Liisa Hirvonen edited Method.tex  over 8 years ago

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\subsection{Sample preparation}  All protein solutions were diluted with sterile phosphate buffered saline (PBS; Sigma; pH~7.4) to 5mg/mL and then dialyzed twice against phosphate buffered saline (PBS) pH 7.4 using D-Tube Midi Dialyzer units from Novagen (6-8~kD cut-off). Subsequently, the purity of the dialysed proteins was confirmed by standard SDS-PAGE. The proteins were then conjugated to the ruthenium dye. This was achieved by reacting the succinimidyl ester-modified dye, Bis(2,2′-bipyridine)-4′-methyl-4-carboxybipyridine-ruthenium N-succinimidyl ester-bis(hexafluorophosphate) (synonym, Ru(bpy)$_2$(mcbpy-O-Su-ester)(PF$_6$)$_2$, Sigma-Aldrich) by using a succinimidyl ester-modified fluorophore with a short linker (Invitrogen, F6130). Conjugation reactions were performed in PBS adjusted with bicine buffer to pH 8.6 at 2~mg/ml protein concentration with the activated fluorophore ester being used in excess (2-fold and 3.5-fold for proteins >60~kD $>$60~kD  and ranibizumab, respectively). The reaction was stopped after two hours and conjugated proteins were separated from remaining free dye by size exclusion chromatography (two times via 7~kD cut-off Zeba\textregistered spin columns (Thermo Fisher, UK)). Using this method we generated the various proteins conjugated to the fluorophore in the following dye:protein ratios: ranibizumab 1.1:1; BSA 1.2:1; aflibercept 1:1.8; 1.8:1;  bevacizumab 1.3:1. Azide (2.0~mM) was added to all dye-conjugated drugs to protect them from microbial deterioration. \subsection{Anisotropy measurements}