortex of db/db mice and HG-induced HK2 cells in vitro. Knocking down GSDMD can reduce HG-induced HK2 cell death, indicating that HG triggers pyroptosis in HK2 cells. Furthermore, HG-induced pyroptosis was mitigated in HK2 cells with AIM2 knockdown using siRNA. Additionally, reducing ROS levels using NAC was able to attenuate HG-induced HK2 cells DNA damage, AIM2 activation, and pyroptosis. Notably, AIM2 upregulation was observed in renal biopsies from DN patients, with expression levels positively correlating with serum creatinine and inversely with estimated glomerular filtration rate (eGFR). Collectively, DNA damage caused by HG could result in the activation of the AIM2 inflammasome, leading to the pyroptosis of proximal tubular epithelial cells, indicating that targeting AIM2 could be a potential novel approach for treating DN.

Interpreting CRISPR-Cas12a enzyme kinetics through free energy change of nucleic acids.

While CRISPR has revolutionized biotechnology, predicting CRISPR-Cas nuclease activity remains a challenge. Herein, through the trans-cleavage feature of CRISPR-Cas12a, we investigate the correlation between CRISPR enzyme kinetics and the free energy change of crRNA and DNA targets from their initial thermodynamic states to a presumed transition state before hybridization. By subjecting computationally designed CRISPR RNAs (crRNAs), we unravel a linear correlation between the trans-cleavage kinetics of Cas12a and the energy barrier for crRNA spacer and single-stranded DNA target unwinding. This correlation shifts to a parabolic relationship with the energy consumption required for double-stranded DNA target separation. We further validate these correlations using ∼100 randomly selected crRNA/DNA pairs from viral genomes. Through machine learning methods, we reveal the synergistic effect of free energy change of crRNA and DNA on categorizing Cas12a activity on a two-dimensional map. Furthermore, by examining other potential factors, we find that the free energy change is the predominant factor governing Cas12a kinetics. This study will not only empower sequence design for numerous applications of CRISPR-Cas12a systems, but can also extend to activity prediction for a variety of enzymatic reactions driven by nucleic acid dynamics.

Validation of a Novel Strategy for Fluorescence Quenching for a Self-Quenching Fluorogenic Probe and Its Application for Visual Loop-Mediated Isothermal Amplification Detection During Food Safety Analysis

The self-quenching fluorogenic probe facilitates precise identification of LAMP (loop-mediated isothermal amplification) amplicons, unaffected by non-specific products resulting from primer dimers. However, low quenching efficiency by surrounding nucleobases leads to high background signal, posing significant challenges for visual inspection with the naked eye. The present study aims to identify an oligonucleotide sequence that is complementary to the self-quenching fluorogenic probe, and to employ the fluorescence super-quenching mechanism of double-stranded DNA to establish a visualization system for the LAMP assay. The results indicated that the incorporation of a sequence fully complementary to the probe could significantly reduce the system’s background fluorescence (p &lt; 0.05). When the melting temperature exceeds room temperature, truncating the complementary sequence from the 3′ end does not compromise the probe’s quenching efficiency. The LAMP visualization system, using a 10–13-base complementary sequence of the loop primer-based probe, could effectively minimize background fluorescence and yield straightforward visual results post-reaction. Applied to rainbow trout and Atlantic salmon detection, the system detected 1 pg DNA in a closed-tube format. In conclusion, a suitable complementary sequence can reduce the background fluorescence of the self-quenching fluorogenic probe. Employing this sequence alongside the self-quenching fluorogenic probe to develop a low-background fluorescence LAMP system demonstrates great potential for successful visual detection and holds considerable promotional merit.