Following anticancer drug activity in cell lysates with DNA devices

A Redox-Reversible Switch of DNA Hydrogen Bonding and Structure

Modulating molecular structure and function at the nanoscale drives innovation across wide-ranging technologies. Electrical control of the bonding of individual DNA base pairs endows DNA with precise nanoscale structural reconfigurability, benefiting efforts in DNA origami and actuation. Here, alloxazine DNA base surrogates were synthesized and incorporated into DNA duplexes to function as a redox-active switch of hydrogen bonding. Circular dichroism (CD) revealed that 24-mer DNA duplexes containing one or two alloxazines exhibited CD spectra and melting transitions similar to DNA with only canonical bases, indicating that the constructs adopt a B-form conformation. However, duplexes were not formed when four or more alloxazines were incorporated into a 24-mer strand. Thiolated duplexes incorporating alloxazines were self-assembled onto multiplexed gold electrodes and probed electrochemically. Square-wave voltammetry (SWV) revealed a substantial reduction peak centered at -0.272 V vs Ag/AgCl reference. Alternating between alloxazine oxidizing and reducing conditions modulated the SWV peak in a manner consistent with the formation and loss of hydrogen bonding, which disrupts the base pair stacking and redox efficiency of the DNA construct. These alternating signals support the assertion that alloxazine can function as a redox-active switch of hydrogen bonding, useful in controlling DNA and bioinspired assemblies.

β-Glucuronidase-Activated Bioluminescence Probe for In Vivo Tumor Imaging

β-Glucuronidase (GLU) is a hallmark enzyme for many malignant tumors, but bioluminescence (BL) probes that enable GLU imaging in vivo have not been reported. Herein, we rationally designed the BL probe Glc-Luc to address this issue. In vitro results demonstrated the specific responsiveness of Glc-Luc toward GLU with a calculated catalytic efficiency (kcat/Km) of 0.0109 μM-1 min-1 and a limit of detection (LOD) of 1.39 U/mL. Moreover, Glc-Luc rendered 3.1-fold and 15.9-fold higher BL intensities over the control groups in cell lysates and tumor-bearing mice, respectively. We anticipate that Glc-Luc could be further applied for the sensitive diagnosis of GLU-related diseases.

Novel NQO1 substrates bearing two nitrogen redox centers: Design, synthesis, molecular dynamics simulations, and antitumor evaluation

By analyzing the crystal structure of NQO1, an additional binding region for the ligand was discovered. In this study, a series of derivatives with a novel skeleton bearing two nitrogen redox centers were designed by introducing amines or hydrazines to fit with the novel binding region of NQO1. Compound 24 with a (4-fluorophenyl)hydrazine substituent was identified as the most efficient substrate for NQO1 with the reduction rate and catalytic efficiency of 1972 ± 82 μmol NADPH/min/μmol NQO1 and 6.4 ± 0.4 × 10⁶ M^-1s^-1, respectively. Molecular dynamics (MD) simulation revealed that the distances between the nitrogen atom of the redox centers and the key Tyr128 and Tyr126 residues were 3.5 Å (N₁-Tyr128) and 3.4 Å (N₂-Tyr126), respectively. Compound 24 (IC₅₀/A549 = 0.69 ± 0.09 μM) showed potent antitumor activity against A549 cells both in vitro and in vivo through ROS generation via NQO1-mediated redox cycling, leading to a promising NQO1-targeting antitumor candidate.

Bleomycin-Fe(II) agent with potentiality for treating drug-resistant H1N1 influenza virus: A study using electrochemical RNA beacons

Rapid emergence of new strains of drug-resistant H1N1 influenza viruses calls for effective drugs for the controls prior to their outbreaks. In the present work, electrochemical H1N1 RNA beacons have been newly designed for exploring the potentiality of an anticancer agent of Bleomycin (BLM) with Fe (ΙΙ) ions (BLM-Fe(ΙΙ)) alternatively the treatment of drug-resistant H1N1 strains with H274Y gene mutation. Herein, biotinylated (-) ssRNA of H1N1 virus and its complementary (+) ssRNA were labeled with electrochemical signal probes of ferrocene and anthraquinone, respectively. The resultants were hybridized and conjugated with avidin-modified magnetic beads to create electrochemical RNA beacons. The electrochemical signal variation of the H1N1 RNA beacon treated with the RNA degradation agent of BLM-Fe(ΙΙ) were monitored. Results indicate that the BLM-Fe(ΙΙ) agent could effectively cleave both H1N1 dsRNAs and ssRNAs at selective cutting sites, as evidenced by the mass spectrometry analysis. This indicates that the BLM-Fe(II) agent could be utilized to block the viral-host infection process by curbing the host-cell viral RNA-mRNA transcription or inactivate the viruses through the cleavage of viral genomes. The efficiency of the BLM-Fe(ΙΙ) agent was verified with clinical seasonal H1N1 samples using real-time polymerase chain reaction. The therapeutic gene drug of BLM-Fe(ΙΙ) holds great potential for controlling new strains of H1N1 virus resistant to clinical antiviral drugs. More importantly, the so designed RNA beacons may provide a rapid, sensitive and cost-effective platform of drug screening by monitoring the drug-DNA/RNA interactions.

DNA Electrochemistry: Charge-Transport Pathways through DNA Films on Gold

Over the past 25 years, collective evidence has demonstrated that the DNA base-pair stack serves as a medium for charge transport chemistry in solution and on DNA-modified gold surfaces. Since this charge transport depends sensitively upon the integrity of the DNA base pair stack, perturbations in base stacking, as may occur with DNA base mismatches, lesions, and protein binding, interrupt DNA charge transport (DNA CT). This sensitivity has led to the development of powerful DNA electrochemical sensors. Given the utility of DNA electrochemistry for sensing and in response to recent literature, we describe critical protocols and characterizations necessary for performing DNA-mediated electrochemistry. We demonstrate DNA electrochemistry with a fully AT DNA sequence using a thiolated preformed DNA duplex and distinguish this DNA-mediated chemistry from that of electrochemistry of largely single-stranded DNA adsorbed to the surface. We also demonstrate the dependence of DNA CT on a fully stacked duplex. An increase in the percentage of mismatches within the DNA monolayer leads to a linear decrease in current flow for a DNA-bound intercalator, where the reaction is DNA-mediated; in contrast, for ruthenium hexammine, which binds electrostatically to DNA and the redox chemistry is not DNA-mediated, there is no effect on current flow with mismatches. We find that, with DNA as a well hybridized duplex, upon assembly, a DNA-mediated pathway facilitates the electron transfer between a well coupled redox probe and the gold surface. Overall, this report highlights critical points to be emphasized when utilizing DNA electrochemistry and offers explanations and controls for analyzing confounding results.

Detecting Attomolar DNA-Damaging Anticancer Drug Activity in Cell Lysates with Electrochemical DNA Devices

Here, we utilize electrochemical DNA devices to quantify and understand the cancer-specific DNA-damaging activity of an emerging drug in cellular lysates at femtomolar and attomolar concentrations. Isobutyl-deoxynyboquinone (IB-DNQ), a potent and tumor-selective NAD(P)H quinone oxidoreductase 1 (NQO1) bioactivatable drug, was prepared and biochemically verified in cancer cells highly expressing NQO1 (NQO1+) and knockdowns with low NQO1 expression (NQO1-) by Western blot, NQO1 activity analysis, survival assays, oxygen consumption rate, extracellular acidification rate, and peroxide production. Lysates from these cells and the IB-DNQ drug were then introduced to a chip system bearing an array of DNA-modified electrodes, and their DNA-damaging activity was quantified by changes in DNA-mediated electrochemistry arising from base-excision repair. Device-level controls of NQO1 activity and kinetic analysis were used to verify and further understand the IB-DNQ activity. A 380 aM IB-DNQ limit of detection and a 1.3 fM midpoint of damage were observed in NQO1+ lysates, both metrics 2 orders of magnitude lower than NQO1- lysates, indicating the high IB-DNQ potency and selectivity for NQO1+ cancers. The device-level damage midpoint concentration in NQO1+ lysates was over 8 orders of magnitude lower than cell survival benchmarks, likely due to poor IB-DNQ cellular uptake, demonstrating that these devices can identify promising drugs requiring improved cell permeability. Ultimately, these results indicate the noteworthy potency and selectivity of IB-DNQ and the high sensitivity and precision of electrochemical DNA devices to analyze agents/drugs involved in DNA-damaging chemotherapies.

A pharmacological review of dicoumarol: An old natural anticoagulant agent

Dicoumarol is an oral anticoagulant agent prescribed in clinical for decades. It is a natural hydroxycoumarin discovered from the spoilage of Melilotus officinalis (L.) Pall and is originally discovered as a rodenticide. Due to its structural similarity to that of vitamin K, it significantly inhibits vitamin K epoxide reductase and acts as a vitamin K antagonist. Dicoumarol is mainly used as an anticoagulant to prevent thrombogenesis and to cure vascular thrombosis. Other biological activities besides anticoagulants such as anticancer, antimicrobial, antiviral, etc., have also been documented. The side effects of dicoumarol raise safety concerns for clinical application. In this review, the physicochemical property, the pharmacological activities, the side effects, and the pharmacokinetics of dicoumarol were summarized, aiming to provide a whole picture of the "old" anticoagulant.