DNA integrity under alkaline conditions: An investigation of factors affecting the comet assay

Bioinspired hybrid DNA/dendrimer-based films with supramolecular chirality

Bioinspired hybrid DNA/dendrimer films were obtained by heating long double-stranded DNA (dsDNA) above its melting temperature and, while in the denatured state, mixing it with poly(amidoamine) (PAMAM) dendrimers, followed by controlled cooling. The formation of these new types of films was found to be dependent on several parameters, including the initial heating temperature, pH, buffer composition, dendrimer generation, amine/phosphate (N/P) ratio, and cooling speed. In addition to the PAMAM dendrimers (generations 3, 4, and 5), films could also be produced with branched poly(ethylenimine) with a molecular weight of 25 kDa. The results indicated that these films were formed not only through electrostatic interactions established between the negatively charged DNA molecules and the positive dendrimers, as expected, but also through random rehybridization of the single-stranded DNA (ssDNA) during the cooling process. The resulting films are water-insoluble, transparent when thin, highly elastic when air-dried, exceptionally stable over extended periods, cytocompatible, and easily scalable. Notably, the slow cooling process allowed for the establishment of at least a partially ordered structure in the films, as revealed by circular dichroism, providing evidence of supramolecular chirality. It is envisioned that these films may have significant potential in biomedical applications, such as drug/gene delivery systems, platforms for cell-free DNA transcription and components in biosensors.

The effect of commonly employed forensic DNA extraction protocols on ssDNA/dsDNA proportion and DNA integrity

The utilisation of massively parallel sequencing (MPS) in forensic DNA analysis is on the rise, driven by the expansion of targeted MPS panels in the market and the introduction of forensic investigative genetic genealogy. The MPS library preparation process, integral to both whole-genome sequencing (WGS) and targeted MPS panel data generation, is largely based on converting double-stranded DNA (dsDNA) into sequencing libraries. In the current study, we examined the effect of seven routinely used forensic DNA extraction methods on the strandedness (single-stranded or double-stranded) and the fragment size of the DNA extracted from buccal swab, blood, bone and tooth samples. Our findings reveal a variation in the proportion of dsDNA and single-stranded DNA (ssDNA), with the phenol-chloroform and silica column-based extraction methods tested predominantly yielding dsDNA, while the tested Chelex and magnetic bead-based extraction methods predominantly yielded ssDNA. Additionally, fragment size analysis showed that high molecular weight dsDNA was recovered from buccal swab samples with all of the extraction methods except Chelex, which yielded relatively short dsDNA fragments. DNA extracted from tooth samples with tested magnetic bead-based extraction methods resulted in longer dsDNA fragments compared to the silica column-based extraction protocol.

Supramolecular interactions-driven aggregation to prepare lipoic acid-bioadhesives for seawater-immersed wounds

Seawater-immersed wounds can be threatened by high pH, high permeability and infection, which may lead to the development of chronic wounds. The present study develops an aggregation strategy for the rapid preparation of α-lipoic acid (LA)-based bioadhesives at room temperature with strong and underwater adhesion for emergency treatment of trauma in maritime activities. The bioadhesives are fabricated from the aggregation of LA, MXene and Ag+ through their supramolecular interactions, which can be rapidly formed in mild environments, showing strong interface adhesion without adhesive failure caused by depolymerization, while exhibiting mechanical self-reinforcing. To further improve the adhesive strength, the formation of MXene/Ag+/LA interactions was integrated into poly(2-hydroxyethyl methacrylate) (pHEMA) electrospinning to manufacture electrospun film with the adhesion strength as high as 2 MPa. The bioadhesives are sensitive to alkaline environments and can lead to deprotonation of LA. The released H+ can instantly adjust the pH of weakly alkaline seawater-immersed wounds to normal pH, while deprotonated LA is released into wounds to exert anti-inflammatory functions. Together with antibacterial property, bioadhesives applied to seawater-immersed wounds provide stable barrier protection and correct adverse microenvironment, promoting wound healing.

Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling

In the comet assay, tails are formed after single-cell gel electrophoresis if the cells have been exposed to genotoxic agents. These tails include a mixture of both DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). However, these two types of strand breaks cannot be distinguished using comet assay protocols with conventional DNA stains. Since DSBs are more problematic for the cells, it would be useful if the SSBs and DSBs could be differentially identified in the same comet. In order to be able to distinguish between SSBs and DSBs, we designed a protocol for polymerase-assisted DNA damage analysis (PADDA) to be used in combination with the Flash comet protocol, or on fixed cells. By using DNA polymerase I to label SSBs and terminal deoxynucleotidyl transferase to label DSBs with fluorophore-labelled nucleotides. Herein, TK6-cells or HaCat cells were exposed to either hydrogen peroxide (H2O2), ionising radiation (X-rays) or DNA cutting enzymes, and then subjected to a comet protocol followed by PADDA. PADDA offers a wider detection range, unveiling previously undetected DNA strand breaks.