Supplementary information for Multivalent binding and DNA length-dependent photo-adduct formation of Ru ( TAP )

DNA substrates. For the magnetic tweezer measurements a 7.9-kbp DNA construct, prepared as described previously 1, was used. In brief, PCR-generated DNA fragments (~600 bp) labeled with multiple biotin or digoxigenin groups were ligated to the DNA, to bind magnetic beads and the flow cell surface, respectively. Linear DNA fragments (486 bp) used for atomic force microscopy imaging were obtained by PCR amplification of a synthetic DNA fragment (gBlock fragment; Integrated DNA Technologies). PCR products were purified from primers, proteins and salts using a PCR Cleanup kit (QIAquick PCR Purification Kit – Qiagen) and resuspended in 10 mM phosphate buffer. To test the effect of DNA length on the spectroscopic properties of Ru(TAP)3, we used phage lambda DNA (NEB; N3011L) that was dialyzed overnight against 10 mM phosphate buffer to remove the EDTA used for storage. In addition we tested a 32 bp double stranded fragment that was obtained by annealing the complementary oligodeoxynucleotides 5' ACG TCA GTC AGC ATC AGA GTT TTC CCG TGA AG 3' and 5' CTT CAC GGG AAA ACT CTG ATG CTG ACT GAC GT 3'.