Lignin Nanoparticles Deliver Novel Thymine Biomimetic Photo-Adducts with Antimelanoma Activity

We report here the synthesis of novel thymine biomimetic photo-adducts bearing an alkane spacer between nucleobases and characterized by antimelanoma activity against two mutated cancer cell lines overexpressing human Topoisomerase 1 (TOP1), namely SKMEL28 and RPMI7951. Among them, Dewar Valence photo-adducts showed a selectivity index higher than the corresponding pyrimidine-(6-4)-pyrimidone and cyclobutane counterpart and were characterized by the highest affinity towards TOP1/DNA complex as evaluated by molecular docking analysis. The antimelanoma activity of novel photo-adducts was retained after loading into UV photo-protective lignin nanoparticles as stabilizing agent and efficient drug delivery system. Overall, these results support a combined antimelanoma and UV sunscreen strategy involving the use of photo-protective lignin nanoparticles for the controlled release of thymine dimers on the skin followed by their sacrificial transformation into photo-adducts and successive inhibition of melanoma and alert of cellular UV machinery repair pathways.

Variable inhibition of unwinding rates of DNA catalyzed by the SARS-Cov-2 (COV19) helicase nsp13 by structurally distinct single DNA lesions.

The SARS 2 (Covid 19) helicase nsp13 plays a critically important role in the replication of the Corona virus by unwinding double-stranded RNA (and DNA) with a 5 prime to 3 prime strand polarity. Here we explored the impact of single, structurally defined covalent DNA lesions on the helicase activity of nsp13 in aqueous solutions, The objectives were to derive mechanistic insights into the relationships between the structures of DNA lesions, the DNA distortions that they engender, and the inhibition of helicase activity. The lesions included two bulky stereoisomeric N2-guanine adducts derived from the reactions of benzo[a]pyrene diol epoxide with DNA. The trans-adduct assumes a minor groove conformation, while the cis-product adopts a base-displaced intercalated conformation. The non-bulky DNA lesions included the intra-strand cross-linked thymine dimers, the cis-syn-cyclobutane pyrimidine dimer, and the pyrimidine (6–4) pyrimidone photoproduct. All four lesions strongly inhibit the helicase activity of nsp13, The UV photolesions feature a 2 - 5-fold smaller inhibition of the nsp13 unwinding activity than the bulky DNA adducts, and the kinetics of these two pairs of DNA lesions are also different. The connections between the structural features of these four DNA lesions and their impact on nsp13 unwinding efficiencies are discussed.

The interplay of supercoiling and thymine dimers in DNA

Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here we introduce a model of thymine dimers in the oxDNA forcefield, and validate it by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.

Molecular Dynamic and Docking Simulation to Prevent Thymine Dimer as the Main Reason for Skin Cancer

Two major types can be repaired UV-induced DNA lesions. The first one is a light-dependent process that reverts UV damage applying particular wavelengths. The second is a light-independent process that excises the light-damaged region under novo synthesis of an intact DNA. The iGEMDOCK has been used for this study, and the acceptable thymine dimer can be defined for the binding site in whole DNA structures. The DNA is worked with two thymine in a segment of nucleic acids, and iGEMDOCK can help to prepare a suitable binding between them. The total energies of the model systems are a total of several partial energies as follows: E(system) = E(bond) + E(angle) + E(torsion) +E(over) +E(vdW) + E(Coulomb) + E(Specific). EvdW +E(Coulomb) represents the dispersive and electrostatic energies contribution between all atoms, respectively. Finally, E(Specific) is system-specific energy such as lone-pair, conjugation, and hydrogen binding. The DFT and HF calculations of the thymine dimer exhibited that the ring fusion at the C5 and C6 atoms of two thymine bases produced a four-member cyclo-butane puckered ring, as well as the feature, is seen with the MPn or Moller-Pleset level. In addition, the UV radiations between 360 nm to 200 nm have been investigated for the study of thymine dimers.

Thymine dissociation and dimer formation: A Raman and synchronous fluorescence spectroscopic study

In this study, absorption, fluorescence, synchronous fluorescence, and Raman spectra of nonirradiated and ultraviolet (UV)-irradiated thymine solutions were recorded in order to detect thymine dimer formation. The thymine dimer formation, as a function of irradiation dose, was determined by Raman spectroscopy. In addition, the formation of a mutagenic (6-4) photoproduct was identified by its synchronous fluorescence spectrum. Our spectroscopic data suggest that the rate of conversion of thymine to thymine dimer decreases after 20 min of UV irradiation, owing to the formation of an equilibrium between the thymine dimers and monomers. However, the formation of the (6-4) photoproduct continued to increase with UV irradiation. In addition, the Raman spectra of nonirradiated and irradiated calf thymus DNA were recorded, and the formation of thymine dimers was detected. The spectroscopic data presented make it possible to determine the mechanism of thymine dimer formation, which is known to be responsible for the inhibition of DNA replication that causes bacteria inactivation.

Immunological detection of thymine dimers in indigenous genomic DNA from pre-disinfection drinking water as an ultraviolet disinfection dosimeter

A linear UV dose response is demonstrated using an ELISA assay that measures thymine dimers formed in the genomic DNA extracted from the mixed species of microorganisms filtered from UV treated pre-disinfection drinking water.

UV rays induced DNA damage: Protection by polyphenols enriched extract of mint leaves

DNA of live cells is damaged when exposed to harmful Ultraviolet rays. If the cells are exposed to UV rays exposure time more duration of time, more thymine dimers are formed in the DNA and the greater the risk of an incorrect repair or a missed dimer. To analyze the effect of UV rays Calf thymus DNA and prevention by polyphenol enriched extract of Mint leaves and also its non toxic nature. The above study was done by using submarine gel electrophoresis where UV rays are used to damage the DNA and BHA (400µM) used as positive control. The polyphenol enriched extract was taken at 15μg concentration prevent UV rays induced DNA fragmentation in submarine agarose gel electrophoresis which provides same protection when compared to standard antioxidant BHA (400μM). The cytotoxicity studies showed that, the extract and BHA provides a protection of 54% whereas, the extract of Mint leaves extract showed 72%. In conclusion, the Mint leaves extract showed a promising DNA protectant activity against UV rays induced DNA damage.

Experimental and theoretical studies on thymine photodimerization mediated by oxidatively generated DNA lesions and epigenetic intermediates

Combined spectroscopic and computational studies reveal that, in spite of their structural similarities, 5-formyluracil and 5-formylcytosine photosensitize cyclobutane thymine dimers through two different types of mechanisms.