Molecular weight and polydispersity of calf-thymus DNA: static light-scattering and size-exclusion chromatography with dual detection

Determination of the optimal pH for doxorubicin encapsulation in polymeric micelles

HYPOTHESIS

The anticancer drug doxorubicin hydrochloride (DX) shows a high solubility in aqueous media thanks to the positive charge in the ammonium group. This feature, however, affects the drug encapsulation in the hydrophobic domains of polymeric micelles (PMs) used for the targeted delivery of the drug. At basic pH, DX deprotonates but also acquires a negative charge in the phenolic groups of the anthracycline structure. Both the efficiency and the rate of encapsulation will be increased by choosing an appropriate pH such that the drug molecule is in neutral form.

EXPERIMENTS

An optimal pH for the encapsulation of the DX in PMs based on commercial poloxamers and on the diblock copolymer methoxy-poly(ethylene glycol)17-b-poly(ε-caprolactone)9 was determined by fluorescence spectroscopy, following the time evolution of both the intensity ratio of the first and the second emission bands of DX and its fluorescence lifetime, both sensitive to the environment polarity. Intracellular delivery of PMs encapsulated drug was followed by Confocal Scanning Laser Microscopy (CSLM). Cell viability was assessed with the sulforhodamine B (SRB) assay.

FINDINGS

By adjusting pH to 8.1 a high yield of incorporation of DX in the PMs was achieved coupled to an appreciable increase (one order of magnitude) in the drug encapsulation rate. In-vitro tests in selected cancer cell lines showed the slow release of the drug and a delay in the cytotoxic response in comparison to free DX as detected by CSLM and SRB assay. The proposed methodology paves the way for a greener, faster and more efficient encapsulation of DX in PMs.

Directional migration propensity of calf thymus DNA in a gradient of metal ions

The migration propensity and spatially modulated surface deposition of calf thymus DNA have been reported in response to gradients of different monovalent and divalent ions.

Thermoplastic nanofluidic devices for identifying abasic sites in single DNA molecules

DNA damage can take many forms such as double-strand breaks and/or the formation of abasic (apurinic/apyrimidinic; AP) sites. The presence of AP sites can be used to determine therapeutic efficacy of many drugs, such as doxorubicin. While there are different assays to search for DNA damage, they are fraught with limitations, such as the need for large amounts of DNA secured from millions of cells. This is challenging due to the growing importance of using liquid biopsies as a source of biomarkers for many in vitro diagnostic assays. To accommodate the mass limits imposed by the use of liquid biopsies, we report a single-molecule DNA damage assay that uses plastic nanofluidic chips to stretch DNA to near its full contour length when the channel dimensions (width and depth) are near the persistence length (∼50 nm) of double-stranded (ds) DNA. The nanofluidic chip consisted of input funnels for high loading efficiency of single DNA molecules, entropic traps to store the DNA and simultaneously load a series of nanochannels for high throughput processing, and an array of stretching nanochannels to read the AP sites. Single dsDNA molecules, which were labeled with an intercalating dye and a biotinylated aldehyde reactive probe (bARP), could be parked in the stretching nanochannels, where the AP sites were read directly using a dual-color fluorescence microscope equipped with an EMCCD camera. One color of the microscope was used to read the DNA length and the second color detected the AP sites. The nanofluidic chip was made from thermoplastics via nanoimprint lithography, which obviated the need for direct writing the devices in glass or quartz using focused ion beam milling. We show that we can read the frequency of AP sites in single dsDNA molecules with the frequency of AP sites determined by associating fluorescently-labeled streptavidin with bARP through a biotin/streptavidin complex.

Poloxamer/sodium cholate co-formulation for micellar encapsulation of doxorubicin with high efficiency for intracellular delivery: An in-vitro bioavailability study

HYPOTHESIS

Doxorubicin hydrochloride (DX) is widely used as a chemotherapeutic agent, though its severe side-effects limit its clinical use. A way to overcome these limitations is to increase DX latency through encapsulation in suitable carriers. However, DX has a high solubility in water, hindering encapsulation. The formulation of DX with sodium cholate (NaC) will reduce aqueous solubility through charge neutralization and hydrophobic interactions thus facilitating DX encapsulation into poloxamer (F127) micelles, increasing drug latency.

EXPERIMENTS

DX/NaC/PEO-PPO-PEO triblock copolymer (F127) formulations with high DX content (DX-PMs) have been prepared and characterized by scattering techniques, transmission electron microscopy and fluorescence spectroscopy. Cell proliferation has been evaluated after DX-PMs uptake in three cell lines (A549, Hela, 4T1). Cell uptake of DX has been studied by means of confocal laser scanning microscopy and flow cytometry.

FINDINGS

DX-PMs formulations result in small and stable pluronic micelles, with the drug located in the apolar core of the polymeric micelles. Cell proliferation assays show a delayed cell toxicity for the encapsulated DX compared with the free drug. Data show a good correlation between cytotoxic response and slow DX delivery to nuclei. DX-PMs offer the means to restrict DX delivery to the cell interior in a highly stable and biocompatible formulation, suitable for cancer therapy.

Detection by Flow Cytometry of Anti-DNA Autoantibodies and Circulating DNA Immune Complexes in Lupus Erythematosus

A new method for the detection by flow cytometry of anti-double-stranded DNA antibodies and of circulating immune complexes (IC) containing endogenous DNA (IC-eDNA) is described. From each serum sample, two samples were taken, one was used to detect IC-eDNA. The other to detect anti-DNA antibodies was incubated with calf thymus DNA. ICs were isolated by polyethylene glycol precipitation or by cryoprecipitation, after which immunoglobulins were labeled with FITC-conjugated anti-human globulin. Serum samples from 63 systemic lupus erythematosus (SLE) patients, 32 incomplete lupus, and 87 control patients were tested. Detection of anti-dsDNA antibodies by flow cytometry had a diagnostic sensitivity and specificity almost comparable to routine tests, the fluorescent enzyme immunoassay EliA™-dsDNA test, and the ultrasensitive Crithidia luciliae indirect immunofluorescence test. In 21 (33%) out of 63 SLE serum samples, IC-eDNA was detected. In these samples, free anti-dsDNA antibodies were hardly detectable or undetectable by flow cytometry or by routine tests. When anti-DNA antibodies are neutralized by endogenous DNA and can no longer be detected by routine tests, the serologic diagnosis and the follow-up of relapses in patients with SLE is compromised. To overcome this obstacle, we propose an accessible solution: the detection of circulating IC-eDNA by flow cytometry.

A Supramolecular Interaction of a Ruthenium Complex With Calf-Thymus DNA: A Ligand Binding Approach by NMR Spectroscopy

Lawsone itself exhibits interesting biological activities, and its complexation with a metal center can improve the potency. In this context a cytotoxic Ru-complex, [Ru(law)(dppb)(bipy)] (law = lawsone, dppb = 1,4-bis(diphenylphosphino)butane and bipy = 2,2'-bipyridine), named as CBLAU, was prepared as reported. In this work, NMR binding-target studies were performed to bring to light the most accessible interaction sites of this Ru-complex toward Calf-Thymus DNA (CT-DNA, used as a model), in a similar approach used for other metallic complexes with anti-cancer activity, such as cisplatin and carboplatin. Advanced and robust NMR binding-target studies, among them Saturation Transfer Difference (STD)-NMR and longitudinal relaxometry (T1), were explored. The 1H and 31P -NMR data indicate that the structure of Ru-complex remains preserved in the presence of CT-DNA, and some linewidth broadening is also observed for all the signals, pointing out some interaction. Looking at the binding efficiency, the T1 values are highly influenced by the formation of the CBLAU-DNA adduct, decreasing from 11.4 s (without DNA) to 1.4 s (with DNA), where the difference is bigger for the lawsone protons. Besides, the STD-NMR titration experiments revealed a stronger interaction (KD = 5.9 mM) for CBLAU-DNA in comparison to non-complexed lawsone-DNA (KD = 34.0 mM). The epitope map, obtained by STD-NMR, shows that aromatic protons from the complexed lawsone exhibits higher saturation transfer, in comparison to other Ru-ligands (DPPB and bipy), suggesting the supramolecular contact with CT-DNA takes place by the lawsone face of the Ru-complex, possibly by a spatial π-π stacking involving π-bonds on nucleic acids segments of the DNA chain and the naphthoquinone group.

Direct determination of molecular weight distribution of calf-thymus DNAs and study of their fragmentation under ultrasonic and low-energy infrared irradiations. A charge detection mass spectrometry investigation

RATIONALE

Calf-thymus (CT-DNA) is widely used as a binding agent. The commercial samples are known to be "highly polymerized DNA" samples. CT-DNA is known to be fragile in particular upon ultrasonic wave irradiation. Degradation products could have dramatic consequences on its bio-sensing activity, and an accurate determination of the molecular weight distribution and stability of commercial samples is highly demanded.

METHODS

We investigated the sensitivity of charge detection mass spectrometry (CDMS), a single-molecule MS method, both with single-pass and ion trap CDMS ("Benner" trap) modes to the determination of the composition and stability (under multiphoton IR irradiation) of calf-thymus DNAs. We also investigated the changes in molecular weight distributions in the course of sonication by irradiating ultrasonic waves to CT-DNA.

RESULTS

We report, for the first time, the direct molecular weight (MW) distribution of DNA sodium salt from calf-thymus revealing two populations at high (~10 MDa) and low (~3 MDa) molecular weights. We evidence a transition between the high-MW to the low-MW distribution, confirming that the low-MW distribution results from degradation of CT-DNA. Finally, we report also IRMPD experiments carried out on trapped single-stranded linear DNAs from calf-thymus allowing extraction of their activation energy for unimolecular dissociation.

CONCLUSIONS

We show that single-pass CDMS is a direct, efficient and accurate MS-based approach to determine the composition of calf-thymus DNAs. Furthermore, ion trap CDMS allows us to evaluate the stability (both under multiphoton IR irradiation and in the course of sonication by irradiating ultrasonic wave) of calf-thymus DNAs.

Photophysical and thermodynamic evaluation on the in vitro and in silico binding profile of Camptothecin with DNA

Camptothecin (CMT) is an anti-tumour alkaloid drug exhibiting selective topoisomerase-I inhibitory activity by eventually hindering dynamic functions of DNA duplex via initiating apoptosis. Unravelling the binding mechanism of CMT with bio macromolecular systems can offer fundamental information regarding the mechanism of actions which can lead to the design of rational proactive drugs. This study endeavoured the binding interactions of CMT with calf thymus DNA (ct-DNA) along with the structural alterations attained by the DNA duplex owing to CMT interactions through multi-spectroscopic, calorimetric and molecular docking studies. The UV-visible absorbance and fluorescence quenching studies revealed the binding strength of CMT with ct-DNA, evident from the binding constants K₁ = 3.79 × 10³ M^-1 and Kq = 2 × 10³ M^-1. The time-resolved lifetime measurements inferred that the quenching was static due to the non-fluorescent ground state complex formation. The dye displacement study, temperature melting and viscosity measurements established a typical non-intercalative binding mode of CMT with ct-DNA. The binding isotherm deduced from ITC was found to be spontaneous and exothermic exerting a promising ΔG value of -6.2 kcal mol^-1. The thermal kinetic parameters implied that the forces primarily involved in the CMT-ct-DNA complexation are hydrogen bonding and van der Waals interactions. Moreover, the structural alterations of DNA duplex reflected in the CD and FTIR spectra could undeniably confirm the groove binding manner of CMT. The in silico extra precision docking study explored more accurate molecular illustrations of sequence specific minor groove binding mechanism evolved between CMT and DNA corroborating well with the experimental results. These innovative findings may shorten the path towards the development of novel and more effective CMT drug derivatives.

Fluorescence correlation spectroscopy for multiple-site equilibrium binding: a case of doxorubicin–DNA interaction

Quantification of multiple equilibrium binding on the example of doxorubicin–DNA interaction using fluorescence correlation spectroscopy.

Autoantibody Profiling in Lupus Patients using Synthetic Nucleic Acids

Autoantibodies to nuclear components of cells (antinuclear antibodies, ANA), including DNA (a-DNA), are widely used in the diagnosis and subtyping of certain autoimmune diseases, including systemic lupus erythematosus (SLE). Despite clinical use over decades, precise, reproducible measurement of a-DNA titers remains difficult, likely due to the substantial sequence and length heterogeneity of DNA purified from natural sources. We designed and tested a panel of synthetic nucleic acid molecules composed of native deoxyribonucleotide units to measure a-DNA. ELISA assays using these antigens show specificity and reproducibility. Applying the ELISA tests to serological studies of pediatric and adult SLE, we identified novel clinical correlations. We also observed preferential recognition of a specific synthetic antigen by antibodies in SLE sera. We determined the probable basis for this finding using computational analyses, providing valuable structural information for future development of DNA antigens. Synthetic nucleic acid molecules offer the opportunity to standardize assays and to dissect antibody-antigen interactions.

Controlled potential electro-oxidation of genomic DNA

Exposure of mammalian cells to oxidative stress can result in DNA damage that adversely affects many cell processes. Lack of dependable DNA damage reference materials and standardized measurement methods, despite many case-control studies hampers the wider recognition of the link between oxidatively degraded DNA and disease risk. We used bulk electrolysis in an electrochemical system and gas chromatographic mass spectrometric analysis (GC/MS/MS) to control and measure, respectively, the effect of electrochemically produced reactive oxygen species on calf thymus DNA (ct-DNA). DNA was electro-oxidized for 1 h at four fixed oxidizing potentials (E = 0.5 V, 1.0 V, 1.5 V and 2 V (vs Ag/AgCl)) using a high surface area boron-doped diamond (BDD) working electrode (WE) and the resulting DNA damage in the form of oxidatively-modified DNA lesions was measured using GC/MS/MS. We have shown that there are two distinct base lesion formation modes in the explored electrode potential range, corresponding to 0.5 V < E < 1.5 V and E > 1.5 V. Amounts of all four purine lesions were close to a negative control levels up to E = 1.5 V with evidence suggesting higher levels at the lowest potential of this range (E = 0.5 V). A rapid increase in all base lesion yields was measured when ct-DNA was exposed at E = 2 V, the potential at which hydroxyl radicals were efficiently produced by the BDD electrode. The present results demonstrate that controlled potential preparative electrooxidation of double-stranded DNA can be used to purposely increase the levels of oxidatively modified DNA lesions in discrete samples. It is envisioned that these DNA samples may potentially serve as analytical control or quality assurance reference materials for the determination of oxidatively induced DNA damage.

Properties of polyplexes formed through interaction between hydrophobically-modified poly(ethylene imine)s and calf thymus DNA in aqueous solution

Polycationic polymers and DNA form soluble complexes in aqueous solution, which allows the transfer of genetic material into cells. Therefore, these chemically-modified polymers are of interest for use in studies aimed at better transfection efficiency and gene expression along with reduced cytotoxicity. In this study, branched poly(ethylene imine) (PEI) was modified by alkylation with n-alkyl groups (n = 4, 6, 8 and 12 carbons). The polyplexes formed through interaction of the modified PEIs and calf thymus DNA (ctDNA) were investigated using UV-Vis spectrophotometry, ethidium bromide fluorescence emission, circular dichroism spectroscopy, dynamic light scattering, and small-angle X-ray scattering techniques along with the determination of the zeta potential and viscosity. According to the results obtained, the formation of ctDNA-PEI polyplexes occurs in three steps. Firstly, when a small amount of polyelectrolyte is present the ctDNA chains are partially compacted. Subsequently, with the addition of more polyelectrolyte, the complexes have a null charge density and micrometric size. Lastly, with a higher concentration of PEI, the ctDNA is fully compacted by the PEI chains, leading to positively charged complexes with R_h values in the range of 52.0-86.0 nm. The viscosity and SAXS analysis suggested that the unmodified PEI exhibits the strongest interaction and promotes the best ctDNA condensation.

Texture formation in DNA films with alkali metal chlorides

The formation of textures in DNA films with LiCl, NaCl, KCl, RbCl, and CsCl salts has been studied. The films are prepared by evaporation of water solution with highly polymerized calf thymus DNA and excess salt of specific type. For DNA solution with 10 mM concentration of NaCl, KCl, and RbCl the films with dendritic textures have been obtained, whereas in case of CsCl the textures in the films appear only at 30 mM concentration of excess salt in the initial solution. In the solution with LiCl, the textures in DNA films have not been observed within the whole range of concentration of excess salt under consideration. The analysis of parameters of DNA films with different salts has showed that evaporation of solution leads to crystallization of salt ions on DNA macromolecule and formation of DNA-salt complexes. Electrostatic energy of the system of crystalline ordered ions and charges of DNA chains has been estimated to study the stability of DNA-salt complexes. The results obtained for different salts have been showed that the presence of DNA macromolecule enhances crystallization as compared with solution without DNA. The property of excess salt to form the crystalline structures has been found to decrease in the following order: KCl > NaCl > RbCl > CsCl > LiCl. The results of estimation are in good agreement with the experimentally observed dependence of texture formation on excess salt type.

Conformation and Rheological Properties of Calf-Thymus DNA in Solution

Studies of DNA molecule behavior in aqueous solutions performed through different approaches allow assessment of the solute-solvent interactions and examination of the strong influence of conformation on its physicochemical properties, in the presence of different ionic species and ionic concentrations. Firstly, the conformational behavior of calf-thymus DNA molecules in TE buffer solution is presented as a function of temperature. Secondly, their rheological behavior is discussed, as well as the evidence of the critical concentrations, i.e., the overlap and the entanglement concentrations (C* and C_e, respectively) from steady state flow and oscillatory dynamic shear experiments. The determination of the viscosity in the Newtonian plateau obtained from flow curves η (γ˙) allows estimation of the intrinsic viscosity and the specific viscosities at zero shear when C[η] < 40. At end, a generalized master curve is obtained from the variation of the specific viscosity as a function of the overlap parameter C[η]. The variation of the exponent s obtained from the power law η~γ˙^−s for both flow and dynamic results is discussed in terms of Graessley’s analysis. In the semi-dilute regime with entanglements, a dynamic master curve is obtained as a function of DNA concentration (C_DNA > 2.0 mg/mL) and temperature (10 °C < T < 40 °C).

A spectroscopic study to decipher the mode of interaction of some common acridine derivatives with CT DNA within nanosecond and femtosecond time domains

Our spectroscopic investigation with acridine derivatives presents the electronic control of their substituents on intercalation, solvation and PET with DNA.

Stopped-flow kinetic studies of poly(amidoamine) dendrimer-calf thymus DNA to form dendriplexes

Poly(amidoamine) (PAMAM) dendrimers are known to be highly efficient nonviral carriers in gene delivery. Dendrimer-mediated transfection is known to be a function of the dendrimer to DNA charge ratio as well as the size of the dendrimer. In the present study, the binding kinetics of four PAMAM dendrimers (G1, G2, G3, and G4) with calf thymus DNA (CT-DNA) has been studied using stopped-flow fluorescence spectroscopy. The effect of dendrimer-to-DNA charge ratio and dendrimer generation on the binding kinetics was investigated. In most cases, the results of dendrimer-CT-DNA binding can be explained by a two-step reaction mechanism: a rapid electrostatic binding between the dendrimer and DNA, followed by a conformational change of the dendrimer-DNA complex that ultimately leads to DNA condensation. It was observed that the charge ratio on the dendrimer and the DNA phosphate groups, as well as the dendrimer generation (size), has a marked effect on the kinetics of binding between the DNA and the dendrimers. The rate constant (k'1) of the first step was much higher compared to that of the second step (k'2), and both were found to increase with an increase in dendrimer concentration. Among the four generations of dendrimers, G4 exhibited significantly faster binding kinetics compared to the three smaller generation dendrimers.

Fluorochrome-functionalized nanoparticles for imaging DNA in biological systems

Attaching DNA binding fluorochromes to nanoparticles (NPs) provides a way of obtaining NPs that bind to DNA through fluorochrome mediated interactions. To obtain a nanoparticle (NP) that bound to the DNA in biological systems, we attached the DNA binding fluorochrome, TO-PRO 1 (TO), to the surface of the Feraheme (FH) NP, to obtain a fluorochrome-functionalized NP denoted TO-FH. When reacted with DNA in vitro, TO-FH formed microaggregates that were characterized by fluorescence, light scattering, and T2 changes. The formation of DNA/TO-FH microaggregates was also characterized by AFM, with microaggregates exhibiting a median size of 200 nm, and consisting of DNA and multiple TO-FH NPs whose individual diameters were only 25-35 nm. TO-FH failed to bind normal cells in culture, but treatment with chemotherapeutic agents or detergents yielded necrotic cells that bound TO-FH and vital fluorochromes similarly. The uptake of TO-FH by HT-29 xenografts (treated with 5-FU and oxaliplatin) was evident by surface fluorescence and MRI. Attaching multiple DNA binding fluorochromes to magnetic nanoparticles provides a way of generating DNA binding NPs that can be used to detect DNA detection by microaggregate formation in vitro, for imaging the DNA of necrotic cells in culture, and for imaging the DNA of a tumor treated with a chemotherapeutic agent. Fluorochrome functionalized NPs are a multimodal (magnetic and fluorescent), highly multivalent (n ≈ 10 fluorochromes/NP) nanomaterials useful for imaging the DNA of biological systems.