Tively. doi:10.1371/journal.pone.0048251.gIn order to evaluate the SG binding mode, we checked the alterations in fluorescence upon adding the electrolyte of NaCl. As shown in Figure 6, addition of NaCl does not seriously affect the emission of SG bound to DNA1-Ys, whereas NaCl induces a concentration-dependent increase in fluorescence for the FMDNA, indicating release of the bound SG from the FM-DNA upon increasing the Na+ concentration. These results confirm that the chromophore moiety of SG can mainly intercalate into the AP site. By contrast, a main minor groove binding of SG to FM-DNA [45] is expected because the minor groove site is the second strong Na+ binding site besides the phosphate backbone. The fluorescence lifetime measurements were further used to evaluate the AP site binding of SG and the results were listed in Table 1. It is evidenced that the excited-state SG alone in aqueous solution decays according to a lifetime of 3.20 ns at 415 
nm and of 2.45 ns at 586 nm for the alkanolamine form and iminium form, respectively, which is in good agreement with the previously reported values [46]. At 415 nm, the presence of FM-DNA, DNA1-A, and GW 0742 DNA1-G produces only one lifetime of 3.25, 3.32, and 3.30 ns respectively that is comparable with that for SG alone,Table 1. Fluorescence decay fitting parameters (t1 and t2) of 5 mM SG in the absence and presence of 5 mM DNAsD.x2 1.047 1.029 1.048 12.05 11.65 14.05 DNA1-G 3.30 2.28 DNA1-T 2.a b a b a bt1 (ns) DNA free 3.20a 2.45b DNA1-A 3.at2 (ns)2.90b (8.12 ) DNA1-C 2.a(91.88 ) (25.73 )1.123 1.003 1.032 1.(74.27 )showing that the alkanolamine form does not bind to these DNAs. The unfavorable binding of the alkanolamine form to FM-DNA has also been reported [37]. Nevertheless, besides the short-lived decays, 18055761 both DNA1-C and -T induce another 842-07-9 web long-lived lifetime at this wavelength, implying that the alkanolamine form can bind to these AP sites. This could be explained by the fact that the smallsized pyrimidines opposite the AP site would provide more space in the AP site to effectively accommodate the more bulky SG alkanolamine nonplanar structure. Importantly, the increased average lifetimes for DNA1-C and -T (5.05 and 4.60 ns, in comparison to 3.20 ns for SG alone) and the increased excitation intensities at 336 nm (Figure 3A) would predict an enhanced emission at 415 nm. However, sharply decreased emissions were observed (Figure 3B), showing that a large population of the alkanolamine form converts to the iminium form. On the other hand, from the measured lifetimes at 586 nm (listed in Table 1), the SG iminium form is capable of binding to the FM-DNA and all DNA1-Ys. In comparison with a short-lived decay and a longlived decay for DNA1-A and -G, only one long-lived decay was found for DNA1-C and -T, indicating a strong association of the iminium form to the AP site opposed by pyrimidines. For example, the intrinsic binding constants of 1.76107 M21 and 8.36105 M21 for DNA1-C and the FM-DNA respectively were derived from fluorescence titration experiments (Figure S3). The value for the FM-DNA without the AP site is in good agreement with the ones reported for natural and oligomeric DNAs [31]. Note that here only the binding modes related to the strongest DNA binding site for both DNA1-C and the FM-DNA 
were considered in calculating the corresponding binding parameters. Interestingly, the long-lived decay lifetimes of 14.05, 13.61, 12.05, and 11.75 ns for DNA1-C, -T, -A, and -G are just roug.Tively. doi:10.1371/journal.pone.0048251.gIn order to evaluate the SG binding mode, we checked the alterations in fluorescence upon adding the electrolyte of NaCl. As shown in Figure 6, addition of NaCl does not seriously affect the emission of SG bound to DNA1-Ys, whereas NaCl induces a concentration-dependent increase in fluorescence for the FMDNA, indicating release of the bound SG from the FM-DNA upon increasing the Na+ concentration. These results confirm that the chromophore moiety of SG can mainly intercalate into the AP site. By contrast, a main minor groove binding of SG to FM-DNA [45] is expected because the minor groove site is the second strong Na+ binding site besides the phosphate backbone. The fluorescence lifetime measurements were further used to evaluate the AP site binding of SG and the results were listed in Table 1. It is evidenced that the excited-state SG alone in aqueous solution decays according to a lifetime of 3.20 ns at 415 nm and of 2.45 ns at 586 nm for the alkanolamine form and iminium form, respectively, which is in good agreement with the previously reported values [46]. At 415 nm, the presence of FM-DNA, DNA1-A, and DNA1-G produces only one lifetime of 3.25, 3.32, and 3.30 ns respectively that is comparable with that for SG alone,Table 1. Fluorescence decay fitting parameters (t1 and t2) of 5 mM SG in the absence and presence of 5 mM DNAsD.x2 1.047 1.029 1.048 12.05 11.65 14.05 DNA1-G 3.30 2.28 DNA1-T 2.a b a b a bt1 (ns) DNA free 3.20a 2.45b DNA1-A 3.at2 (ns)2.90b (8.12 ) DNA1-C 2.a(91.88 ) (25.73 )1.123 1.003 1.032 1.(74.27 )showing that the alkanolamine form does not bind to these DNAs. The unfavorable binding of the alkanolamine form to FM-DNA has also been reported [37]. Nevertheless, besides the short-lived decays, 18055761 both DNA1-C and -T induce another long-lived lifetime at this wavelength, implying that the alkanolamine form can bind to these AP sites. This could be explained by the fact that the smallsized pyrimidines opposite the AP site would provide more space in the AP site to effectively accommodate the more bulky SG alkanolamine nonplanar structure. Importantly, the increased average lifetimes for DNA1-C and -T (5.05 and 4.60 ns, in comparison to 3.20 ns for SG alone) and the increased excitation intensities at 336 nm (Figure 3A) would predict an enhanced emission at 415 nm. However, sharply decreased emissions were observed (Figure 3B), showing that a large population of the alkanolamine form converts to the iminium form. On the other hand, from the measured lifetimes at 586 nm (listed in Table 1), the SG iminium form is capable of binding to the FM-DNA and all DNA1-Ys. In comparison with a short-lived decay and a longlived decay for DNA1-A and -G, only one long-lived decay was found for DNA1-C and -T, indicating a strong association of the iminium form to the AP site opposed by pyrimidines. For example, the intrinsic binding constants of 1.76107 M21 and 8.36105 M21 for DNA1-C and the FM-DNA respectively were derived from fluorescence titration experiments (Figure S3). The value for the FM-DNA without the AP site is in good agreement with the ones reported for natural and oligomeric DNAs [31]. Note that here only the binding modes related to the strongest DNA binding site for both DNA1-C and the FM-DNA were considered in calculating the corresponding binding parameters. Interestingly, the long-lived decay lifetimes of 14.05, 13.61, 12.05, and 11.75 ns for DNA1-C, -T, -A, and -G are just roug.
