Supporting Information: Effect of Mechanical Stretching on DNA Conductance. Christopher Bruot, Limin Xiang, Julio L. Palma, and Nongjian Tao

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1 Supporting Information: Effect of Mechanical Stretching on DNA Conductance Christopher Bruot, Limin Xiang, Julio L. Palma, and Nongjian Tao Center for Bioelectronics and Biosensors, Biodesign Institute, School of Electrical, Energy and Computer Engineering, Arizona State University, Tempe, Arizona Alkanedithiol Conductance and Stretching Length vs. Molecular Length Figure S1 shows the molecular conductance and stretching length characteristics for n- alkanedithiol molecules (n=4,6,8) vs molecular length. The molecular conductance, Figure S1a, is seen to decrease exponentially with molecular length, as has been reported for alkane chain molecules by numerous groups. We observe that the stretching length is independent on molecular length, in agreement with previous experiments. The measured stretching length for alkanedithiol molecules is ~0.23nm.

2 Figure S1: Average conductance and stretching length vs. molecular length for alkanedithiol molecules. Red lines intended to guide the eye. Amine-linker DNA Figure S2 shows the chemical structure of the 3` -thiol and amine linker groups used in this study. The thiol linker groups are attached to the phosphate-sugar backbone while the amine linker group is attached directly to the terminal thymine base. Figure S3 shows example conductance and stretching length histograms for 8 base pair (denoted as 5 -A(CG) 3 T-3 in S3a

3 and S3b) and 14 base pair ( denoted as 5 -A(CG) 6 T-3 in S3c and S3d) long molecules. The effect of the amine linker bonding directly to the terminal thymine base is seen as an overall increase in conductance for amine terminated dsdna molecules, due to the decrease in contact resistance caused by fewer saturated bonds between the electrode and first hopping site. We observe a weak decrease in conductance with molecular length for amine terminated bonds, in agreement with the hopping model. Furthermore, the stretching length for 8 base pair and 14 base pair long amine terminated dsdna molecules is ~0.13nm, within experimental error of the thiol linker dsdna molecules. This adds further evidence that the short stretching length required to abruptly decrease conductance in dsdna molecules is a unique property of the dsdna molecule, not the linker group. Figure S2: Structures of two different linker groups. (a) Structure of the thiol linker group in dsdna molecule. (b) Structure of the amine linker group in dsdna molecule.

4 Figure S3: Conductance and stretching length characteristics of amine linked dsdna molecules. (a) Conductance and (b) stretching length histograms for 8 base pair (5 -A(CG) 3 T-3 ) amine linked dsdna molecule. (c) Conductance and (d) stretching length for 14 base pair (5 - A(CG) 6 T-3 ) amine linked dsdna molecule. Additional Compression/Stretching Data Figure S4 shows additional 2-dimensional histograms of conductance vs. tip displacement for 26 base pair thiol linker dsdna (Figure S4a) and octanedithiol (Figure S4b). The slope of the logarithm of conductance vs. tip displacement in region I is ~7.4±2nm -1 for the dsdna and ~9.3±2nm -1 for octanedithiol, which are similar to the tunneling decay constant of the solvent. The exponential dependence on tip displacement suggests that tunneling between the tip and substrate is a major contribution. Furthermore, the small difference in slope between dsdna and octanedithiol suggests that the transport mechanism of the molecule plays little role in this regime.

5 Figure S4: 2-dimensional conductance vs. tip displacement histograms. (a) Log(conductance) dependence on tip displacement for 26 base pair (5 -A(CG) 12 T-3 ) dsdna molecule (shown in (c)). (b) Log(conductance) dependence on tip displacement for octanedithiol (shown in (d)). PAGE Gel Preparation and Data The double strand DNA structure was confirmed by native polyacrylamide gel electrophoresis (PAGE). Electrophoretic measurements were performed at 20 C with a voltage of

6 200V for ~3 hours using 50pmol of each sample and 10% native PAGE gels in 1xTAE Mg 2+ buffer. The gels were then stained with ethidium bromide (EB) and scanned in a Biorad Gel Doc XR+ system for sample visualization. Figure S5 shows the DNA samples measured with PAGE with and without Mg 2+. Figure S5a shows 14, 20, 26, and 36 base pair samples annealed without Mg 2+ ions (just in Phosphate buffer) using the annealing procedure described in the methods section. We see that the concentration of hairpin band (bottom band) increases in lengths more than 14 base pair, suggesting that the DNA favorably forms hairpin structures after the annealing. Figure S5b shows 20 and 36 base pair samples annealed with and without 10mM Mg 2+. With Mg 2+ (columns 2 and 5) the double strand DNA (top band) is the main product while without Mg 2+ the hairpin structure (bottom band) are more likely to form. For all experiments shown in the main text the molecules were annealed in phosphate buffer solution containing 10mM Mg 2+.

7 Figure S5: Native Polyacrylamide gel electrophoresis. (a) dsdna annealed in phosphate buffer without Mg 2+. From 1 to 4 the sequence is 5 -A(CG) 6 T-3, 5 -A(CG) 9 T-3, 5 -A(CG) 12 T-3, and 5 -A(CG) 17 T-3. (b) dsdna annealed in phosphate buffer with Mg 2+ (columns 2 and 5) and without Mg 2+ (the rest). Column 1 is 5 -A(CG) 6 T-3 in phosphate buffer annealed for 3 hrs, 2 is 5 -A(CG) 6 T-3 in phosphate buffer with Mg 2+ annealed for 3 hrs, 3 is 5 -A(CG) 6 T-3 in phosphate buffer annealed for 13 hrs, 4 is 5 -A(CG) 17 T-3 in phosphate buffer annealed for 3 hrs 5 is 5 -A(CG) 17 T-3 in phosphate buffer with Mg 2+ annealed for 3 hrs, 6 is 5 -A(CG) 17 T-3 in phosphate buffer annealed for 13 hrs.