Supporting Material for “Measuring single molecule DNA hybridization by active control of DNA in a nanopore” 1 Target DNA and binding oligodeoxynucleotide (ODN) purity

In our experimental studies of DNA hybridization as a function of fishing (exposure) time and the subsequent dissociation of bound oligomers, we compared the behaviors of two syntheses of the 59 mer target (labeled 59A and 59B) and 10 mer ODN (labeled 10A and 10B) in different experiments. The two syntheses yield significantly different results. For instance, the fraction of detectable hybridization at a long fishing time is near 100% for 59A whereas the fraction of detectable hybridization at a long fishing time is only about 80% for 59B (see Figure 2 in the text). Since the experimental conditions were set to be the same for the two syntheses, the cause of the different behaviors is likely to be the impurity in the syntheses. Gels were run to establish the purity of the target DNA and ODN samples. 59A and 59B were run on 14% denaturing PAGE gels at 20 W for 5 hours. 10A and 10B were run on a 20% denaturing PAGE gel at 28 W for 1.5 hours. Gels were stained with SYBR gold (Invitrogen) according to manufacturer’s protocol, and imaged on a UVP gel documentation system. The relative intensities of the imaged bands in each lane were analyzed used ImageJ[1]. For 59A, the full length product comprises 81% of the relative intensity of the lane, whereas for 59B the full length product comprises only 29% of the relative intensity seen in the sample (Fig. S1, I and II). Both 10A and 10B showed comparable and high purity (Fig. S1 III). The results of gel experiments indicate i) target DNA 59B is significantly less pure than 59A, which is consistent with the results of hybridization experiments (see Fig. 2 in the main text); and ii) ODN 10A and 10B both have high purity.