Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes

Table 1 Typing of cyanobacterial strains using the cynD/AoaB SYTO9 melting curve assay.

Species	Strain	Peak 1 T_m °C	Peak 2 T_m °C	Toxic
C. raciborskii	AWT205	84.9	87.0	yes
C. raciborskii	CYLI-19	-	-	no
C. raciborskii	CYLI-29	-	-	no
C. raciborskii	CYLI-31	-	-	no
C. raciborskii	CYLI-42	-	-	no
C. raciborskii	CYLI-53	-	-	no
C. raciborskii	CYLI-75	-	-	no
C. raciborskii	CYP003A	85.0	87.0	yes
C. raciborskii	CYP005F	85.0	87.0	yes
C. raciborskii	CYP009A	84.9	86.8	yes
C. raciborskii	CYP010A	84.9	86.8	yes
C. raciborskii	CYP014A	-	-	no
C. raciborskii	CYP023A	85.0	87.0	yes
C. raciborskii	CYP024C	85.0	87.0	yes
C. raciborskii	CYP025B	85.0	87.0	yes
C. raciborskii	CYP026J	85.0	87.0	yes
C. raciborskii	CYP030	85.0	87.0	yes
C. raciborskii	CYP033	84.9	87.0	yes
A. bergii	ANA360D	-	-	no
A. bergii	ANA360H	-	-	no
A. bergii	ANA366A	86.3	-	yes
A. bergii	ANA283A	86.6	-	yes
A. ovalisporum	APH028A	-	-	no
A. ovalisporum	APH031G	86.4	-	yes
A. ovalisporum	APH033C	86.4	-	yes
A. ovalisporum	APH035E	86.4	-	yes
A. ovalisporum	APH035F	86.4	-	yes

Typing of cylindrospermopsin-producing and non-producing cyanobacterial strains using a SYTO9 melting curve assay for the cynD/AoaB gene designed in silico using the POLAND software. The T_m for each melt peak observed in cynD/AoaB positive samples is reported to one decimal place. All cynD/AoaB negative samples are indicated by "-". Toxin production confirmed by LC-MS with a detection limit of 0.2 μg/L ([34]).

ISSN: 1471-2105