ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity.

Motivation: Genetically engineering food crops involves introducing proteins from other species into crop plant species or modifying already existing proteins with gene editing techniques. In addition, newly synthesized proteins can be used as therapeutic protein drugs against diseases. For both research and safety regulation purposes, being able to assess the potential toxicity of newly introduced/synthesized proteins is of high importance.

Fluorescence anisotropy: from single molecules to live cells.

The polarization of light emitted by fluorescent probes is an easily accessible physical quantity that is related to a multitude of molecular parameters including conformation, orientation, size and the nanoscale environment conditions, such as dynamic viscosity and temperature. In analytical biochemistry and analytical chemistry applied to biological problems, fluorescence anisotropy is widely used for measuring the folding state of proteins and nucleic acids, and the affinity constant of ligands through titration experiments. The emphasis of this review is on new multi-parameter single-molecule detection schemes and their bioanalytical applications, and on the use of ensemble polarization assays to study binding and conformational dynamics of proteins and aptamers and for high-throughput discovery of small-molecule drugs.

A mixed film composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) brushes to enhance selectivity for detection of single nucleotide polymorphisms.

Preliminary studies of mixed films composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) (PHEMA) have recently been shown to enhance the selectivity for detection of 3 base-pair mismatched (3 bpm) oligonucleotide targets. Evaluation of selectivity for detection of single nucleotide polymorphisms (SNP) using such mixed films has now been completed. The selectivity was quantitatively determined by considering the sharpness of melt curves and melting temperature differences (DeltaT(m)) for fully complementary targets and SNPs.