DNA Structure Research Articles

N vacancy and self-enhancement induced high anodic electrochemiluminescence of 3D g-C3N4 for sensitive staphylococcus aureus analysis

Here, 3D g-C3N4 with dense N vacancy in its 3D porous interconnected open-framework was synthesized, and the co-reactive 3-(dibutylamino)propylamine (DBAPA) was further covalently coupled onto the surface, resulting in a strong self-enhanced anodic electrochemiluminescence (ECL). Through introduction of high-density N vacancy, for the obtained 3D g–C3N4–NV, the band gap was broadened and the electrical conductivity was enhanced, realizing an obvious ECL improvement. Moreover, after the covalent binding of co-reactive DBAPA, the obtained 3D g–C3N4–NV-DBAPA exhibited a more intensive self-enhanced ECL signal due to the higher co-reaction efficiency originated from shorter electron transfer distance and lower energy loss. Based on the high initial signal of the proposed 3D g–C3N4–NV-DBAPA, a sensitive ECL biosensor with signal “on-off” was fabricated in assistance with multiple horizontal ordered hybridization chain reaction (HO-HCR). Through orderly fixing the reacted DNA chains on the Y-shape DNA structure on the electrode could effectively decrease diffusion process and improve the reaction efficiency of HCR process, resulting in the formation of numerous long horizontal double-strand DNA that could immobilize abundant ferrocene-doxorubicin (Fc-Dox) with ECL quenching effect. Meanwhile, compared to the traditional vertical HCR, the HO-HCR could make the quench reagent closer to the ECL emitter on the electrode surface and obtain a more effective quenching effect to enhance the sensing sensitivity. As a result, the proposed ECL biosensor archived the sensitive measurement of staphylococcus aureus with a detection limit of 10.3 aM.

A ratiometric electrochemical biosensor based on ARGET ATRP for detection of HER2 gene

Human epidermal growth factor receptor 2 (HER2), a common proto-oncogene, is overexpressed in a subset of breast cancer patients. It is essential to track HER2 expression for early breast cancer diagnosis. Herein, a ratiometric electrochemical biosensor for detection of HER2 based on activators generated by electron transfer for atom transfer radical polymerisation (AGET ATRP) and hairpin DNA was developed. Specifically, hairpin DNA was first self-assembled on the gold electrode by Au–S bond. Upon capturing HER2, the stem-loop structure of hairpin DNA was unfolded, the signal value of methylene blue (MB) decreased as it moved away from the electrode surface. cDNA was linked with HER2 by complementary base pairing to introduce amino group. Then, the initiator 2-bromo-2-methylpropionic acid (BMP) were connected to the amino group on the cDNA to activate ARGET ATRP. The detection performance of biosensors for HER2 was explored by the ratio signal between two signal molecules. Under optimal conditions, this ratiometric electrochemical biosensor shows good selectivity and stability with a wide detection range of 1–1 × 106 pM and a detection limit of 78.47 fM. Furthermore, the biosensor exhibits satisfactory anti-interference ability due to the hairpin DNA and dual signal system, and has promising application prospects in the detection of other DNA disease markers.

Dumbbell Dual-Hairpin Triggered DNA Nanonet Assembly for Cascade-Amplified Sensing of Exosomal MicroRNA.

Exosomal microRNAs (miRNAs) are valuable biomarkers closely associated with cancer progression. Therefore, sensitive and specific exosomal miRNA biosensing has been employed for cancer diagnosis, prognosis, and prediction. In this study, a miRNA-based DNA nanonet assembly strategy is proposed, enabling the biosensing of exosomal miRNAs through dumbbell dual-hairpin under isothermal enzyme-free conditions. This strategy dexterously designs a specific dumbbell dual-hairpin that can selectively recognize exosomal miRNA, inducing conformational changes to cascade-generated X-shaped DNA structures, facilitating the extension of the X-shaped DNA in three-dimensional space, ultimately forming a DNA nanonet assembly. On the basis of the target miRNA, our design enriches the fluorescence signal through the cascade assembly of DNA nanonet and realizes the secondary signal amplification. Using exosomal miR-141 as the target, the resultant fluorescence sensing demonstrates an impressive detection limit of 57.6 pM and could identify miRNA sequences with single-base variants with high specificity. Through the analysis of plasma and urine samples, this method effectively distinguishes between benign prostatic hyperplasia, prostate cancer, and metastatic prostate cancer. Serving as a novel noninvasive and accurate screening and diagnostic tool for prostate cancer, this dumbbell dual-hairpin triggered DNA nanonet assembly strategy is promising for clinical applications.

Selective Ru(II)/benzoate complexes against triple-negative breast tumor cells and their interactions with DNA and BSA

New ruthenium(II) complexes bearing benzoate (AB) ligand with the general formula [Ru(AB)(bipy)(PP)]PF6, where 2,2′-bipyridine (bipy) and different diphosphine ligands, (PP) = 1,2′-bis(diphenylphosphine)ethane (dppe, 1), 1,3′-bis(diphenylphosphine)propane (dppp, 2) and 1,2′-bis(diphenylphosphine)ferrocene (dppf, 3), were synthesized. The compounds were characterized by molar conductivity, elemental analysis, cyclic voltammetry, infrared and UV–Vis spectroscopies, NMR, and by single-crystal X-ray diffraction for complexes 1 and 2. The complexes showed a weak interaction to CT-DNA through DNA minor groove, with Kb values at around 103-104 M−1. CT-DNA interaction assays by viscosity and circular dichroism (CD) suggested that the compounds do not significantly alter the secondary DNA structure. The complexes are cytotoxic against MDA-MB-231, MCF-7 (breast) and A549 (lung) tumor cell lines, with IC50 values in the range of 1 to 17 µM. The compounds 1-3 showed high selectivity against triple-negative breast tumor cells. Remarkably, complexes 1 and 3 show greater cytotoxic activity against cells than cisplatin, being promising agents for tumor treatment.

Precision miRNA profiling: Electrochemiluminescence powered by CRISPR-Cas13a and hybridization chain reaction

The article details a groundbreaking platform for detecting microRNAs (miRNAs), crucial biomolecules involved in gene regulation and linked to various diseases. This innovative platform combines the CRISPR-Cas13a system's precise ability to specifically target and cleave RNA molecules with the amplification capabilities of the hybridization chain reaction (HCR). HCR aids in signal enhancement by creating branched DNA structures. Additionally, the platform employs electrochemiluminescence (ECL) for detection, noted for its high sensitivity and low background noise, making it particularly effective. A key application of this technology is in the detection of miR-17, a biomarker associated with multiple cancer types. It exhibits remarkable detection capabilities, characterized by low detection limits (14.38 aM) and high specificity. Furthermore, the platform's ability to distinguish between similar miRNA sequences and accurately quantify miR-17 in cell lysates underscores its significant potential in clinical and biomedical fields. This combination of precise targeting, signal amplification, and sensitive detection positions the platform as a powerful tool for miRNA analysis in medical diagnostics and research.

Synthesis, Characterization and DNA Binding Study of Silver N-Heterocyclic Carbene Complex [Bis (1,3-Dipentyl-1,3-Dihydro-2-Imidazole-2-Ylidene) Silver (I) hexafluorophosphate (V)] by Surface-Enhanced Raman Spectroscopy (SERS)

The silver organometallic compounds favorably target DNA in cancerous cells and stop their growth by inhibiting DNA replication. Specific properties of these compounds help in their action as drugs and different changes occur in the structure of DNA. In-depth study of the binding mechanism of drugs is of potential use for novel drug synthesis. Surface-enhanced Raman spectroscopy (SERS) coupled with multivariate data analysis was employed to probe the interaction of silver N-heterocyclic carbene complex (drug) with DNA. In this study, silver N-heterocyclic carbene complex was synthesized and various concentrations were exposed to known concentrations of DNA. Silver nanoparticles were used for enhancement of Raman signals, which enabled sensitive detection and characterization of molecular changes occurring during binding process. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were applied to extract meaningful information from the spectral data. Changes in intensity and position of significant SERS signals were noted, which gave an indication of the bonding of the drug with DNA. The results reveal the strong intercalative binding of drug with nitrogenous bases of DNA. PCA and PLS-DA provide evidence for successful DNA-drug interaction.

RNAscape: geometric mapping and customizable visualization of RNA structure.

Analyzing and visualizing the tertiary structure and complex interactions of RNA is essential for being able to mechanistically decipher their molecular functions in vivo. Secondary structure visualization software can portray many aspects of RNA; however, these layouts are often unable to preserve topological correspondence since they do not consider tertiary interactions between different regions of an RNA molecule. Likewise, quaternary interactions between two or more interacting RNA molecules are not considered in secondary structure visualization tools. The RNAscape webserver produces visualizations that can preserve topological correspondence while remaining both visually intuitive and structurally insightful. RNAscape achieves this by designing a mathematical structural mapping algorithm which prioritizes the helical segments, reflecting their tertiary organization. Non-helical segments are mapped in a way that minimizes structural clutter. RNAscape runs a plotting script that is designed to generate publication-quality images. RNAscape natively supports non-standard nucleotides, multiple base-pairing annotation stylesand requires no programming experience. RNAscape can also be used to analyze RNA/DNA hybrid structures and DNA topologies, including G-quadruplexes. Users can upload their own three-dimensional structures or enter a Protein Data Bank (PDB) ID of an existing structure. The RNAscape webserver allows users to customize visualizations through various settings as desired. URL: https://rnascape.usc.edu/.

Monitoring of DNA structural changes after incorporation of the phenylpyrazole insecticide fipronil

The use of insecticides presents a risk to the environment because they can accumulate in the water, soil, air, and organisms, endangering human and animal health. It is therefore essential to investigate the effects of different groups of insecticides on individual biomacromolecules such as DNA. We studied fipronil, which belongs to the group of phenylpyrazole insecticides. The interaction of fipronil with calf thymus DNA was investigated using spectroscopic methods (absorption and fluorescence spectroscopy) complemented with infrared spectroscopy and viscosity measurement. Fluorescence emission spectroscopy showed the formation of a fipronil/DNA complex with a combined static and dynamic type of quenching. The binding constant was 4.15 × 103 L/mol. Viscosity changes were recorded to confirm/disconfirm the intercalation mode of interaction. A slight change in DNA viscosity in the presence of fipronil was observed. The phenylpyrazole insecticide does not cause significant conformational changes in DNA structure or increase of its chain length. We hypothesize that fipronil is incorporated into the minor groove of the DNA macromolecule via hydrogen interactions as indicated by FT-IR and CD measurements.

Phthalates Boost Natural Transformation of Extracellular Antibiotic Resistance Genes through Enhancing Bacterial Motility and DNA Environmental Persistence.

The environmental dissemination of extracellular antibiotic resistance genes (eARGs) in wastewater and natural water bodies has aroused growing ecological concerns. The coexisting chemical pollutants in water are known to markedly affect the eARGs transfer behaviors of the environmental microbial community, but the detailed interactions and specific impacts remain elusive so far. Here, we revealed a concentration-dependent impact of dimethyl phthalate (DMP) and several other types of phthalate esters (common water pollutants released from plastics) on the natural transformation of eARGs. The DMP exposure at an environmentally relevant concentration (10 μg/L) resulted in a 4.8-times raised transformation frequency of Acinetobacter baylyi but severely suppressed the transformation at a high concentration (1000 μg/L). The promotion by low-concentration DMP was attributed to multiple mechanisms, including increased bacterial mobility and membrane permeability to facilitate eARGs uptake and improved resistance of the DMP-bounded eARGs (via noncovalent interaction) to enzymatic degradation (with suppressed DNase activity). Similar promoting effects of DMP on the eARGs transformation were also found in real wastewater and biofilm systems. In contrast, higher-concentration DMP suppressed the eARGs transformation by disrupting the DNA structure. Our findings highlight a potentially underestimated eARGs spreading in aquatic environments due to the impacts of coexisting chemical pollutants and deepen our understanding of the risks of biological-chemical combined pollution in wastewater and environmental water bodies.

The Characterization of G-Quadruplexes in Tobacco Genome and Their Function under Abiotic Stress.

Tobacco is an ideal model plant in scientific research. G-quadruplex is a guanine-rich DNA structure, which regulates transcription and translation. In this study, the prevalence and potential function of G-quadruplexes in tobacco were systematically analyzed. In tobacco genomes, there were 2,924,271,002 G-quadruplexes in the nuclear genome, 430,597 in the mitochondrial genome, and 155,943 in the chloroplast genome. The density of the G-quadruplex in the organelle genome was higher than that in the nuclear genome. G-quadruplexes were abundant in the transcription regulatory region of the genome, and a difference in G-quadruplex density in two DNA strands was also observed. The promoter of 60.4% genes contained at least one G-quadruplex. Compared with up-regulated differentially expressed genes (DEGs), the G-quadruplex density in down-regulated DEGs was generally higher under drought stress and salt stress. The G-quadruplex formed by simple sequence repeat (SSR) and its flanking sequence in the promoter region of the NtBBX (Nitab4.5_0002943g0010) gene might enhance the drought tolerance of tobacco. This study lays a solid foundation for further research on G-quadruplex function in tobacco and other plants.

DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context.

Molecular details for the impact of DNA damage on folding of potential G-quadruplex sequences (PQSs) to noncanonical DNA structures involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, termed a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest the formation of G4 motifs and demonstrated a folding dependency on the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.

DNA damage in inhabitants exposed to heavy metals near Hudiara drain, Lahore, Pakistan

The current study was conducted on the inhabitants living in the area adjacent to the Hudiara drain using bore water and vegetables adjacent to the Hudiara drain. Toxic heavy metals badly affect human health because of industrial environmental contamination. Particularly hundreds of millions of individuals globally have faced the consequences of consuming water and food tainted with pollutants. Concentrations of heavy metals in human blood were elevated in Hudiara drainings in Lahore city, Pakistan, due to highly polluted industrial effluents. The study determined the health effects of high levels of heavy metals (Cd, Cu, Zn, Fe, Pb, Ni, Hg, Cr) on residents of the Hudiara draining area, including serum MDA, 8-Isoprostane, 8-hydroxyguanosine, and creatinine levels. An absorption spectrophotometer was used to determine heavy metals in wate water, drinking water, soil, plants and human beings blood sampleas and ELISA kits were used to assess the level of 8-hydroxyguanosine, MDA, 8-Isoprostane in plasma serum creatinine level. Waste water samples, irrigation water samples, drinking water samples, Soil samples, Plants samples and blood specimens of adult of different weights and ages were collected from the polluted area of the Hudiara drain (Laloo and Mohanwal), and control samples were obtained from the unpolluted site Sheiikhpura, 60 km away from the site. Toxic heavy metals in blood damage the cell membrane and DNA structures, increasing the 8-hydroxyguanosine, MDA, creatinine, and 8-Isoprostane. Toxic metals contaminated bore water and vegetables, resulting in increased levels of creatinine, MDA, Isoprostane, and 8-hydroxy-2-guanosine in the blood of inhabitants from the adjacent area Hudiara drain compared to the control group. In addition,. This study also investigated heavy metal concentrations in meat and milk samples from buffaloes, cows, and goats. In meat, cow samples showed the highest Cd, Cu, Fe and Mn concentrations. In milk also, cows exhibited elevated Cu and Fe levels compared to goats. The results highlight species-specific variations in heavy metal accumulation, emphasizing the need for targeted monitoring to address potential health risks. The significant difference between the two groups i.e., the control group and the affected group, in all traits of the respondents (weight, age, heavy metal values MDA, 8-Isoprostane, 8-hydroxyguaniosine, and serum creatinine level). Pearson’s correlation coefficient was calculated. The study has shown that the level of serum MDA, 8-Isoprostane, 8-hydroxyguaniosine, or creatinine has not significantly correlated with age, so it is independent of age. This study has proved that in Pakistan, the selected area of Lahore in the villages of Laloo and Mohanwal, excess of heavy metals in the human body damages the DNA and increases the level of 8-Isoprostane, MDA, creatinine, and 8-hydroxyguaniosine. As a result, National and international cooperation must take major steps to control exposure to heavy metals.

Host-Guest Recognition-Mediated Supramolecular Aggregation-Induced Electrochemiluminescence of Iridium(III) Complexes for Nucleic Acid Bioassay.

Currently reported aggregation-induced electroluminescence (AIECL) is usually based on the electrostatic integration of luminous monomers, and its application is still limited by the low ECL efficiency and poor structural stability of electrostatic integration-based AIECL emitters. Herein, host-guest recognition-mediated supramolecular AIECL was creatively developed to overcome the defects of electrostatic-integration-based AIECL. Cucurbit[8]uril (CB[8]) as the host recognized tris (2-phenylpyridine) iridium(III) [Ir(ppy)3] as the guest to form a novel supramolecular complex Ir-CB[8]. CB[8] can not only provide a large hydrophobic cavity to efficiently load Ir(ppy)3 and enrich coreactant tripropylamine but also utilize its carbonyl-laced portals to form intramolecular hydrogen bonds to stabilize the supramolecular structure, so Ir-CB[8] revealed excellent AIECL performance. The AIECL emitter Ir-CB[8] coupled the efficient DNA walker to construct a sensing system for miRNA-16 detection. Au nanoparticles@norepinephrine (AuNPs@NE) trapped by single-strand S1 was developed to significantly quench the ECL emission of Ir-CB[8]. When the target microRNA-16 (miRNA-16) existed, H1 was opened and the sequential assembly from H2 to H7 was triggered, forming "windmill"-like DNA walker with six Pb2+-dependent leg DNA. The assembled DNA walker, which was centered on DNA structure, had high efficiency and biocompatibility and can cut S1 to keep the DNA fragment-carrying quencher AuNPs@NE away from the electrode surface, thus restoring the ECL emission of Ir-CB[8] and realizing ultrasensitive detection of miRNA-16. Supramolecular AIECL mediated by host-guest recognition provides a new way for constructing AIECL emitters with excellent structural stability and AIECL efficiency, and an Ir-CB[8] coupling "windmill"-like DNA walker builds a promising ECL-sensing system for bioassay.

Inactivation of Alicyclobacillus acidoterrestris in apple juice using pulsed light

We aimed to investigate the effect of pulsed light (PL) on inactivating Alicyclobacillus acidoterrestris in apple juice, the mechanism behind the inactivation, and the resultant effects on the quality of the juice. Our results showed that PL had a good inactivation effect on both spores and vegetative cells of A. acidoterrestris in apple juice, with a reduction of 3.5 ± 0.1 and 2.1 ± 0.1 log CFU/mL, respectively, following 3 s of treatment. This effect was better when lower concentrations of apple juice and lower liquid layer depths were used. Transmission electron microscopy (TEM) showed that the morphology and structure of A. acidoterrestris spores did not change significantly before and after treatment. When we compared the dipicolinic acid (DPA) release rate and death rate of the spores, we hypothesized that PL might have damaged the cortical proteins on A. acidoterrestris that are associated with the resistance of the spores, thus leading to their death. However, TEM revealed that the cell membranes of vegetative cells of A. acidoterrestris were intact and smooth before the treatment, but significantly wrinkled afterward. Raman spectroscopy revealed that the main targets of PL on A. acidoterrestris vegetative cells were: amide I on the proteins, nucleic acids [adenine(A) and guanine (G), in particular] and DNA (O–P–O‾ stretching) structures, and lipids (C–H2 deformation). The PL treatment increased the sugar content significantly, while having little to no effect on the other basic physicochemical parameters of apple juice.

Creation of Quasi‐DNA Origami at the Air/Water Interface Using the Collapsed Mechanism of Langmuir Monolayer

AbstractIt has achieved the preparation of quasi‐deoxyribonucleic acid (DNA) origami using the techniques of organized molecular films. After the adsorption of DNA from the subphase onto a Langmuir monolayer of polymers containing diamino‐s‐triazine rings, the monolayer collapses owing to high surface pressure, resulting in the formation of a three‐dimensional folded structure of DNA. A homopolymer featuring a diamino‐s‐triazine ring and a copolymer containing 20 % long alkyl chains are used to form the Langmuir monolayer. A‐T base pairs of salmon testis‐derived DNA from the subphase are hydrogen‐bonded and adsorbed onto each Langmuir monolayer. Following the collapse of the Langmuir monolayer, the film height almost doubles, indicating the formation of a bilayer structure consisting of a bioadsorbed polymer monolayer, especially evident in copolymer‐collapsed films. During this period, the bioconjugated bilayer structure adopts a mesoscopic linear morphology within the plane. In this quasi‐DNA origami structure, the chirality in the DNA molecule is maintained, as evidenced by the circular dichroism (CD) spectra displaying a positive Cotton effect. These results correspond to the proposal of a new DNA morphology control technology.

Synthetic DNA-based Swimmers Driven by Enzyme Catalysis.

Here, we report DNA-based synthetic nanostructures decorated with enzymes (hereafter referred to as DNA-enzyme swimmers) that self-propel by converting the enzymatic substrate to the product in solution. The DNA-enzyme swimmers are obtained from tubular DNA structures that self-assemble spontaneously by the hybridization of DNA tiles. We functionalize these DNA structures with two different enzymes, urease and catalase, and show that they exhibit concentration-dependent movement and enhanced diffusion upon addition of the enzymatic substrate (i.e., urea and H2O2). To demonstrate the programmability of such DNA-based swimmers, we also engineer DNA strands that displace the enzyme from the DNA scaffold, thus acting as molecular "brakes" on the DNA swimmers. These results serve as a first proof of principle for the development of synthetic DNA-based enzyme-powered swimmers that can self-propel in fluids.

Exploring the Roles of Different DNA Repair Proteins in Short Inverted Repeat Mediated Genomic Instability: A Pilot Study

Repetitive DNA sequences are abundant in the human genome and can adopt alternative (i.e., non-B) DNA structures. These sequences contribute to diverse biological functions, including genomic instability. Previously, we found that Z-DNA-, H-DNA- and cruciform DNA-forming sequences are mutagenic, implicating them in cancer etiology. These sequences can stimulate the formation of DNA double-strand breaks (DSBs), causing deletions via cleavage by the endonuclease ERCC1-XPF. Interestingly, the activity of ERCC1-XPF in H-DNA-induced mutagenesis is nucleotide excision repair (NER)-dependent, but its role in Z-DNA-induced mutagenesis is NER-independent. Instead, Z-DNA is processed by ERCC1-XPF in a mechanism dependent on the mismatch repair (MMR) complex, MSH2-MSH3. These observations indicate distinct mechanisms of non-B-induced genomic instability. However, the roles of NER and MMR proteins, as well as additional nucleases (CtIP and MRE11), in the processing of cruciform DNA remain unknown. Here, we present data on the processing of cruciform-forming short inverted repeats (IRs) by DNA repair proteins using mammalian cell-based systems. From this pilot study, we show that, in contrast to H-DNA and Z-DNA, short IRs are processed in a NER- and MMR-independent manner, and the nucleases CtIP and MRE11 suppress short IR-induced genomic instability in mammalian cells.

Abstract LB180: Non-cardiotoxic properties of annamycin, a clinically evaluated anthracycline and potent topoisomerase 2β poison

Abstract Introduction. Cardiotoxicity is an important side effect limiting the clinical use of all anthracyclines, including doxorubicin (DOX). DOX targets topoisomerase II alpha (Top2α) and beta (Top2β), two enzymes that regulate DNA topology. Top2β is present in cardiomyocytes and has been proposed as a major contributor to DOX-induced cardiotoxicity. Annamycin (ANN), a novel clinically evaluated DOX analog, displays suppressed or no cardiotoxic properties in preclinical in vivo experiments. The objective of this study was to directly assess and compare the potency of DOX and ANN against Top2α and Top2β and determine their impact on physiology of human cardiomyocytes and mice hearts following chronic exposure. Our initial data are clearly aligned with lack of drug-related cardiotoxic events in ANN-treated patients in ongoing clinical trials. Methods. The potency of ANN and DOX to inhibit Top2 was tested in DNA relaxation assays using recombinant Top2α and Top2β with kinetoplast as the DNA substrate. ANN and DOX cytotoxicity was assessed in a panel of cancer cell lines cardiomyocytes (murine and human). In addition, the effects on cardiomyocyte physiology (beating rate, contraction, electric potential,) were assessed in human cardiomyocytes using the xCELLigence RTCA CardioECR. The pathophysiology of the heart after chronic exposure to the drugs was also evaluated in mice models. Cardiotoxicity of liposome formulated ANN (L-ANN) is currently being examined in ongoing clinical studies of subjects with acute myeloid leukemia (NCT05319587) or soft tissue sarcoma with metastases to the lungs (NCT04887298). Results. The nanomolar range potency of ANN in tested cancer cell lines was 2-10 times greater than that of DOX. The DNA relaxation assay demonstrated high potency of ANN against recombinant Top2α and Topβ with IC50 values 0.23±0.06 and 0.22± 0.06 µM, respectively, whereas the IC50 for DOX was 0.65± 0.22 and 0.34± 0.31µM, respectively. Importantly, ANN did not significantly affect electric potential, contractility, and viability of human cardiomyocytes up to highest tested dose of 1,500 nM (72h exposure). In contrast, DOX caused a dramatic change in heart beating rate and decreased in contractility and field potential amplitude. In rat cardiomyocyte culture (H92C), ANN was 14-fold less cytotoxic than DOX (IC50 1,264 nM for ANN vs. 88 nM for DOX). No cardiotoxicity of L-ANN was detected in myocardium of nude mice exposed weekly for 12 weeks to therapeutic doses of L-ANN (4 mg/kg, 40% of LD10). Finally, data from ongoing clinical trials revealed no drug related cardiac events in patients receiving L-ANN (confirmed by an independent review of the Duke’s ECHO core laboratory, USA). Conclusions. Our preclinical studies demonstrate non-cardiotoxic properties of ANN. These data are clearly aligned with lack of drug-related cardiotoxic events in ANN-treated patients in ongoing clinical trials. Interestingly, ANN appeared to be a significantly more potent inhibitor of Top2β than DOX, suggesting that Top2β may not be a universal mediator of cardiotoxicity of anthracyclines. Additional studies are needed to reevaluate the role of Top2β in anthracycline-induced cardiotoxicity. Citation Format: Rafal J. Zielinski, Krzysztof Grela, Roberto Cardenas-Zuniga, Stanislaw Skora, Izabela Fokt, Mihai Gagea, Wolfram Dempke, Waldemar Priebe. Non-cardiotoxic properties of annamycin, a clinically evaluated anthracycline and potent topoisomerase 2β poison [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB180.

Abstract ND11: Chemoproteomic-enabled discovery of VVD-214, a synthetic lethal allosteric inhibitor of WRN helicase

Abstract WRN helicase is a promising target for treating cancers with microsatellite instability (MSI) due to its essential role in resolving deleterious non-canonical DNA structures that accumulate in cells with faulty mismatch repair mechanisms. Currently, there are no approved drugs directly targeting human DNA or RNA helicases, in part due to the challenging nature of developing potent and selective compounds to this class of proteins. Here we describe the chemical proteomic-enabled discovery of a clinical-stage, covalent allosteric inhibitor of WRN. The clinical lead, VVD-214, covalently engages cysteine 727 of WRN in a nucleotide cooperative manner and inhibits ATP hydrolysis and helicase activity, resulting in widespread double-stranded DNA breaks, nuclear swelling, and cell death in MSI-high, but not microsatellite stable cells. VVD-214 provided robust tumor regression in multiple MSI-high colorectal cancer cell lines and patient derived xenograft models, including models derived from patients progressing on immune checkpoint therapies. VVD-214 was exceptionally well tolerated, and constitutes a promising oral drug candidate for patients with MSI-high cancers. Citation Format: Shota Kikuchi, Piergiorgio Pettazzoni, Kristen A. Baltgalvis, Kelsey N. Lamb, Kent T. Symons, Chu-Chiao Wu, Melissa A. Hoffman, Aaron N. Snead, Xiaodan Song, Thomas Glaza, Jason C. Green, Donald C. Rogness, Betty Lam, Maria E. Rodriguez-Aguirre, David R. Woody, Christie L. Eissler, Socorro Rodiles, Seth M. Negron, Steffen M. Bernard, Eileen Tran, Jonathan Pollock, Ali Tabatabaei, Victor Contreras, Heather N. Williams, Martha K. Pastuszka, John J. Sigler, Markus G. Rudolph, Moritz Classen, Doris Brugger, Christopher Claiborne, Jean-Marc Plancher, Isabel Cuartas, Joan Seoane, Laurence E. Burgess, Robert T. Abraham, David S. Weinstein, Gabriel M. Simon, Matthew P. Patricelli, Todd M. Kinsella. Chemoproteomic-enabled discovery of VVD-214, a synthetic lethal allosteric inhibitor of WRN helicase [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr ND11.

Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.

DNA motifs are crucial patterns in gene regulation. DNA-binding proteins (DBPs), including transcription factors, can bind to specific DNA motifs to regulate gene expression and other cellular activities. Past studies suggest that DNA shape features could be subtly involved in DNA-DBP interactions. Therefore, the shape motif annotations based on intrinsic DNA topology can deepen theunderstanding of DNA-DBP binding. Nevertheless, high-throughput tools for DNA shape motif discovery that incorporate multiple features altogether remain insufficient. To address it, we propose a series of methods to discover non-redundant DNA shape motifs with the generalization to multiple motifs inmultiple shape features. Specifically, an existingGibbs sampling methodis generalized to multiple DNA motif discovery with multiple shape features. Meanwhile, an expectation-maximization (EM) method and a hybrid method coupling EM with Gibbs sampling are proposed anddeveloped with promisingperformance, convergence capability, and efficiency. The discovered DNA shape motif instances reveal insights intolow-signal ChIP-seq peak summits, complementing the existing sequence motif discovery works. Additionally, our modelling captures the potential interplays across multiple DNA shape features. We provide a valuable platform of tools for DNA shape motif discovery. An R package is built for open accessibility and long-lasting impact: https://zenodo.org/doi/10.5281/zenodo.10558980.