Methods and compositions for selecting siRNA of improved functionality

1. A method for obtaining an siRNA sequence, said method comprising:

(a) accessing a computer and causing said computer to apply a computer program product being embodied in a computer readable storage medium, wherein said computer program product comprises instructions for applying a formula to a set of at least two candidate siRNA sequences that are each between 19 and 30 bases in length and that each comprise a sense strand sequence of 19-30 bases, wherein said sense strand sequence of each siRNA sequence within said set of candidate siRNA sequences is at least 79% similar to a region of a target gene;

(b) determining a predicted relative functionality of at least two siRNA sequences within said set of candidate siRNA sequences, wherein said predicted relative functionality is measured by said computer applying said computer program product to said at least two siRNA sequences and said computer program product further comprises instructions for ascribing a value to each of said at least two siRNA sequences, and said value is generated by a formula, wherein said formula comprises:

(−8)*A 1 +(−1)*A 2 +(12)*A 3 +(7)*A 4 +(18)*A 5 +(12)*A 6 +(19)*A 7 +(6)*A 8 +(−4)*A 9 +(−5)*A 10 +(−2)*A 11 +(−5)*A 12 +(17)*A 13 +(−3)*A 14 +(4)*A 15 +(2)*A 16 +(8)*A 17 +(11)*A 18 +(30)*A 19 +(−13)*U 1 +(−10)*U 2 +(2)*U 3 +(−2)*U 4 +(−5)*U 5 +(5)*U 6 +(−2)*U 7 +(−10)*U 8 +(−5)*U 9 +(15)*U 10 +(−1)*U 11 +(0)*U 12 +(10)*U 13 +(−9)*U 14 +(−13)*U 15 +(−10)*U 16 +(3)*U 17 +(9)*U 18 +(9)*U 19 +(7)*C 1 +(3)*C 2 +(−21)*C 3 +(5)*C 4 +(−9)*C 5 +(−20)*C 6 +(−18)*C 7 +(−5)*C 8 +(5)*C 9 +(1)*C 10 +(2)*C 11 +(−5)*C 12 +(−3)*C 13 +(−6)*C 14 +(−2)*C 15 +(−5)*C 16 +(−3)*C 17 +(−12)*C 18 +(−18)*C 19 +(14)*G 1 +(8)*G 2 +(7)*G 3 +(−10)*G 4 +(−4)*G 5 +(2)*G 6 +(1)*G 7 +(9)*G 8 +(5)*G 9 +(−11)*G 10 +(1)*G 11 +(9)*G 12 +(−24)*G 13 +(18)*G 14 +(11)*G 15 +(13)*G 16 +(−7)*G 17 +(−9)*G 18 ±(−22)*G 19 +6*(number of A+U in position 15-19)−3*(number of G+C in whole siRNA),

and

A 1 =1 if A is the base at position 1 of the sense strand, otherwise its value is 0;

A 2 =1 if A is the base at position 2 of the sense strand, otherwise its value is 0;

A 3 =1 if A is the base at position 3 of the sense strand, otherwise its value is 0;

A 4 =1 if A is the base at position 4 of the sense strand, otherwise its value is 0;

A 5 =1 if A is the base at position 5 of the sense strand, otherwise its value is 0;

A 6 =1 if A is the base at position 6 of the sense strand, otherwise its value is 0;

A 7 =1 if A is the base at position 7 of the sense strand, otherwise its value is 0;

A 8 =1 if A is the base at position 8 of the sense strand, otherwise its value is 0;

A 9 =1 if A is the base at position 9 of the sense strand, otherwise its value is 0;

A 10 =1 if A is the base at position 10 of the sense strand, otherwise its value is 0;

A 11 =1 if A is the base at position 11 of the sense strand, otherwise its value is 0;

A 12 =1 if A is the base at position 12 of the sense strand, otherwise its value is 0;

A 13 =1 if A is the base at position 13 of the sense strand, otherwise its value is 0;

A 14 =1 if A is the base at position 14 of the sense strand, otherwise its value is 0;

A 15 =1 if A is the base at position 15 of the sense strand, otherwise its value is 0;

A 16 =1 if A is the base at position 16 of the sense strand, otherwise its value is 0;

A 17 =1 if A is the base at position 17 of the sense strand, otherwise its value is 0;

A 18 =1 if A is the base at position 18 of the sense strand, otherwise its value is 0;

A 19 =1 if A is the base at position 19 of the sense strand, otherwise its value is 0;

C 1 =1 if C is the base at position 1 of the sense strand, otherwise its value is 0;

C 2 =1 if C is the base at position 2 of the sense strand, otherwise its value is 0;

C 3 =1 if C is the base at position 3 of the sense strand, otherwise its value is 0;

C 4 =1 if C is the base at position 4 of the sense strand, otherwise its value is 0;

C 5 =1 if C is the base at position 5 of the sense strand, otherwise its value is 0;

C 6 =1 if C is the base at position 6 of the sense strand, otherwise its value is 0;

C 7 =1 if C is the base at position 7 of the sense strand, otherwise its value is 0;

C 8 =1 if C is the base at position 8 of the sense strand, otherwise its value is 0;

C 9 =1 if C is the base at position 9 of the sense strand, otherwise its value is 0;

C 10 =1 if C is the base at position 10 of the sense strand, otherwise its value is 0;

C 11 =1 if C is the base at position 11 of the sense strand, otherwise its value is 0;

C 12 =1 if C is the base at position 12 of the sense strand, otherwise its value is 0;

C 13 =1 if C is the base at position 13 of the sense strand, otherwise its value is 0;

C 14 =1 if C is the base at position 14 of the sense strand, otherwise its value is 0;

C 15 =1 if C is the base at position 15 of the sense strand, otherwise its value is 0;

C 16 =1 if C is the base at position 16 of the sense strand, otherwise its value is 0;

C 17 =1 if C is the base at position 17 of the sense strand, otherwise its value is 0;

C 18 =1 if C is the base at position 18 of the sense strand, otherwise its value is 0;

C 19 =1 if C is the base at position 19 of the sense strand, otherwise its value is 0;

G 1 =1 if G is the base at position 1 on the sense strand, otherwise its value is 0;

G 2 =1 if G is the base at position 2 of the sense strand, otherwise its value is 0;

G 3 =1 if G is the base at position 3 of the sense strand, otherwise its value is 0;

G 4 =1 if G is the base at position 4 of the sense strand, otherwise its value is 0;

G 5 =1 if G is the base at position 5 of the sense strand, otherwise its value is 0;

G 6 =1 if G is the base at position 6 of the sense strand, otherwise its value is 0;

G 7 =1 if G is the base at position 7 of the sense strand, otherwise its value is 0;

G 8 =1 if G is the base at position 8 on the sense strand, otherwise its value is 0;

G 9 =1 if G is the base at position 9 of the sense strand, otherwise its value is 0;

G 10 =1 if G is the base at position 10 on the sense strand, otherwise its value is 0;

G 11 =1 if G is the base at position 11 of the sense strand, otherwise its value is 0;

G 12 =1 if G is the base at position 12 of the sense strand, otherwise its value is 0;

G 13 =1 if G is the base at position 13 on the sense strand, otherwise its value is 0;

G 14 =1 if G is the base at position 14 of the sense strand, otherwise its value is 0;

G 15 =1 if G is the base at position 15 of the sense strand, otherwise its value is 0;

G 16 =1 if G is the base at position 16 of the sense strand, otherwise its value is 0;

G 17 =1 if G is the base at position 17 of the sense strand, otherwise its value is 0;

G 18 =1 if G is the base at position 18 of the sense strand, otherwise its value is 0;

G 19 =1 if G is the base at position 19 of the sense strand, otherwise its value is 0;

U 1 =1 if U is the base at position 1 on the sense strand, otherwise its value is 0;

U 2 =1 if U is the base at position 2 on the sense strand, otherwise its value is 0;

U 3 =1 if U is the base at position 3 on the sense strand, otherwise its value is 0;

U 4 =1 if U is the base at position 4 on the sense strand, otherwise its value is 0;

U 5 =1 if U is the base at position 5 of the sense strand, otherwise its value is 0;

U 6 =1 if U is the base at position 6 of the sense strand, otherwise its value is 0;

U 7 =1 if U is the base at position 7 on the sense strand, otherwise its value is 0;

U 8 =1 if U is the base at position 8 of the sense strand, otherwise its value is 0;

U 9 =1 if U is the base at position 9 on the sense strand, otherwise its value is 0;

U 10 =1 if U is the base at position 10 on the sense strand, otherwise its value is 0;

U 11 =1 if U is the base at position 11 of the sense strand, otherwise its value is 0;

U 12 =1 if U is the base at position 12 of the sense strand, otherwise its value is 0;

U 13 =1 if U is the base at position 13 of the sense strand, otherwise its value is 0;

U 14 =1 if U is the base at position 14 of the sense strand, otherwise its value is 0;

U 15 =1 if U is the base at position 15 on the sense strand, otherwise its value is 0;

U 16 =1 if U is the base at position 16 on the sense strand, otherwise its value is 0;

U 17 =1 if U is the base at position 17 on the sense strand, otherwise its value is 0;

U 18 =1 if U is the base at position 18 on the sense strand, otherwise its value is 0;

U 19 =1 if U is the base at position 19 of the sense strand, otherwise its value is 0;

wherein

(i) when there are nineteen bases present in said sense strand, positions 1-19 are defined relative to the 5′ end of the sense strand, and

(ii) when there are twenty to thirty bases present in said sense strand, positions 1-19 are the 3′ most positions within the sense strand, wherein position 1 is the 5′ most position within said positions 1-19 and position 19 is the 3′ most position within said positions 1-19;

(c) selecting from said set of at least two candidate siRNA sequences, an siRNA sequence for gene silencing based on said predicted relative functionality, wherein a higher value generated by said formula is indicative of greater predicted functionality and said siRNA for gene silencing that is selected has the highest value from within said set of at least two siRNA sequences; and

(d) generating an output comprising said siRNA sequence for gene silencing that is selected, wherein said output is generated by said computer and is in a form that is readable by a user, thereby obtaining said siRNA sequence for gene silencing.

2. The method according to claim 1 , further comprising selecting either for or against sequences that contain motifs that induce cellular stress.

3. The method according to claim 1 , further comprising selecting either for or against sequences that have low or high internal thermodynamic stability.

4. A method of gene silencing, comprising obtaining an siRNA sequence for gene silencing according to the method of claim 1 , synthesizing an siRNA molecule for gene silencing comprising said siRNA sequence for gene silencing and introducing into a cell said siRNA molecule for gene silencing.

5. The method according to claim 4 , wherein said introducing is by allowing passive uptake of the siRNA molecule for gene silencing.

6. The method according to claim 4 , wherein said siRNA molecule for gene silencing is unimolecular.

7. The method according to claim 4 , wherein said siRNA molecule for gene silencing is comprised of two separate polynucleotide strands.

8. The method according to claim 4 , wherein said siRNA molecule for gene silencing is expressed from one or more vectors.

9. The method according to claim 4 , wherein two or more genes are silenced by a single administration of said siRNA molecule for gene silencing.

10. A method for obtaining an siRNA sequence for a target gene, wherein said siRNA sequence comprises 19-30 nucleotide bases, said method comprising the steps:

(a) selecting a target gene;

(b) generating a set of candidate siRNA sequences that are between 19 and 30 bases in length, wherein each of said candidate siRNA sequences comprises a sense region of 19-30 bases, wherein said sense region comprises a sense sequence of 19 bases that is at least 79% similar to a region of the target gene;

(c) accessing a computer and causing said computer to apply a computer program product being embodied in a computer readable storage medium, wherein said computer program product comprises instructions for applying to said set of candidate siRNA sequences a set of one or more criteria selected from the group consisting of

(i) a base other than an A at position 2 of the sense sequence,

(ii) an A base at position 4 of the sense sequence,

(iii) an A base at position 6 of the sense sequence,

(iv) an A base at position 7 of the sense sequence,

(v) an A base at position 8 of the sense sequence,

(vi) a base other than an A at position 9 of the sense sequence,

(vii) a base other than an A at position 12 of the sense sequence,

(viii) a base other than a U at position 2 of the sense sequence,

(ix) a U base at position 3 of the sense sequence,

(x) a base other than a U at position 4 of the sense sequence,

(xi) a U base at position 6 of the sense sequence,

(xii) a base other than a U at position 7 of the sense sequence,

(xiii) a base other than a U at position 8 of the sense sequence,

(xiv) a base other than a U at position 9 of the sense sequence,

(xv) a C base at position 2 of the sense sequence,

(xvi) a C base at position 4 of the sense sequence,

(xvii) a base other than a C at position 6 of the sense sequence,

(xviii) a base other than a C at position 7 of the sense sequence,

(xix) a base other than a C at position 8 of the sense sequence,

(xx) a C base at position 9 of the sense sequence,

(xxi) a C base at position 10 of the sense sequence,

(xxii) a base other than a C at position 12 of the sense sequence,

(xxiii) a G base at position 2 of the sense sequence,

(xxiv) a G base at position 3 of the sense sequence,

(xxv) a base other than a G at position 4 of the sense sequence,

(xxvi) a G base at position 6 of the sense sequence,

(xxvii) a G base at position 7 of the sense sequence,

(xxviii) a G base at position 8 of the sense sequence,

(xxix) a G base at position 9 of the sense sequence,

(xxx) a G base at position 11 of the sense sequence,

(xxxi) a G base at position 12 of the sense sequence,

(xxxii) a G base at position 14 of the sense sequence,

(xxxiii) a G base at position 15 of the sense sequence, and

(xxxiv) a G base at position 16 of the sense sequence;

(d) selecting an siRNA sequence from the set of candidate siRNA sequences of step (b) as a selected siRNA sequence for the target gene, wherein said selected siRNA for the target gene satisfies said one or more criteria, wherein said sense sequence occupies positions 1-19 of the sense region, and wherein when said candidate siRNA sequence is 20-30 bases, bases that are within the sense region that are not within said sense sequence occupy positions − 1 to − 11 of the sense region and positions − 1 to − 11 of the sense region are immediately 5′ of the 5′ end of the sense sequence; and

(e) generating an output comprising said selected siRNA sequence for the target gene, wherein said generating is performed by said computer and said output is in a form that is readable by a user, thereby obtaining said siRNA sequence for the target gene.

11. The method according to claim 10 , wherein in step (c) at least two of said criteria are applied and in step (d) said selected siRNA sequence for the target gene satisfies the at least two of said criteria.

12. The method according to claim 10 , wherein in step (c) at least three of said criteria are applied and in step (d) said selected siRNA sequence for the target gene satisfies the at least three of said criteria.

13. The method according to claim 10 , wherein in step (c) at least four of said criteria are applied and in step (d) said selected siRNA sequence for the target gene satisfies the at least four of said criteria.

14. The method according to claim 10 , wherein in step (c) at least five of said criteria are applied and in step (d) said selected siRNA sequence for the target gene satisfies the at least five of said criteria.

15. The method according to claim 10 further comprising applying at least one additional criteria selected from the group consisting of the presence of A at position 19 of the sense sequence, the presence of A at position 3 of the sense sequence, the presence of U at position 10 of the sense sequence, the presence of A at position 14 of the sense sequence, the absence of C at position 19 of the sense sequence, the absence of G at position 13 of the sense sequence, the absence of U at position 5 of the sense sequence, the absence of A at position 1 of the sense sequence, the presence of A at position 5 of the sense sequence, the absence of A at position 10 of the sense sequence, the absence of A at position 11 of the sense sequence, the presence of A at position 13 of the sense sequence, the absence of A at position 14 of the sense sequence, the presence of A at position 15 of the sense sequence, the presence of A at position 16 of the sense sequence, the presence of A at position 17 of the sense sequence, the presence of A at position 18 of the sense sequence, the absence of U at position 1 of the sense sequence, the absence of U at position 5 of the sense sequence, the absence of U at position 11 of the sense sequence, the presence of U at position 13 of the sense sequence, the absence of U at position 14 of the sense sequence, the absence of U at position 15 of the sense sequence, the absence of U at position 16 of the sense sequence, the presence of U at position 17 of the sense sequence, the presence of U at position 18 of the sense sequence, the presence of U at position 19 of the sense sequence, the presence of C at position 1 of the sense sequence, the absence of C at position 3 of the sense sequence, the absence of C at position 5 of the sense sequence, the presence of C at position 11 of the sense sequence, the absence of C at position 13 of the sense sequence, the absence of C at position 14 of the sense sequence, the absence of C at position 15 of the sense sequence, the absence of C at position 16 of the sense sequence, the absence of C at position 17 of the sense sequence, the absence of C at position 18 of the sense sequence, the presence of G at position 1 of the sense sequence, the absence of G at position 5 of the sense sequence, the absence of G at position 10 of the sense sequence, the absence of G at position 17 of the sense sequence, the absence of G at position 18 of the sense sequence and the absence of G at position 19 of the sense sequence and wherein in step (d) said selected siRNA sequence for gene silencing satisfies the at least one additional criteria.

16. The method according to claim 15 , wherein said at least one additional criteria comprises the presence of A at position 5 of the sense sequence.

17. The method according to claim 10 , wherein the set of one or more criteria includes an A base at position 7 of the sense sequence.

18. The method according to claim 17 , wherein said at least one additional criteria comprises the absence of C at position 3 of the sense sequence.

19. The method according to claim 10 , wherein the set of one or more criteria includes a base other than C at position 6 of the sense sequence.

20. The method according to claim 10 , wherein the set of one or more criteria includes a base other than C at position 7 of the sense sequence.

21. The method according to claim 10 , wherein the set of one or more criteria includes the presence of G at position 14 of the sense sequence.

22. The method according to claim 1 , wherein said output is displayed by a computer.

23. The method according to claim 4 , wherein said output is displayed by a computer.

24. The method of claim 17 , wherein said applying at least one additional criteria comprises applying at least two of said additional criteria.

25. The method of claim 17 , wherein said applying at least one additional criteria comprises applying at least five of said additional criteria.

26. The method of claim 17 , wherein said applying at least one additional criteria comprises applying at least ten of said additional criteria.

27. The method of claim 17 , wherein said applying at least one additional criteria comprises applying at least fifteen of said additional criteria.

28. A method of gene silencing, comprising obtaining an siRNA sequence for gene silencing according to the method of claim 10 , synthesizing an siRNA molecule for gene silencing comprising said siRNA sequence for gene silencing and introducing into a cell said siRNA molecule for gene silencing.

29. A method of gene silencing, comprising obtaining an siRNA sequence for gene silencing according to the method of claim 17 , synthesizing an siRNA molecule for gene silencing comprising said siRNA sequence for gene silencing and introducing into a cell said siRNA molecule for gene silencing.

30. The method according to claim 10 , wherein the sense region is 19 bases in length.

31. The method according to claim 10 , wherein each sense region within said set of candidate siRNAs is 100% similar to said region of said target gene.