Table 4 Modification of algorithm scores based upon shRNA central duplex ΔG. The percent knockdown data represents the average knockdown as shown in Table 3. shRNAs with a central ΔG equal to or less than -12.9 kcal/mol are underlined. These were assigned minimum scores according to the algorithm modification. Minimum scores are: Amarzguioui et al. algorithm, -4; Ui-Tei et al. algorithm, -2; Takasaki et al. algorithm, -13.26. The three shRNAs that scored high in the original Takasaki et al. algorithm but have poor knockdown efficacy are marked with asterisks. The modification minimized scoring for these shRNAs, thus increasing specificity of the algorithm.

shASC-721

91

-9.7

2

2

8.07

shASC-743

74

-10.6

4

2

7.33

shCLR16.2-482

37

-12.9

-4

-2

-13.26 *

shCLR16.2-716

64

-11.3

4

3

5.05

shCLR16.2-3394

74

-12

3

4

0

shCLR16.2-1630

59

-9.6

5

4

4.81

shCLR19.3-667

71

-13

-4

-2

-13.26

shCLR19.3-991

13

-13.1

-4

-2

-13.26 *

shCLR19.3-1504

70

-10.9

0

0

8.42

shCLR19.6-888

<10%

-7.8

2

1

-2.6

shCLR19.6-1549

<10%

-13.1

-4

-2

-13.26 *

shCLR19.6-2249

<10%

-10.9

2

2

3.78

shMAL-1374

69

-11.2

2

2

-11

shMAL-1504

65

-11.8

0

1

-3.8

shMYD88-1830

73

-9.8

1

3

2.7

shMYD88-2207

53

-9.6

1

2

-4

shTLR2-1625

59

-7.1

3

4

3.13

shTLR2-2271

57

-10.6

1

0

14.7

shTLR4-2377

79

-7.3

1

-2

-6.6

shTLR4-1923

<10%

-8.5

4

3

-0.1

shTLR4-806

<10%

-9.8

-2

-2

-0.7

shTRAF6-936

51

-10.9

3

4

0

shTRAF6-1326

62

-9.7

3

3

13.1

shTRAF6-1563

53

-9.8

3

0

7.38

shTRAM-290

<10%

-11

1

2

-8.9

shTRAM-482

<10%

-12.9

-4

-2

-13.26

shTRIF-1786

<10%

-8.69

0

0

1.03