DNA Interaction Research Articles

Competitive Binding Strategy for Reliable Signal-off Surface Enhanced Raman Scattering Sensing in Protecting Apples from Patulin without External Interference

Patulin is a toxin that can be found in damaged or moldy fruits, especially apples. Very high detection sensitivity can be achieved using the SERS (Surface Enhanced Raman Scattering) technique, which provides information about molecular vibrations. However, unexpected desorption of target toxins from the surface of the SERS substrate and interference from other substances pose a major challenge. Here we investigate a competitive binding strategy for reliable SERS analysis of PAT. Core-Raman molecule-shell (CMS) structures and programmable, specific DNA interactions are utilized to regulate Raman signal intensity without affecting the embedded Raman molecules. Specfically, aptamer-functionalized CMS structures are combined with metal-organic scaffold nanoparticles that possess complementary DNA sequences. In the presence of PAT, binding of the aptamer to the toxin leads to degradation of the hybrid nano assembly, which can be measured by a change in the SERS signal. This SERS strategy enables turn-off sensing in apple juice over a wide range (10pg/mL to 1μg/mL), with a detection limit as low as 0.02ng/mL. Analysis of real samples gives results consistent with high-performance liquid chromatography (HPLC) test. The excellent selectivity and sensitivity of the SERS sensor demonstrate its potential for a wide range of SERS sensor applications.

Synthesis, characterization, DNA, BSA, antimicrobial, antioxidant and molecular docking studies of gadolinium(III) based complexes

The present study reports the synthesis of two new gadolinium-metal-based complexes with mixed ligands, [Gd(L1)2(py)(H2O)3] (C1) and [Gd (L2)2(phen)(H2O)2] (C2), where L1 represents 3-(4 cyanophenyl) acrylate and L2 as 3-(4 fluorophenyl) acrylate. The complexes were characterized by various analytical techniques including FT-IR, PXRD, TGA, DSC, SEM and EDX to determine structural elucidation, binding mode, crystallinity, thermal stability, morphology and elemental composition, respectively. The synthesized complexes were tested for DNA (salmon sperm) and BSA interaction studies to infer their antitumor potential. The binding constants obtained for C1 and C2 with SS DNA were 3.03 × 104 and 3.2 × 104 while with BSA observed as 1.59 × 105 and 1.22 × 105, respectively. In vitro antimicrobial potential of both complexes was determined against various bacterial and fungal strains. Experimental results showed complex C2 is more active than C1 against all selected bacterial strains and showed higher antibacterial potential against E. coli with a zone of inhibition (ZOI) of 35 mm. The antibacterial potential of C2 was further investigated by calculating the MIC (IC50) value. MIC of complex C2 was assessed using visual inspection (turbidity) and spectrophotometric assay at 600 nm. The findings of the spectrophotometric approach have greater sensitivity than the standard disc diffusion assays. The molecular docking studies were conducted to validate further and compare the findings of experimental results which exhibited that complex C2 has an excellent binding capacity with the target protein (5CDQ) with free binding energy −12.23 kcal/mol. Antioxidant potentials of the complexes were assessed using phosphomolybdenum assay, which demonstrated that complex C2 exhibits higher antioxidant activity than complex C1.

UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation.

The RING E3 ubiquitin ligase UHRF1 is an established cofactor for DNA methylation inheritance. The model posits that nucleosomal engagement through histone and DNA interactions directs UHRF1 ubiquitin ligase activity toward lysines on histone H3 tails, creating binding sites for DNMT1 through ubiquitin interacting motifs (UIM1 and UIM2). However, the extent to which DNMT1 relies on ubiquitin signaling through UHRF1 in support of DNA methylation maintenance remains unclear. Here, with integrative epigenomic and biochemical analyses, we reveal that DNA methylation maintenance at low-density cytosine-guanine dinucleotides (CpGs) is particularly vulnerable to disruption of UHRF1 ubiquitin ligase activity and DNMT1 ubiquitin reading activity through UIM1. Hypomethylation of low-density CpGs in this manner induces formation of partially methylated domains (PMDs), a methylation signature observed across human cancers. In contrast, UIM2 disruption completely abolishes the DNA methylation maintenance function of DNMT1 in a CpG density-independent manner. In the context of DNA methylation recovery following acute DNMT1 depletion, we further reveal a 'bookmarking' function for UHRF1 ubiquitin ligase activity in support of DNA re-methylation. Collectively, these studies show that DNMT1-dependent DNA methylation inheritance is a ubiquitin-regulated process that is partially reliant on UHRF1 and suggest a disrupted UHRF1-DNMT1 ubiquitin signaling axis contributes to PMD formation in cancers.

Structural basis for C. elegans pairing center DNA binding specificity by the ZIM/HIM-8 family proteins

Pairing center (PC) on each chromosome of Caenorhabditis elegans is crucial for homolog pairing and initiating synapsis. Within each PC, clusters of 11/12 bp DNA motif recruit one of four paralogous meiosis-specific proteins: ZIM-1, ZIM-2, ZIM-3, or HIM-8. However, the mechanistic basis underlying the specificity of ZIM/HIM-8-PC DNA interaction remains elusive. Here, we describe crystal structures of HIM-8, ZIM-1 and ZIM-2 DNA binding domains (ZF1, ZF2 and CTD) in complex with their cognate PC DNA motifs, respectively. These structures demonstrated the ZF1-2-CTD folds as an integrated structural unit crucial for its DNA binding specificity. Base-specific DNA-contacting residues are exclusively distributed on ZF1-2 and highly conserved. Furthermore, the CTD potentially contributes to the conformational diversity of ZF1-2, imparting binding specificity to distinct PC DNA motifs. These findings shed light on the mechanism governing PC DNA motif recognition by ZIM/HIM-8 proteins, suggesting a co-evolution relationship between PC DNA motifs and ZF1-2-CTD in shaping the specific recognition.

Mechanistic Insights into Oxygen-Independent DNA Photodegradation by Pheophorbide a: Implications for Future Photodynamic Therapy Applications.

This study explores the unique properties of Pheophorbidea(Pheda) in the photodegradation of G-quadruplex DNA under anoxic conditions, emphasizing its potential for photodynamic therapy (PDT) in hypoxic tumor environments. We used electron spin resonance (ESR), circular dichroism (CD), and nuclear magnetic resonance (NMR) spectroscopies to assess the radical generation and DNA interaction capabilities of Phedacompared to Pyropheophorbidea(Pyroa) under both oxygenated and anoxic conditions. Our results reveal that Phedaeffectively degrades G-quadruplex DNA in the absence of oxygen, whereas Pyroadoes not. Under anoxic conditions, Phedagenerates unique carbon-centered radicals, as indicated by distinctive ESR signals, which are not observed in aerobic environments or with Pyroa. These radicals facilitate DNA decomposition without relying on reactive oxygen species (ROS). Pheda's ability to degrade DNA independently of oxygen underscores its potential as a versatile and effective PDT agent, especially for hypoxic tumors where traditional photosensitizers are ineffective. This study paves the way for the development of new PDT agents that can operate under different oxygen levels. Pheda's radical generation and oxygen-independent DNA degradation mechanisms make it a promising candidate for future PDT applications.

Synthesis of derived Cu(II) complex from Schiff base of Vitamin B6 and antihypertensive hydralazine: DNA interaction, biological application and molecular docking studies

A novel Schiff base ligand (E)-5-(hydroxymethyl)-2-methyl-4-((2-(phthalazin-1-yl)hydrazineylidene)methyl)pyridin-3-ol was synthesized through the condensation of antihypertensive hydralazine and Pyridoxal (Vitamin B6) ligands. This fabricated Schiff base (L) was a precursor for developing a unique Cu(II) complex. TheSchiff base ligand and Cu(II) complex structureswere characterized using various analytical tools, including IR, UV–Vis Spectroscopy and NMR. An octahedron geometry of this complex was proposed for the assigned molecular formula [Cu(L)2].3H2O. The molecular structures of theSchiff base ligand and its Cu(II) complex have been optimized using the B3LYP functional and the 6-311G++(d,p) basis set. Investigating the interaction of this prepared Cu(II) complex with calf thymus DNA (CT-DNA) molecules was operated using UV–Vis spectrophotometry, viscosity measurement, electrochemical studies, gel electrophoresis, and molecular docking. In vitro cytotoxicity was conducted using the MTT assay on four human tumor cell lines including hepatocellular carcinoma, estrogen-dependent breast cancer, melanoma, triple-negative breast cancer as well as healthy human skin fibroblasts.

Tryptamine-Derived Schiff Bases: Potent Antimicrobial Agents and Evaluation of Cytotoxicity, ADME and DNA Binding Properties.

Inspired by the fact that the introduction of indole pharmacophore in organic scaffolds could enable interesting pharmacological properties, the series of novel tryptamine-derived Schiff bases was synthetized. Tryptamine was used as a source of indole pattern, as well as an example of biogenic amines which chemical transformations lead to the compounds with prominent biological activities. The obtained results for antimicrobial activity against a range of bacterial and fungal strains and cytotoxic activities have revealed that Schiff base TSB4 combining the tryptamine and p-nitro aryl patterns in the structure showed better antifungal activity at low concentrations than standard drug Fluconazole, while compound TSB6 with molecular scaffold composed from tryptamine and quinoline moieties showed certain cytotoxic effect on HCT-116 cell line with a strongly expressed selectivity about healthy fibroblast cells, MRC-5. For these two selected compounds, additional ADME analysis and DNA interactions were performed. to obtain better insight into their pharmacokinetics and determination of binding mode for DNA molecules. As results suggested, strong binding of examined compounds to CT-DNA was observed, while the ADME screening showed that selected compounds possess suitable physicochemical properties for oral bioavailability and druglikeness.

RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions.

Many RNAs associate with chromatin, either directly or indirectly. Several technologies for mapping regions where RNAs interact across the genome have been developed to investigate the function of these RNAs. Obtaining information on the proteins involved in these RNA-chromatin interactions is critical for further analysis. Here, we developed RADIP [RNA and DNA interacting complexes ligated and sequenced (RADICL-seq) with immunoprecipitation], a novel technology that combines RADICL-seq technology with chromatin immunoprecipitation to characterize RNA-chromatin interactions mediated by individual proteins. Building upon the foundational principles of RADICL-seq, RADIP extends its advantages by increasing genomic coverage and unique mapping rate efficiency compared to existing methods. To demonstrate its effectiveness, we applied an anti-H3K27me3 antibody to the RADIP technology and generated libraries from mouse embryonic stem cells (mESCs). We identified a multitude of RNAs, including RNAs from protein-coding genes and non-coding RNAs, that are associated with chromatin via H3K27me3 and that likely facilitate the spread of Polycomb repressive complexes over broad regions of the mammalian genome, thereby affecting gene expression, chromatin structures and pluripotency of mESCs. Our study demonstrates the applicability of RADIP to investigations of the functions of chromatin-associated RNAs.

Enlightening the blind spot of the Michaelis–Menten rate law: The role of relaxation dynamics in molecular complex formation

The century-long Michaelis–Menten rate law and its modifications in the modeling of biochemical rate processes stand on the assumption that the concentration of the complex of interacting molecules, at each moment, rapidly approaches an equilibrium (quasi-steady state) compared to the pace of molecular concentration changes. Yet, in the case of actively time-varying molecular concentrations with transient or oscillatory dynamics, the deviation of the complex profile from the quasi-steady state becomes relevant. A recent theoretical approach, known as the effective time-delay scheme (ETS), suggests that the delay from the relaxation time of molecular complex formation contributes to the substantial breakdown of the quasi-steady state assumption. Here, we systematically expand this ETS and inquire into the comprehensive roles of relaxation dynamics in complex formation. Through the modeling of rhythmic protein–protein and protein–DNA interactions and the mammalian circadian clock, our analysis reveals the effect of the relaxation dynamics beyond the time delay, which extends to the dampening of changes in the complex concentration with a reduction in the oscillation amplitude compared to the quasi-steady state. Interestingly, the combined effect of the time delay and amplitude reduction shapes both qualitative and quantitative oscillatory patterns such as the emergence and variability of the mammalian circadian rhythms. These findings highlight the downside of the routine assumption of quasi-steady states and enhance the mechanistic understanding of rich time-varying biomolecular processes.

Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence

The basic helix-loop-helix (bHLH) domain via critical amino acid residues on basic region binding to E-box (5′-CANNTG-3′) is known in embryophyte. However, the dictated E-box types selection by bHLH dimers and the significant impact of these critical amino acid residues along embryophyte evolution remain unclear. The Arabidopsis thaliana PIF3-bHLH (AtPIF3-bHLH) recombinant protein and a series of AtPIF3-bHLH mutants were synthesized and analyzed. The reduced DNA binding ability and affinity of AtPIF3-bHLH point-mutation proteins, observed via fluorescence-based electrophoretic mobility shift assay (fEMSA) and isothermal titration calorimetry (ITC), suggest the critical role of these DNA-recognition sites in maintaining the AtPIF3-bHLH–DNA interaction. The purifying selection signals and the DNA-recognition-site conservation at the species level suggest the invariant roles of these sites throughout embryophyte evolution. The G-box outcompeted other types of E-box for binding in our competitive fEMSAs. The dynamic hydrogen bond formed between AtPIF3-bHLH and the G-box core indicates flexible identification of the core region. These features highlight a fast fixation of the bHLH-G-box recognition mechanism through embryophyte evolution and serve as a blueprint for studying DNA recognition determinants of other TF families.

Heparan sulphate binding controls in vivo half-life of the HpARI protein family

The parasitic nematode Heligmosomoides polygyrus bakeri secretes the HpARI family, which bind to IL-33, either suppressing (HpARI1 and HpARI2) or enhancing (HpARI3) responses to the cytokine. We previously showed that HpARI2 also bound to DNA via its first complement control protein (CCP1) domain. Here, we find that HpARI1 can also bind DNA, while HpARI3 cannot. Through the production of HpARI2/HpARI3 CCP1 domain-swapped chimeras, DNA-binding ability can be transferred, and correlates with in vivo half-life of administered proteins. We found that HpARI1 and HpARI2 (but not HpARI3) also binds to the extracellular matrix component heparan sulphate (HS), and structural modelling showed a basic charged patch in the CCP1 domain of HpARI1 and HpARI2 (but not HpARI3) which could facilitate these interactions. Finally, a mutant of HpARI2 was produced which lacked DNA and HS binding, and was also shown to have a short half-life in vivo. Therefore, we propose that during infection the suppressive HpARI1 and HpARI2 proteins have long-lasting effects at the site of deposition due to DNA and/or extracellular matrix interactions, while HpARI3 has a shorter half-life due to a lack of these interactions.

Heparan sulphate binding controls in vivo half-life of the HpARI protein family.

The parasitic nematode Heligmosomoides polygyrus bakeri secretes the HpARI family, which bind to IL-33, either suppressing (HpARI1 and HpARI2) or enhancing (HpARI3) responses to the cytokine. We previously showed that HpARI2 also bound to DNA via its first complement control protein (CCP1) domain. Here, we find that HpARI1 can also bind DNA, while HpARI3 cannot. Through the production of HpARI2/HpARI3 CCP1 domain-swapped chimeras, DNA-binding ability can be transferred, and correlates with in vivo half-life of administered proteins. We found that HpARI1 and HpARI2 (but not HpARI3) also binds to the extracellular matrix component heparan sulphate (HS), and structural modelling showed a basic charged patch in the CCP1 domain of HpARI1 and HpARI2 (but not HpARI3) which could facilitate these interactions. Finally, a mutant of HpARI2 was produced which lacked DNA and HS binding, and was also shown to have a short half-life in vivo. Therefore, we propose that during infection the suppressive HpARI1 and HpARI2 proteins have long-lasting effects at the site of deposition due to DNA and/or extracellular matrix interactions, while HpARI3 has a shorter half-life due to a lack of these interactions.

A Novel Quinoline Inhibitor of the Canonical NF-κB Transcription Factor Pathway.

The NF-κB family of transcription factors is a master regulator of cellular responses during inflammation, and its dysregulation has been linked to chronic inflammatory diseases, such as inflammatory bowel disease. It is therefore of vital importance to design and test new effective NF-κB inhibitors that have the potential to be utilized in clinical practice. In this study, we used a commercial transgenic HeLa cell line as an NF-κB activation reporter to test a novel quinoline molecule, Q3, as a potential inhibitor of the canonical NF-κB pathway. Q3 inhibited NF-κB-induced luciferase in concentrations as low as 5 μM and did not interfere with cell survival or induced cell death. A real-time PCR analysis revealed that Q3 could inhibit the TNF-induced transcription of the luciferase gene, as well as the TNF gene, a known downstream target gene. Immunocytochemistry studies revealed that Q3 moderately interferes with TNF-induced NF-κB nuclear translocation. Moreover, docking and molecular dynamics analyses confirmed that Q3 could potentially modulate transcriptional activity by inhibiting the interaction of NF-κB and DNA. Therefore, Q3 could be potentially developed for further in vivo studies as an NF-κB inhibitor.

Towards development of the 4c-based method detecting interactions of plasmid dna with host genome

Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and optimize protocol to allow high detection rate of contacts between the plasmid and host DNA.

The cohesin complex: structure and principles of interaction with dna

Accurate duplication and separation of long linear genomic DNA molecules is associated with a number of purely mechanical problems. SMC complexes are key components of the cellular machinery that ensures decatenation of sister chromosomes and compaction of genomic DNA during division. Cohesin, one of the essential eukaryotic SMC complexes, has a typical ring structure with intersubunit pore through which DNA molecules can be threaded. The capacity of cohesin for such topological entrapment of DNA is crucial for the phenomenon of post-replicative association of sister chromatids better known as cohesion. Recently, it became apparent that cohesin and other SMC complexes are in fact motor proteins with a very peculiar movement pattern leading to the formation of DNA loops. This specific process was called loop extrusion. Extrusion underlies multiple cohesin’s functions beyond cohesion, but the molecular mechanism of the process remains a mystery. In this review, we have summarized data on the molecular architecture of cohesin, the influence of ATP hydrolysis cycle on this architecture, and the known modes of cohesin–DNA interactions. Many of the seemingly disparate facts presented here will probably be incorporated in a unified mechanistic model of loop extrusion in a not so far future.

Comprehensive assessment of schiff base derived from 4-Chloroaniline and 2-Formylphenol: Molecular architecture, experimental with computational bioactivity profiling, emphasizing anticancer efficacy against pulmonary and mammary carcinoma cell models

This study thoroughly analyses the structural and biological properties of a Schiff base compound synthesized from the condensation of 2-formyl phenol and 4-chloroaniline. Single crystal X-ray diffraction examination indicated that the compound crystallizes in the monoclinic space group P21/c, with unit cell parameters a = 13.4232(15) Å, b = 5.7860(6) Å, c = 14.699(2) Å, β = 106.048(6) °, and Z = 4. The molecular structure has an E configuration around the C = N double bond, with a bond length of 1.266(2) Å, and includes an intramolecular O—H⋯N hydrogen bond. Hirshfeld surface analysis elucidated intermolecular interactions inside the crystal lattice, emphasizing dominant hydrogen-hydrogen, hydrogen-chlorine, and carbon-hydrogen contacts. The chemical exhibited concentration-dependent antioxidant and anti-inflammatory effects. Studies on DNA interactions indicate van der Waals forces between the ligand and nucleic acid, whereas it demonstrated considerable binding affinity for BSA with a ΔG value of -6.9 kcal/mol. ADME study revealed values within the recommended range, indicating advantageous pharmacokinetic characteristics. PASS filter-based cytotoxicity predictions indicated significant anti-cancer efficacy against breast adenocarcinoma, small cell lung carcinoma, and lung cancer. Toxicological assessments in diverse models indicated no possible irritation to skin and ocular tissues, highlighting its safety profile for therapeutic use. This research advances our comprehension of Schiff bases with halogen substituents and their prospective uses in chemistry and biology.

Electrochemical investigation of the antimicrobial agent daptomycin utilizing disposable pencil graphite electrode and DNA interaction with green techniques

Electrochemical investigation of the antimicrobial agent daptomycin utilizing disposable pencil graphite electrode and DNA interaction with green techniques

Shikonin Stimulates Mitochondria-Mediated Apoptosis by Enhancing Intracellular Reactive Oxygen Species Production and DNA Damage in Oral Cancer Cells.

Phytotherapy has rendered a new insight towards the treatment of various cancers, including oral cancer with fewer side effects, over the traditional chemotherapeutic drugs to overcome chemoresistance. Shikonin (Shk) is a natural biologically active alkaloid found in the Lithospermum erythrorhizon plant's root. It has potent cytotoxic activities against various cancers. Our study revealed the release time and anticancer potential of Shk on the SCC9 and H357 oral cancer cell lines. We investigated the antiproliferative, antimigratory, cell cycle arresting and apoptosis promoting activity of Shk in oral cancer cells by performing MTT and morphological assay, colony, and tumor sphere formation assay, AO/EtBr and DAPI staining, Annexin V-FITC/PI staining, assay for reactive oxygen species (ROS) and mitochondrial membrane potential (MMP) measurement, comet assay, qRT-PCR, and western blot analysis. We also checked the interaction of DNA and Shk by docking and CD spectroscopy and EtBr displacement assay. As a result, we found that Shk reduced the viability, proliferation, and tumorigenicity of SCC9 and H357 cells in a time and concentration-dependent manner. We obtained half-maximal inhibitory concentration (IC50) at 0.5 µM for SCC9 and 1.25 µM for H357. It promotes apoptosis via overexpressing proapoptotic Bax and caspase 3 via enhancing ROS that leads to MMP depletion and DNA damage and arrests cells at the G2/M & G2/S phase. The antimigratory activity of Shk was performed by analyzing the expression of markers of epithelial-mesenchymal transition like E-cadherin, ZO-1, N-cadherin, and vimentin. These overall results recommended that Shk shows potent anticancer activity against oral cancer cell lines in both in vitro and ex vivo conditions. So, it could be an excellent agent for the treatment of oral cancer.

Pharmacoinformatics, Molecular Dynamics Simulation, and Quantum Mechanics Calculation Based Phytochemical Screening of Croton bonplandianum Against Breast Cancer by Targeting Estrogen Receptor-α (ERα)

Breast cancer progression is strongly influenced by estrogen receptor-α (ERα), a ligand-activated transcription factor that regulates hormone binding, DNA interaction, and transcriptional activation. ERα plays a key role in promoting cell proliferation in breast tissue, and its overexpression is associated with the advancement of breast cancer through estrogen-mediated signaling pathways. Targeting ERα is, therefore, a promising therapeutic strategy for breast cancer. However, there are currently no phytochemical-based drug candidates approved for effectively inhibiting breast cancer progression driven by elevated ERα expression. This study aims to identify phytochemical inhibitors from Croton bonplandianum against ERα using pharmacoinformatics approaches. Eighty-three bioactive compounds from C. bonplandianum were retrieved from the IMPPAT (Indian Medicinal Plants, Phytochemistry, and Therapeutics) database and screened through molecular docking for their binding affinity to ERα. The top candidates were further evaluated through molecular dynamics simulations, ADME analysis, toxicity assessment, and quantum mechanics-based DFT calculations. The thermodynamic properties and HOMO-LUMO energy gap values indicated that the selected compounds were both stable and active. Among them, 2,3-oxidosqualene (CID-5366020) and 5,8,11-eicosatriynoic acid, trimethylsilyl ester (CID-91696396) demonstrated the most potent inhibitory activity against ERα. These findings suggest that these compounds have significant potential as therapeutic agents for breast cancer treatment by targeting ERα.

Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference

CRISPR-Cas mediated DNA-interference typically relies on sequence-specific binding and nucleolytic degradation of foreign genetic material. Type IV-A CRISPR-Cas systems diverge from this general mechanism, using a nuclease-independent interference pathway to suppress gene expression for gene regulation and plasmid competition. To understand how the type IV-A system associated effector complex achieves this interference, we determine cryo-EM structures of two evolutionarily distinct type IV-A complexes (types IV-A1 and IV-A3) bound to cognate DNA-targets in the presence and absence of the type IV-A signature DinG effector helicase. The structures reveal how the effector complexes recognize the protospacer adjacent motif and target-strand DNA to form an R-loop structure. Additionally, we reveal differences between types IV-A1 and IV-A3 in DNA interactions and structural motifs that allow for in trans recruitment of DinG. Our study provides a detailed view of type IV-A mediated DNA-interference and presents a structural foundation for engineering type IV-A-based genome editing tools.