The SYBR-green approach eliminates the time-consuming agarose gels and reduces the risk of contamination. Selleckchem Go6983 Results Analytical sensitivity and specificity The analytical sensitivity
of the assay was determined with serial concentrations of cloned replicon DNA ranging from 5 ng to 50 fg. For all different clones the PCR showed a clear melting curve position ranging from 82,1°C to 88,9°C (see Table 1). The DNA concentrations varied from 5 ng to 5 fg of vector DNA (estimated number of plasmids for 5 fg: ~1087). Comparison of the melting curve analysis with agarose gel electrophoresis results showed that the sensitivity of the melting curve analysis was tenfold higher than the sensitivity of the agarose method (see Figure 1). Table 1 Average melting temperature of reference amplicons with CV% and SDs Replicon name Size of reference plasmid and amplicon (bp) Melting check details temperature of amplicon (°C) Average TM SD CV% A/C 4365 86.3 86.3 0.05 0.06 B/O 4059 85.1 85.1 0.17 0.20 ColE 4087 86.4 86.4 0.20 0.23 ColEtp 4006 84.9 84.9 0.13
0.16 F 4170 84.2 84.2 0.24 0.29 FIA 4362 84.0 84 0.17 0.21 FIB 4602 86.4 86.4 0.07 0.08 FIC 4162 83.6 83.6 0.15 3-oxoacyl-(acyl-carrier-protein) reductase 0.18 FIIs 4170 87.7 87.7 0.18 0.20 HI1 4371 83.6 83.6 0.18 0.21 HI2 4544 86.3 86.3 0.11 0.13 I1 4039 83.3 83.3 0.12 0.15
K 4060 85.2 85.2 0.09 0.10 L/M 4685 84.7 84.7 0.08 0.10 N 4459 86.5 86.5 0.17 0.19 P 4434 88.4 88.4 0.15 0.17 R 4151 84.4 84.4 0.18 0.21 T 4650 83.8 83.8 0.19 0.23 U 4743 88.9 88.9 0.09 0.10 W 4142 88.9 88.9 0.09 0.10 X 4276 82.1 82.1 0.22 0.27 Y 4665 86.6 86.6 0.31 0.36 Reference plasmids, sizes and average melting temperatures obtained from at least five crude lysates of the cloned replicon plasmid. The average melting temperatures for replicons from WT strains were identical to those of the cloned replicons. Figure 1 Melting curves of serial dilutions of the FIIs replicon. The melting curves intensity differences based on 10-1 to 10-9 dilutions of the FIIs replicon (melting peak at 87.4 average for this experiment). For each melting curve the corresponding agarose band is presented in the grey box. Shown in pairs are the curves that gave a positive result both as melting curve and after visualization on agarose gel (blue = 10-1, purple = 10-2, green = 10-3, red = 10-4 and turquoise = 10-5). The dilutions from 10-6 to 10-8 are visible as peaks of 4300 y (10-6) to 4117 y (10-8). These are not shown as agarose bands because they were not visible on agarose gel. Specificity of the method was tested by mixing of 3 different plasmids containing cloned replicons in a multiplex PCR reaction (i.e.