A shRNA Automatic Design
and Selection Tool
During their project, 2016 wet-lab team NJU-China needed a tool that can automatically design shRNA sequence
and select the most appropriate ones according to the given target DNA or mRNA sequence.
Our collaboration can also be seen in the Collaboration site of NJU-China
Demands: In their experiment, they needed to design a shRNA for K-ras in A549. They needed a small tool to design
shRNA with given DNA or mRNA sequence and select the most appropriate ones. The design of shRNA should fulfill
the following 19 requirements.
1. content of G and C should range from 30% to 52%
2. 15th to 19th bases in sense chain should contain at least three A/Us
3. the 19th base in sense chain should be A
4. the 3rd base in sense chain should be A
5. the 10th base in sense chain should be U
6. the 19th base in sense chain should not be G or C
7. the 13th base in sense chain should not be G
8. do not have inverted repeat sequence
9. 5’ end of antisense chain should be A or U
10. 5’ end of sense chain should be G or C
11. first 7 bases of 5’ end in antisense chain should have at least 5 A/Us
12. GC bases should not repeat continuously over 9 times
13. content of A/U in first 3 bases of 3’ end and 5’ end in sense chain should be asymmetric
14. the 1st base in sense chain should be G or C
15. the 6th base in sense chain should be A
16. the 19th base in sense chain should be A or U
17. the 1st base in sense chain should not be U
18. the 19th base in sense chain should not be G
19. number of A/U in first three bases of 3’ end should be at least one more than that of 5’ end
Most importantly, the design shRNA must satisfy at least two points in 14, 15 and 16.
Solution: We wrote a small program with C++. This program asked the user to input their mRNA sequence and it
would generate a series of shRNA sequences with length between 21nt and 23nt. Then the program would check
these sequences how many requirements they satisfied, and ranked them by this number. Download the tool.
Result: NJU-China used our tool and generated the sequence of shRNA targeting to K-ras gene. The predicted se-
quence and its structure was shown in Fig. 1. Their experiment also proved this shRNA could significantly impress
the expression of K-ras in A549 (Fig. 2)
Fig.1 The predicted sequence and structure of this shRNA
Fig. 2 The experiment validate that the designed shRNA performs well
Fig. 3 The result of western blot also expressed shRNA impressed K-ras
From September 2nd to 4th, we helped SYSU-CHINA for their organization of 2016 Sun Yat-sen University Central
China iGEM Consortium in Hedanqing Lecture Hall. 28 iGEM teams around this country and professors from School of
Life Sciences participated in this consortium.
SYSU-CHINA was mainly responsible for this consortium, which consisted of presentation and poster sections, aiming
at simulating the Giant Jamboree. Prof. Yan Zhang and Prof. Junjiu Huang present the opening speech, giving us sincerely
wishes and strengthon our future competition. Senior Haoqian Zhang also shared his experience on iGEM competition
and provide precious advise to us.
During the whole consortium, every iGEM team shared their ideas in their 20 minutes presentation, and their ideas
would be questioned and exchanged in the left 10 minutes by professors and audiences.
For more details please see SYSU-CHINA.
We shared iGEM interlab kits and iGEM plate kits with SYSU-CHINA. During their experiment, their Interlab plasmid
(Device I) can not be transformed well in bacterial culture medium, so we provided our plasmids for them to finish their
Interlab project. SYSU-CHINA also helped us when we used up one of our plate kits (B0015 terminator), and their kindly
help ensured us Interlab project. Reference can be seen in the Collaboration site of SYSU-CHINA