Direct Conjugation of Peptides and 5‑Hydroxymethylcytosine in DNA

Recent discovery of functional 5-hydroxymethylcytosine in vertebrate genomes prompted for elaboration of methods to localize this modification at the nucleotide resolution level. Among several covalent modification-based approaches, atypical activity of cytosine-5 DNA methyltransferases to couple small molecules to 5-hydroxymethylcytosine stands out for acceptance of broad range of ligands. We went further to explore the possibility for methyltransferase-maintained coupling of compounds possessing autonomous functions. Functionalization of DNA was achieved by direct conjugation of chemically synthesized peptides of regular structure. Sequence, residue, and position-specific coupling of DNA containing 5-hydroxy­methylcytosine and different peptides has been demonstrated, with the nature of the resulting conjugates confirmed by protease treatment and mass spectrometry. Coupling products were compatible with affinity-driven separation from the unmodified DNA. This approach highlights an emerging avenue toward the enzymatic, sequence-specific DNA functionalization, enabling a single step merge of the DNA and peptide moieties into a bifunctional entity

Additional file 5 of Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris

Additional file 5: Fig. S2. Terminal complementary sequences in LBVs of Leptomonas pyrrhocoris. Primary structures and/or alignments are shown on the left, secondary structures are on the right. The panhandle-distorting complex structure containing a multi-branched loop, a big bulge, and a short hairpin is outlined

Additional file 4 of Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris

Additional file 4: Fig. S1. Phylogenetic inference of relationships between the RDRP nucleotide sequences of LeppyrLBV3. Numbers at the branches indicate Bayesian posterior probability (PP) and ML bootstrap supports (BS), respectively. Only bootstrap supports BS ≥ 50 are shown, lower values replaced with dashes (-). Circles correspond to maximal statistical support by both methods. The scale bar indicates the number of substitutions per site

Additional file 3 of Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris

Additional file 3: Table S3. Analysis of the incompatibility of tree topologies for different ORFs in LeppyrTLV1

Additional file 6 of Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris

Additional file 6: Fig. S3. Analysis of virus distribution heterogeneity within isolates. Note that not all fragments for a virus (see graphic legend) can be always detected on the gel

Additional file 1 of Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris

Additional file 1: Table S1. Summary of the NGS data obtained for the viral RNAs of the studied trypanosomatid isolates

Additional file 2 of Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris

Additional file 2: Table S2. Sequence variation in LeppyrTLV1 and LeppyrOV1