Puc57 plasmid vector

The type A outer surface protein C (OspC) gene of Borrelia burgdorferi B31 (GenBank accession #AAC66329.1) was designed to include the human tyrosinase signal peptide (MLLAVLYCLLWSFQTSAGHFPRA; GenBank accession #AH003020) at the N-terminus (30 (link), 31 (link)). The coding region was optimized for expression in mice and commercially synthesized in a pUC57 plasmid vector by Bio Basic Inc. (Markham, ON). The OspC gene containing the signal sequence was sub-cloned into a pVAX1 plasmid vector (ThermoFisher, Ottawa, ON), using NotI-HF and EcoRI-HF restriction enzymes (New England Biolabs, Whitby, ON). Large-scale amplifications of the pVAX1-OspC plasmid were generated using the QIAGEN Plasmid Giga Kit (Montreal, QC) according to the manufacturer’s instructions. The genetic sequences were validated by Sanger Sequencing prior to nanoparticle encapsulation.

The DNA substrates used in nucleosome assembly were generated using PCR with a pUC57 plasmid vector from BioBasic (Markham, ON, Canada). A biotinylated reverse primer (IDT, Coralville, IA, USA) was used on all substrates for streptavidin labeling. Substrates containing the Widom 601 motif and the non-specific DNA totaled 377 bp in length, while the substrate containing the α-satellite motif totaled 410 bp in length. Schematics of the substrate designs can be seen in Figure 1. DNA sequences are listed as Figure S3. DNA substrates were separated by gel electrophoresis using 1% SeaKem LE Agarose gel (Lonza Group AG, Basel, Switzerland). The bands were excised and purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany). DNA concentration was then determined using NanoDrop Spectrophotometer ND-1000 (Thermo Fischer, Waltham, MA, USA).

The DNA substrates used in nucleosome assembly were generated using PCR with a pUC57 plasmid vector from BioBasic (Markham, ON, CA). A biotinylated reverse primer (IDT, Coralville, IA) was used on all substrates for streptavidin or rhizavidin labeling.
For the mononucleosome substrates, two constructs were used; one construct featuring 147 bp of the strong positioning Widom 601 sequence^{30 (link)} flanked by plasmid DNA of 113 and 117 bp, and another substrate which replaces the 147 bp of the Widom 601 sequence with a non-specific sequence. Two dinucleosome substrates were also used; one featured the 147 bp of the Widom 601 sequence flanked by 113 and 117 bp, while the other contained two copies of the Widom 601 sequence, separated by 60 bp and flanked by 110 and 114 bp. The substrate constructions are presented in Fig. S1. DNA Sequences are listed as Fig. S7. DNA substrates were separated by gel electrophoresis using 1% SeaKem LE Agarose gel (Lonza Group AG, Basel, Switzerland). The bands were excised and purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany). DNA concentration was then determined using NanoDrop Spectrophotometer ND-1000 (Thermo Fischer, Waltham, MA).