Hycanthone is a thioxanthenone DNA intercalator and inhibits RNA synthesis as well as the DNA topoisomerases I and II. Hycanthone inhibits nucleic acid biosynthesis and inhibits apurinic endonuclease-1 (APE1) by direct protein binding with a K D of 10 nM. Hycanthone is a bioactive metabolite of Lucanthone and has anti-schistosomal agent
In Vitro
Hycanthone has an IC 50 of 80 nM for inhibition of APE1 incision of depurinated plasmid DNA. Hycanthone (0.05-100 µM; for 2 h) promotes APE1 cleavage in presence of Cycloheximide (CHX) and this cleavage is inhibited by 1% DMSO. Hycanthone at 20 mg/mL or more is progressively more detrimental to cell viability. Results reveal that increased concentrations of Hycanthone, ranging from 0.1 to 10 μg/mL, progressively reduces viral interferon yields as much as 73% compare to that of controls. MCE has not independently confirmed the accuracy of these methods. They are for reference only.
In Vivo
Results show that the incorporation of tritiated thymidine into TCA-precipitable material of adult sensitive worms undergo a progressive decrease after treatment with Hycanthone. Immature worms are totally unaffected by Hycanthone at all times tested. Male worms treated with Hycanthone show signs of a possible partial recovery from the initial low levels of incorporation. The incorporation of tritiated leucine by drug-sensitive worms treated with Hycanthone is inhibited by 40 to 50% in the first four days after treatment. Results show that, 7 days after Hycanthone treatment, both ribosomal RNA species are reduced by at least 80% with respect to untreated worms, with some indication of a possible accumulation of heavier precursor molecules. MCE has not independently confirmed the accuracy of these methods. They are for reference only.
Cell Assay
Appropriate quantities of Hycanthone (1 to 100 μg) in 10 mL maintenance medium are added to plastic flasks (75 cm 2 ) containing approximately 3×10 7 LLC-MK2 cells in monolayer, which are then incubated at 35°C for 24 h. Maintenance medium is decanted, and 2 mL influenza virus is added onto cell monolayers and incubated at 35°C for 2 h. The multiplicity of infection is approximately 1.0. Inoculum is removed and 10 mL maintenance medium is added to each flask, which is then incubated at 35°C for 24 h. Supernatant fluid is decanted, centrifuged at 100,000 g for 1 h, dialyzed against HCI-KCI buffer (pH 2.0) at 4°C for 24 h, and then dialyzed against two changes of phosphate-buffered saline (pH 7.1) at 4°C for 24 h. Fluids are passed through filters to obtain sterile preparations. Samples are stored at -80°C until assayed for interferon activity. MCE has not independently confirmed the accuracy of these methods. They are for reference only.
IC50& Target:Topoisomerase I Topoisomerase II
Specifications
Specifications & Purity
10mM in DMSO
Biochemical and Physiological Mechanisms
Hycanthone is a thioxanthenone DNA intercalator and inhibits RNA synthesis as well as the DNA topoisomerases I and II. Hycanthone inhibits nucleic acid biosynthesis and inhibits apurinic endonuclease-1 (APE1) by direct protein binding with a K D of 10 nM.
Storage
Store at -80°C
Shipped In
Dry ice packs + Cold packs
This product requires cold chain shipping. Ground and other economy services are not available.
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Application Protocols
No manufacturer-validated protocols are provided for this item. Below are general, literature-style procedures to guide use as a research tool compound. Adjust to your system and validate experimentally.
DNA intercalation fluorescence competition assay (general)
Prepare calf thymus DNA (ctDNA) at 50 µM base pairs in buffer (10 mM Tris, 50 mM NaCl, pH 7.4).
Pre-equilibrate DNA with ethidium bromide (2 µM). Titrate hycanthone from 0 to 10 µM final, keeping DMSO ≤0.5%.
Record fluorescence (Ex 520 nm/Em 600 nm). Plot quenching vs concentration to estimate binding constant via Stern–Volmer or Scatchard models.
Thermal denaturation assay
Mix 2–10 µM DNA duplex with varying hycanthone equivalents. Monitor absorbance at 260 nm while ramping 20–95°C at 0.5–1.0°C/min. Determine ΔTm relative to control.
LC–MS reference standard preparation
Prepare a 1.0 mg/mL DMSO stock. Dilute to 0.1–10 µg/mL in 50:50 water:ACN + 0.1% formic acid. Store working standards at 4°C (48 h) protected from light; freeze long-term aliquots at −20 to −80°C.
Protein binding by fluorescence quenching
Incubate 1–5 µM serum albumin with 0–10 µM hycanthone in phosphate buffer, pH 7.4. Record intrinsic tryptophan fluorescence decrease to estimate binding constants.
Notes
Include solvent-only and DNA/protein-only controls. Validate linearity and absence of inner-filter effects at higher concentrations.
Biological Roles
Scope
Provided for scientific context only. No medical or clinical claims are made. Hycanthone is a historically studied, cationic, polyaromatic intercalator used as a tool compound in molecular biology and biochemistry (literature/general).
Molecular interactions (literature)
Nucleic acid intercalation: planar chromophore inserts between base pairs, stabilizing the duplex and altering torsional stress; often increases DNA melting temperature (Tm) and can inhibit transcription/replication in cell-free systems.
Protein binding: can associate with serum albumin and nucleic-acid–processing proteins via hydrophobic and electrostatic interactions, influencing distribution and apparent potency in vitro.
Enzymatic effects: reported inhibition/perturbation of topoisomerase activity and nucleases in biochemical assays, consistent with intercalative binding.
Physicochemical determinants (general)
Protonation state modulates affinity: the cationic form enhances electrostatic attraction to the DNA phosphate backbone; ionic strength screens binding.
Photophysical properties may enable label-free readouts (hypochromism, fluorescence changes) upon binding.
Research uses
As a comparator/control molecule in studies of DNA intercalation, structure–activity relationships of thioxanthenone-like scaffolds, and development of analytical methods for cationic intercalators.
Safety note
Due to bioactivity, handle with care; minimize exposure and environmental release. Use appropriate containment during cell-based assays and dispose of waste per institutional biosafety/chemical protocols.
Buffer Applications
Not typically used as a buffering agent.
Practical notes for assay buffers (general guidance)
For nucleic-acid binding assays, common buffers include Tris-HCl, HEPES, or phosphate, with ionic strength carefully controlled (e.g., 10–150 mM NaCl) to modulate intercalation affinity.
When preparing aqueous working solutions, protonation (pH ≤ 6) can increase solubility; alternatively, pre-dissolve in DMSO and dilute into neutral buffer keeping final DMSO low (≤0.1–1% v/v) as the biology allows.
Include light protection (amber vials/wrap) to reduce photochemical artifacts during prolonged incubations.
Green Alternatives
Context
As a solid bioactive research compound, hycanthone itself is not replaced by a “green” alternative. However, greener practices can be applied to its handling, dissolution, and analysis.
Solvent and process considerations (general guidance)
Prefer DMSO or ethanol for stock solutions over higher-toxicity dipolar aprotics (e.g., DMF, NMP) when assay compatibility allows.
For chromatography, water/ethanol or water/acetonitrile systems are generally greener than water/acetonitrile with halogenated modifiers; avoid chlorinated eluents.
Use minimal DMSO carryover into biological assays (≤0.1–0.5% v/v) to reduce solvent burden and cytotoxicity.
Implement microscale workflows (96/384-well plates) to reduce solvent volumes.
Small comparison (general)
DMF vs DMSO: DMSO offers lower toxicity and better biodegradability profile; DMF is classified as reprotoxic. Choose DMSO when feasible.
ACN vs MeOH in LC: ACN provides sharper peaks but has higher supply volatility; MeOH is less hazardous but may require higher backpressure. Evaluate instrument limits and sensitivity.
Waste minimization
Consolidate DMSO/alcohol wastes; avoid mixing with halogenated streams. Use light-protective containers to reduce photodegradation byproducts that complicate waste handling.
Packaging and storage
Aliquot to reduce freeze–thaw cycles and extend shelf life, minimizing disposal of degraded material.
Pharmaceutical Uses
This listing is for research use only and is not intended for human or veterinary use.
Hycanthone can serve as a reference standard in analytical development (e.g., LC–MS/UPLC methods) supporting studies of intercalative chemotypes.
Employed as a system-suitability or retention marker in methods designed to separate cationic, polyaromatic amines.
Useful for forced-degradation studies to establish stability-indicating methods, including sensitivity to light, oxidative stress, and pH.
Pharmacopeial status
No pharmacopeial monograph information is provided with this item. Not specified for this item; refer to CoA/Spec Sheet.
Manufacturing/handling considerations
For GMP-adjacent research (preclinical analytics), maintain full chain-of-custody on batch records, CoA, and storage logs; verify identity/purity by orthogonal methods (LC–MS, NMR). Any clinical or GMP use would require qualification beyond the scope of this research product.
Physical Properties
Item-specific specifications
Appearance: Not specified for this item; refer to CoA/Spec Sheet.
Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
Literature/general values and behavior (do not treat as product specifications)
Phase at ambient conditions: typically an organic solid for small-molecule intercalators of this class (literature, general behavior).
Ionization: contains at least one basic tertiary amine; expected to be protonated in acidic/neutral aqueous media, enhancing solubility (literature/general for this scaffold).
Solubility profile: frequently soluble in polar aprotic solvents (e.g., DMSO, DMF) and in aqueous buffers when acidified; limited solubility expected in nonpolar hydrocarbons (literature/general for cationic polyaromatics).
Partitioning: intercalators with a polyaromatic core often exhibit moderate-to-high logP in the free-base form, with markedly increased apparent solubility and reduced logD when protonated (literature/general trends).
UV–Vis characteristics: planar polyaromatics usually display strong π–π* absorption in the near-UV with potential visible tails depending on substitution (literature/general). Specific λmax values are not provided for this item.
Important note
Quantitative values (mp, bp, density, nD, pKa, exact solubilities) are not provided with this listing. Not specified for this item; refer to CoA/Spec Sheet and SDS for authoritative property data.
Quality & Grades
Item-specific status
Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
Stabilizers/additives: Not specified for this item; refer to CoA/Spec Sheet.
Guidance on interpreting grades (general)
Research grade small-molecule library compounds are typically provided at high chemical purity suitable for discovery biology, assay development, and analytical calibration. When designated as HPLC/LC–MS grade, low nonvolatile residue and defined UV cutoffs are emphasized for chromatographic use; when listed as BioX-grade (if applicable), bioburden/endotoxin targets may be controlled. This specific item does not state a grade—consult CoA.
Recommended verifications upon receipt (best practice)
Confirm identity by LC–MS or HRMS against a reference spectrum; optional 1H NMR in deuterated solvent (e.g., DMSO-d6) to verify structural integrity.
Check purity by HPLC/UPLC with diode-array detection; assess single dominant peak and absence of late-eluting impurities for bioassay use.
For long-term projects, archive a copy of the batch-specific CoA and SDS; record storage conditions and any re-aliquoting dates.
Implications for applications
Analytical standards and quantitative bioassays typically require ≥95% purity; mechanistic or screening assays may tolerate slightly lower levels depending on sensitivity. Without a stated grade, set assay controls accordingly and consider pre-use purification if necessary.
Reaction & Applications
This product is not primarily used as a synthetic reagent or solvent. Its value is as a bioactive research compound and analytical reference. Relevant application domains include:
Biochemical/biophysical research (literature/general)
DNA/RNA intercalation studies: planar polyaromatic scaffold supports intercalation; useful in fluorescence quenching/anisotropy, thermal denaturation (Tm) shifts, and competitive binding assays with ethidium bromide-like probes.
Enzymology: probe compound for DNA-processing enzymes (e.g., topoisomerases, helicases, or nucleases) where intercalation perturbs activity; enables mechanism-of-inhibition studies and kinetic assays.
Photophysics: evaluation of ground- and excited-state interactions with nucleic acids and serum proteins; binding constants via UV–Vis/fluorescence titrations.
Analytical science
Reference standard for LC–MS method development, retention-time locking, and response-factor calibration in studies involving intercalators or environmental fate of cationic polyaromatics.
Spiking/controls in extraction recovery and stability-indicating methods (forced degradation under light, pH, and oxidative stress) to map degradation pathways.
Practical tips (general)
Prepare fresh, light-protected stock solutions; verify concentration by UV–Vis using an experimentally determined ε where available.
Minimize plastic adsorption by using low-binding polypropylene plates/tubes; pre-rinse with dilute DMSO if necessary.
When assaying DNA interactions, control ionic strength and pH meticulously; intercalation affinity often increases at lower ionic strength.
Reaction Conditions
This product is not supplied for use as a reagent in named organic transformations; therefore, no item-specific conditions apply.
General laboratory conditions for its common research uses (literature/general)
Stock preparation: dissolve in anhydrous DMSO (typical 10–50 mM). Vortex and sonicate briefly if needed. Protect from light.
Bioassays (cell-free): dilute stock into assay buffer (e.g., Tris, HEPES, or phosphate) to sub-micromolar to low-micromolar final concentrations; keep final DMSO ≤0.1–1% v/v. Equilibrate 10–30 min for DNA-binding assays before readout.
Thermal denaturation of DNA: record Tm with and without compound across ionic strengths; intercalators commonly induce positive ΔTm proportional to binding affinity.
LC–MS analysis: use water/ACN or water/MeOH with 0.1% formic acid; monitor protonated molecular ion in positive ESI. Validate linear range and assess carryover given cationic, surface-active nature.
Stability checks: evaluate light sensitivity and pH stability by storing aliquots at ambient light vs dark, and pH 2–10, sampling by LC over time.
Yields, catalysts, and temperatures
Not applicable to this item as a reagent. For any synthetic modification of this scaffold, consult primary literature; conditions vary widely with substitution pattern.
Safety & Handling
Regulatory/SDS status for this item
Research Use Only. Not for human or veterinary use.
GHS classification, signal word, pictograms, and H-statements: Not specified for this item; refer to SDS.
General laboratory precautions (good practice)
PPE: lab coat, safety glasses, and appropriate chemical-resistant gloves (e.g., nitrile). Handle powders/solids in a fume hood to minimize inhalation exposure.
Avoid ingestion, inhalation of dust/aerosols, and skin or eye contact. Wash thoroughly after handling.
Given the polyaromatic, cationic nature and historical bioactivity of this scaffold, treat as potentially harmful if swallowed or absorbed; avoid environmental release (literature/general caution).
Incompatibilities and stability (general)
Avoid strong oxidizers and strong acids/bases unless intended for controlled transformations.
Protect from light when feasible; many polyaromatics can photosensitize or degrade upon prolonged exposure (literature/general).
Moisture sensitivity is typically low for the solid, but hygroscopicity can vary; keep container tightly closed with desiccant where practical.
First aid (overview; defer to SDS)
Skin/eye contact: rinse with water for at least 15 minutes; remove contaminated clothing.
Inhalation: move to fresh air; seek medical attention if symptoms persist.
Ingestion: rinse mouth; seek medical attention. Provide SDS to responders.
Waste disposal
Dispose of as organic hazardous waste. Follow institutional, local, and national regulations.
Solvent Selection
Applicability
Hycanthone is a small-molecule, polyaromatic base used primarily in biochemical assays and as an analytical reference. Solvent choice is driven by dissolution for stock solutions and compatibility with the intended assay.
Practical recommendations (general guidance; not product specs)
DMSO: preferred for preparing concentrated stocks (e.g., 10–50 mM) due to strong solvating power for cationic polyaromatics and excellent miscibility with aqueous assay buffers.
DMF or NMP: alternatives when DMSO is unsuitable; consider cytotoxicity/background in cell-based assays.
Aqueous buffers: solubility increases upon protonation (e.g., acetate, citrate, or phosphate buffers at pH ≤ 6). For neutral pH, pre-dissolve in DMSO, then dilute into buffer keeping final DMSO ≤0.1–1% v/v as assay permits.
Alcohols (MeOH, EtOH): moderate solubility; useful for analytical sample prep and LC eluents.
Nonpolar solvents (toluene, hexane): generally poor solvents for this class; avoid for stock preparation.
Compatibility notes
Filter stock solutions (0.2 µm PTFE) to remove particulates before microplate dispensing.
For LC–MS, DMSO or MeOH stocks diluted into water/ACN with 0.1% FA improve ionization and peak shape.
Small comparison (general)
DMSO vs DMF: DMSO is less volatile and generally lower background in bioassays; DMF can wet plastics better but may leach additives—validate for HTS workflows.
Storage & Reconstitution
Item-specific storage and shipping
Storage conditions: Store at -80°C (Product Data). Keep container tightly closed. Minimize freeze–thaw cycles by aliquoting upon first opening.
Shipped in: Dry ice packs + Cold packs (Product Data). Inspect upon receipt; if thawed, re-freeze promptly and assess integrity before use.
Stability guidance (general)
Protect from light to limit photodegradation typical of polyaromatic chromophores. Use amber vials or foil wrap.
For short-term working storage, −20°C to 4°C may be acceptable for prepared solutions; verify by LC–MS/HPLC over the intended timeframe. Solid material remains best preserved at −80°C as specified.
Reconstitution (general, not a specification)
Recommended solvent: anhydrous DMSO to prepare concentrated stocks (e.g., 10–50 mM). Vortex and, if needed, sonicate briefly to fully dissolve. Optionally warm gently (≤37°C) protected from light.
Aqueous working solutions: dilute DMSO stock into buffer; maintain final DMSO at the lowest feasible level (commonly ≤0.1–1% v/v). If direct aqueous dissolution is desired, adjust to mildly acidic pH to increase protonation and solubility.
Sterile filtration: for cell-based assays, pass through 0.2 µm PTFE or PES filter; confirm compatibility.
Documentation
Record lot number, aliquot dates, concentrations, and storage temperatures. For critical assays, determine post-thaw concentration by UV–Vis or LC–MS to confirm stability.
Unspecified parameters
Any item-specific values such as water content, residual solvents, or exact purity are not provided with this listing. Not specified for this item; refer to CoA/Spec Sheet.
Structure & Identity
Item-specific (from Product Data)
SKU: H656298
Product name: Hycanthone
CAS: 3105-97-3
PubChem CID: 3634
Storage note: Store at -80°C (see Storage & Reconstitution)
Structure descriptors
Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
SMILES: Not specified for this item; refer to CoA/Spec Sheet.
InChIKey: Not specified for this item; refer to CoA/Spec Sheet.
Structural features (literature/general)
Hycanthone is a cationic, polyaromatic small molecule known historically as a DNA-intercalating chemotype.
Framework: planar, fused-ring chromophore capable of π–π stacking with nucleobases; typically bears dialkylamino side chain(s) that can be protonated under physiological conditions, enhancing DNA affinity by electrostatic interactions.
Functional group motifs commonly discussed for this scaffold include an anthracenone/thioxanthenone-type chromophore and a basic tertiary amine side chain (literature).
2D description (literature/general)
A rigid, approximately rectangular polycyclic ring system providing a flat aromatic surface; a short linker terminating in a tertiary dialkylamino substituent confers cationic character and aqueous compatibility at lower pH. Such architecture supports intercalation between base pairs and minor-groove interactions.
Synthetic Utility
Hycanthone itself is an end-structure bioactive compound rather than a general-purpose synthetic building block. Nevertheless, chemists may leverage it in the following research contexts (literature/general):
Probe and SAR development
Serves as a reference scaffold for synthesizing analogs (e.g., modifications on the dialkylamino side chain, heteroatom substitutions on the polyaromatic core) to study DNA intercalation and enzyme inhibition structure–activity relationships.
Conjugation and immobilization
The basic amine side chain can form salts with acid chlorides/sulfonyl chlorides or be quaternized to tune aqueous solubility; linkers can be appended for bioconjugation to resins or fluorophores to create affinity probes.
Analytical derivatization
Formation of isotopically labeled standards (e.g., 13C/15N) facilitates quantitative mass spectrometry for environmental fate or in vitro metabolism studies.
Reference in retrosynthetic planning
The scaffold exemplifies late-stage functionalization challenges of polycyclic aromatics—useful for benchmarking C–H activation, photoredox substitutions, or Minisci-type functionalizations on pre-assembled ring systems.
Note
No specific reactivity, mp/bp, or protecting-group guidance is provided for this item. For synthetic campaigns, consult primary literature on thioxanthenone-like intercalators and adapt conditions to the exact substitution pattern.
Target Specificity
Not an antibody, enzyme, or affinity reagent. No antigen/epitope/clone/isotype information applies.
Research context (literature/general)
Hycanthone is often used as a tool compound to study nucleic-acid interactions and the functional consequences on DNA-processing enzymes. It does not possess “target specificity” in the immunochemical sense; binding is primarily physicochemical (intercalation and electrostatics) rather than highly sequence- or epitope-specific.
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