ORF102 and ORF103 of pAL1 were amplified by PCR using Phusion™ Hot Start High-Fidelity DNA Polymerase (Finnzymes Oy, Espoo, Finland), using total DNA of A. nitroguajacolicus Rü61a [pAL1] as the template and the primer sets listed in Supporting Information, Table S1. PCR products were subsequently ligated into pMal-c2x Selleckchem CH5424802 or pART2malE. Competent E. coli and A. nitroguajacolicus Rü61a [pAL1] cells were generated as described by Hanahan (1983)
and Gartemann & Eichenlaub (2001), respectively. All plasmid inserts and flanking regions were verified by sequencing (GATC Biotech AG, Konstanz, Germany). For the preparation of covalent complexes of telomeric pAL1-DNA and MBP-pORF102 or MBP-pORF103, frozen cells of A. nitroguajacolicus Rü61a [pAL1, pART2malE-ORF102] or A. nitroguajacolicus Rü61a [pAL1, pART2malE-ORF103] were thawed in 20 mM Tris/HCl buffer containing 400 mM NaCl, 1 mM
EDTA (pH 7.4) (buffer A), and 1 mM phenylmethylsulfonyl fluoride. After incubation for 30 min with 2 mg mL−1 lysozyme, crude extracts containing soluble proteins were prepared by sonication, followed by centrifugation. Supernatants were applied find more to an amylose column (5 mL bed volume), equilibrated in buffer A. After washing with the same buffer, MBP fusions were eluted with buffer A containing 20 mM maltose. Eluates were loaded to a GF/C Whatman glass microfiber filter (Whatman International Ltd, Kent, UK) (Coombs & Pearson, 1978). The immobilized complexes were washed four times with 1 M NaCl and eluted with 0.5% sodium dodecyl sulfate (SDS), 0.1 M NaCl in water (Bao & Cohen, 2001). Eluted complexes were precipitated twice with 0.1 volume Suplatast tosilate of 3 M sodium acetate and 2.5 volumes of ethanol. Precipitates were redissolved in sterile water. In order to identify the DNA attached to MBP-pORF102, MBP-pORF103, or both, the redissolved complexes were used as templates in PCR reactions with GoTaq® Green DNA polymerase (Promega GmbH, Mannheim, Germany). The primer pairs for amplification of terminal regions of pAL1, an internal segment of pAL1, and a region of the chromosome of A. nitroguajacolicus Rü61a
[pAL1] are listed in Table S1. For the preparation of the MBP-pORF102 fusion protein, 5 g of frozen cells of E. coli K12 ER2508 [pLysSRARE, pMal-c2x-ORF102] were thawed in buffer A. After incubation for 30 min and addition of 1 mM MgCl2 and 10 U mL–1 benzonase, crude extracts were prepared by sonication and centrifugation as described above. The eluate from subsequent amylose affinity chromatography (performed as described above) was applied on HiTrap™ Desalting columns (4 × 5 mL, GE Healthcare, Munich, Germany) equilibrated in buffer B, consisting of 50 mM Tris/HCl (pH 8.0). The desalted eluate was loaded onto a UnoQ column (6 mL bed volume, Bio-Rad Laboratories, Munich, Germany) equilibrated in the same buffer.