Additional file 1 of Dinuclear complex-induced DNA melting
Creators: name: Biere, Niklas
name: Kreft, Dennis
name: Walhorn, Volker
name: Schwarzbich, Sabrina
name: Glaser, Thorsten
name: Anselmetti, Dario
Publisher: name: figshare
Year: 2024
Subjects: Biophysics
Biochemistry
Space Science
Physical Sciences not elsewhere classified
Medicine
Cell Biology
Biotechnology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified

description: Additional file 1: Figure S1. Various stages of the (HtomMe)- complexes. (a) The basic form of the H2tomMe ligand. (b) A methoxymethyl(MOM)-based precursor for synthesis of the metal complexes. (c) The cationic form crystallized with an acetate OAc− counter anion. (d) In aqueous solution the acetate groups are replaces by H2O. (e) The copper ions coordinate to the phosphates of the DNA backbone. Figure S2. λ-DNA subjected to dinuclear copper complexes at various concentrations. Images taken in air in tapping mode. Same length and height scales apply to each image. (a) Untreated λ-DNA (12.5 ng/µl), strand height 0.6 nm. (b) Final complex concentration 0.7 µM, increase of strand height to 1 nm. (c) 1.4 µM, height 0.8 nm. (d) 2 µM, increase of coagulation (indicated by arrows), height 1 nm. (e) 7 µM, height 1 nm. (f) 14 µM, complete coagulation, height 0.4 - 1 nm. (g) 0.4 nM with an incubation time of 45 h. (h) 4 nM. Figure S3. Empirical determination of a suitable complex concentrations: measurements of electrospray depositions of complex-treated DNA under UHV. (a) At 2 µM, a massive residual background is present, the strands appear visibly embedded into a layer (df = - 2.2 Hz, A = 36.1 nm, f0 = 257.4 Hz). (b) At 0.4 nM, still a slight residual molecular background is visible, the gold surface appears to be covered (df = - 2.5 Hz, A = 14.1 nm, f0 = 259.0 Hz). Although technically there should be less complexes than binding sites to the DNA, due to the obvious excess of molecules, it can be assumed that the strands are maximally coated. Figure S4. The [(HtomMe){Cu(OAc)}2]+ complex chemical structure (hydrogen left out) from different perspectives, based on data from [1,2]. (a) Angular view, (b) side view, (c) top view. Figure S5. The puckering of the furanose ring of the DNA backbone changes in humid environments. The (*)-marked C2’ atom switches from the front into the back of the ring plane. The designations C2’- and C3’-endo refer to the atom which is positioned on the side of the C5’ atom. Structural X-ray diffraction data from [3] (1BNA, B-DNA) and [4] (116D, A-DNA). Figure S6. Pseudocode for the analysis of the λ-genome sequence. Firstly, the sequence is reduced for easier counting, then the counting of segments in dependence of the threshold value length occurs. Figure S7. Pseudocode for the adsorption simulation and subsequent analysis. The adsorption routine is depicted in black. Two arrays of singular binding spots, representing the two single strands of one double helix, get subsequently and randomly filled up until no free spots remain. Since the molecules require two adjacent spots, full adsorption will leave randomly distributed singular free spots. In yellow and green depicted are the analysis routines, according to their colors in the graph of Figure 4 in the main paper. The adsorbed strand is reduced for easier identification of molecules. Then two counters are iterated over the arrays, each counting one zigzag phase. The exit conditions for the counting of one segment are that both spots of the same index are either empty or both occupied, meaning the zigzag arrangement would be interrupted either way. In addition, when a GC-pair is present (green).