Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering

Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.     

The Fixation of Tissues Vitally Stained with Trypan Blue

The following fixative is recommended for tissues vitally stained with trypan blue: Chloroform, 2 parts; absolute ethyl alcohol, 2 parts; glacial acetic acid, 1 part; mercuric chloride to the point of saturation.

The tissue should be fixed 1 to 2 hours; transferred to 95% ethyl alcohol for 12 hours; to absolute alcohol for 12 to 24 hours; to a mixture of absolute alcohol and xylol for 1/2 hour, and finally to xylol, before embedding in paraffin. Cedar oil may be used for clearing in the place of xylol; in that case the tissues should be transferred from absolute alcohol to a mixture of absolute alcohol and cedar oil for 24 hours before placing in cedar oil alone.

Various counterstains can be used; Mayer's carmalum is excellent.     

The effect of preparative protocol on the cytoskeleton ultrastructure observed in extracted whole-mount BHK cells

Extracted BHK cells (baby hamster kidney) were prepared for electron microscopy by air-drying (with Freon 113), critical-point-drying, and freeze-drying. Variations in the drying procedures had a marked effect on the resultant cytoskeleton ultrastructure. Air drying had to be done in a Freon-saturated atmosphere, residual water had to be removed from the dehydrating solutions and carbon dioxide for critical-point-dried specimens, and freeze-drying had to be done at temperatures lower than -90 degrees C. Failure to exercise these precautions resulted in a cytoskeleton ultrastructure artifact, possibly caused by fusion of the cytoskeleton filaments.