Construction of pool of interfering nucleic acids covering entire RNA target sequence and related compositions

• US 9,944,928 B2
• Filed: 07/02/2015
• Issued: 04/17/2018
• Est. Priority Date: 07/23/2007
• Status: Active Grant

• Current Assignee: York YuanYuan Zhu
• Original Assignee: York Yuan Yuan Zhu
• Inventors: Zhu, York Yuan Yuan
• Primary Examiner(s): Shin, Dana H
• Application Number:
  US14/791,157
• Publication Number:
  US 20150299707A1
• Time in Patent Office: 1,020 Days
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2330/31 Libraries, arrays
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: C40B 50/06 Biochemical methods, e.g. using enzymes or whole viable microorganisms

Abstract

The present invention provides a PCR based high-throughput method for preparing full-sites siRNA polynucleotide pool, comprising: DNase I random digestion; Loop-1 phosphate linker ligation; single PCR amplification; a type III restriction/modification enzyme digestion; blunt ending; Loop-2 phosphate linker ligation; double primer PCR; FokI digestion and cloning into an siRNA expression vector. The present invention enables the use of a type III restriction/modification enzyme linkers mediated PCR method for high-throughput preparing an siRINA polynucleotide pool, in which the functional length of siRNAs can be controllably distributed from 19-23 bp, thus completely mimic the natural siRNA length diversity, specially suitable for RNAi therapeutic targets screening. The present invention overcomes the bottlenecks and drawbacks of conventional siRNA polynucleotide pool construction technologies.

Claims

1. A DNA duplex comprising a sense strand and an antisense strand, wherein the sense strand comprises a first flanking segment, a middle segment, and a second flanking segment, and the antisense strand comprises a first flanking segment, a middle segment, and a second flanking segment, wherein:

each strand and segment independently has a 5′

end and a 3′

end;

the 3′

end of the first flanking segment of the sense strand and the 5′

end of the middle segment of the sense strand are ligated;

the 3′

end of the middle segment of the sense strand and the 5′

end of the second flanking segment of the sense strand are ligated;

the 3′

end of the first flanking segment of the antisense strand and the 5′

end of the middle segment of the antisense strand are ligated;

the 3′

end of the middle segment of the antisense strand and the 5′

end of the second flanking segment of the antisense strand are ligated;

the middle segment of the sense strand and the middle segment of the antisense strand are complementary and form a duplex that comprises 100-300 base pairs;

the first flanking segment of the sense strand and the second flanking segment of the antisense strand are complementary and form a duplex that comprises;

(a) a first type III restriction enzyme recognition site,

(b) a first poly-A sequence in the sense strand having at least four deoxyadenosine (A) nucleotides, wherein the first poly-A sequence is disposed between the first type III restriction enzyme recognition site and the 5′

end of the middle segment of the sense strand, and is directly linked to the first type III restriction enzyme recognition site, and

(c) a first type II restriction enzyme recognition site nucleotide sequence in the first flanking segment of the sense strand, wherein the first type III restriction enzyme recognition site is disposed between the first type II restriction enzyme recognition site and the first poly-A sequence;

the second flanking segment of the sense strand and the first flanking segment of the antisense strand are complementary and form a duplex that comprises;

(a) a second type III restriction enzyme recognition site,

(b) a second poly-A sequence in the antisense strand having at least four deoxyadenosine nucleotides, wherein the second poly-A sequence is disposed between the second type III restriction enzyme recognition site and the 5′

end of the middle segment of the antisense strand, and is directly linked to the second type III restriction enzyme recognition site and

(c) a second type II restriction enzyme recognition site nucleotide sequence in the first flanking segment of the antisense strand, wherein the second type III restriction enzyme recognition site is disposed between the second type II restriction enzyme recognition site and the second poly-A sequence; and

the first type III restriction enzyme recognition site and the second type III restriction enzyme recognition site are inversely oriented and configured head to head.

2. The DNA duplex of claim 1, wherein the first and second type III restriction enzyme recognition sites are each EcoP15I or EcoP15 recognition sites.

3. The DNA duplex of claim 1, wherein the first and second poly-A sequences each consist of 4, 5, 6, or 7 deoxyadenosine nucleotides.

4. The DNA duplex of claim 3, further comprising:

(a) a deoxyguanosine nucleotide disposed between the first poly-A sequence and the 5′

end of the middle segment of the sense strand, and (b) a deoxyguanosine nucleotide disposed between the second poly-A sequence and the 5′

end of the middle segment of the antisense strand.

5. The DNA duplex of claim 1, wherein the first and second type II restriction enzyme recognition sites are each FokI recognition sites.

6. The DNA duplex of claim 5, wherein the first and second type III restriction enzyme recognition sites are each EcoP15I or EcoP15 recognition sites.

7. The DNA duplex of claim 1, further comprising:

(a) 0, 1, 2, 3, or 4 base pairs disposed between the first type II restriction enzyme recognition site and the first type III restriction enzyme recognition site; and

(b) 0, 1, 2, 3, or 4 base pairs disposed between the second type II restriction enzyme recognition site and the second type III restriction enzyme recognition site.

8. The DNA duplex of claim 7, wherein:

(a) the first flanking segment of the sense strand comprises;

(i) the first poly-A sequence consisting of X₁ deoxyadenosine nucleotides, wherein X₁ is 4, 5, 6, or 7;

(ii) Y₁ deoxyguanosine nucleotides disposed between the first poly-A sequence and the 5′

end of the middle segment, wherein Y₁ is 0 or 1; and

(iii) Z₁ base pairs disposed between the first type II restriction enzyme recognition site and the first type III restriction enzyme recognition site, wherein Z₁ is 0, 1, 2, 3, or 4; and

wherein X₁+Y₁+Z₁=8; and

(b) the first flanking segment of the antisense strand comprises;

(i) the second poly-A sequence consisting of X₂ deoxyadenosine nucleotides, wherein X₂ is 4, 5, 6, or 7;

(ii) Y₂ deoxyguanosine nucleotides disposed between the first poly-A sequence and the 5′

end of the middle segment, wherein Y₂ is 0 or 1; and

(iii) Z₂ base pairs disposed between the second type II restriction enzyme recognition site and the second type III restriction enzyme recognition site, wherein Z₂ is 0, 1, 2, 3, or 4; and

wherein X₂+Y₂+Z₂=8.

9. The DNA duplex of claim 1, having two ends, wherein each end comprises a hairpin loop.

10. The DNA duplex of claim 9, wherein each hairpin loop comprises a duplex stem of 25 base pairs, and each of:

the first or second type III restriction enzyme recognition sites, the first or second poly-A sequences, and the first or second type II restriction enzyme recognition sites of the DNA duplex are located outside of the duplex stem of the hairpin loop.

12. The DNA duplex of claim 1, wherein:

the first flanking segment of the sense strand comprises SEQ ID NO;

80 and the second flanking segment of the antisense strand comprises SEQ ID NO;

79;

the first flanking segment of the sense strand comprises SEQ ID NO;

72 and the second flanking segment of the antisense strand comprises SEQ ID NO;

71;

the first flanking segment of the sense strand comprises SEQ ID NO;

74 and the second flanking segment of the antisense strand comprises SEQ ID NO;

73;

the first flanking segment of the sense strand comprises SEQ ID NO;

76 and the second flanking segment of the antisense strand comprises SEQ ID NO;

75;

or

the first flanking segment of the sense strand comprises SEQ ID NO;

78 and the second flanking segment of the antisense strand comprises SEQ ID NO;

77.

13. The DNA duplex of claim 1, wherein:

the first flanking segment of the sense strand comprises SEQ ID NO;

26 and the second flanking segment of the antisense strand comprises SEQ ID NO;

25;

the first flanking segment of the sense strand comprises SEQ ID NO;

28 and the second flanking segment of the antisense strand comprises SEQ ID NO;

27;

the first flanking segment of the sense strand comprises SEQ ID NO;

30 and the second flanking segment of the antisense strand comprises SEQ ID NO;

29;

the first flanking segment of the sense strand comprises SEQ ID NO;

32 and the second flanking segment of the antisense strand comprises SEQ ID NO;

31;

or

the first flanking segment of the sense strand comprises SEQ ID NO;

34 and the second flanking segment of the antisense strand comprises SEQ ID NO;

33.

14. The DNA duplex of claim 13, wherein the middle segment of the sense strand and the middle segment of the antisense strand are complementary and form a duplex that comprises 100-300 base pairs derived from a full-length cDNA of a SARS coronavirus membrane protein.

15. The DNA duplex of claim 1, wherein the middle segment of the sense strand and the middle segment of the antisense strand are complementary and form a duplex that comprises 100-300 base pairs derived from a full-length cDNA of a SARS coronavirus membrane protein.

16. The DNA duplex of claim 1, wherein the first and second type III restriction enzyme recognition sites are identical, and the first and second type II restriction enzyme recognition sites are identical.

11. A DNA duplex comprising a sense strand and an antisense strand, wherein the sense strand comprises a first flanking segment, a middle segment, and a second flanking segment, and the antisense strand comprises a first flanking segment, a middle segment, and a second flanking segment, wherein:

each strand and segment independently has a 5′

end and a 3′

end;

the 3′

end of the first flanking segment of the sense strand and the 5′

end of the middle segment of the sense strand are ligated;

the 3′

end of the middle segment of the sense strand and the 5′

end of the second flanking segment of the sense strand are ligated;

the 3′

end of the first flanking segment of the antisense strand and the 5′

end of the middle segment of the antisense strand are ligated;

the 3′

end of the middle segment of the antisense strand and the 5′

end of the second flanking segment of the antisense strand are ligated; and

wherein;

(a) the middle segment of the sense strand and the middle segment of the antisense strand are complementary and form a duplex that comprises 100-300 base pairs;

(b) the first flanking segment of the sense strand and the second flanking segment of the antisense strand are complementary and form a duplex that comprises;

(i) a first FokI recognition site;

(ii) a first EcoP15I or EcoP15 recognition site; and

(iii) a first poly-A sequence in the sense strand having X₁ nucleotides, wherein X₁ is 4, 5, 6, or 7;

wherein the first EcoP15I or EcoP15 recognition site is disposed between the first FokI recognition site and the first poly-A sequence, and the first poly-A sequence is disposed between the first EcoP15I or EcoP15 recognition site and 5′

end of the middle segment of the sense strand, and is directly linked to the first EcoP15I or EcoP15 recognition site,

(iv) Y₁ deoxyguanosine nucleotides disposed between the first poly-A sequence and the 5′

end of the middle segment of the sense strand, wherein Y₁ is 0 or 1,

(v) Z₁ base pairs disposed between the first FokI recognition site and the first EcoP15I or EcoP15 recognition site,

wherein X1+Y1+Z1=8; and

(c) the second flanking segment of the sense strand and the first flanking segment of the antisense strand are complementary and form a duplex that comprises;

(i) a second FokI recognition site;

(ii) a second EcoP15I or EcoP15 recognition site; and

(iii) a second poly-A sequence in the antisense strand having X₂ nucleotides, wherein X₂ is 4, 5, 6, or 7;

wherein the second EcoP15I or EcoP15 recognition site is disposed between the second FokI recognition site and the second poly-A sequence, and the second poly-A sequence is disposed between the second EcoP15I or EcoP15 recognition site and the 5′

end of the middle segment of the antisense strand, and is directly linked to the second EcoP15I or EcoP15 recognition site ; and

(iv) Y₂ deoxyguanosine nucleotides disposed between the first poly-A sequence and the 5′

end of the middle segment of the antisense strand, wherein Y₂ is 0 or 1,

(v) Z₂ base pairs disposed between the second FokI recognition site and the second EcoP15I or EcoP15 recognition site,

wherein X₂+Y₂+Z₂=8.