sh-mir designer2013.igem.org › files › poster › amu-poznan.pdf · 2013-11-18 · 1.structure...

Input:One strand or two strands in 5'-3' orientation of siRNA of known efficiency

Concatenation of both given siRNA strands (or one given strand and one added) with flanking sequences and loop sequence of pri-miRNA (caps) taken from created pri-miRNA database.

Analysis of sh-miRNA structure with mfold program. Comparison with structure of endogenous pri-miRNAs

aggcaagaugcuggcauagcuugcuaugccaacauauugccau

CAUAACAACGAAGAGGGAUGGUAUUGCUCCUGUAACUCGGAACUGGAGAGGaggcaagaugcuggcauagcuGUUGAACUGGGAACCugcuaugccaacauauugccauCUUUCCUGUCUGACAGCAGCUUGGCUACCUCCGUCCUGUUCCUCCUUGUCUU

sh-miR Designer is a so�ware aimed for fast and efficient design of effec�ve RNA interference (RNAi) reagents - sh-miRs, also known as ar�ficial miRNAs. sh-miRs are RNA par�cles whose structure is based on miRNA precursor pri-miRNA, but sequence interac�ng with transcript is changed depending on research purpose. Maintenance of structure of pri-miRNA is very important to enable cellular processing (performed mainly by endonucleases Drosha and Dicer) and therefore ensure func�onality of ar�ficial par�cles. sh-miRs delivered to cells on gene�c vectors - plasmids or viral vectors - enter natural RNAi pathway and silence target mRNA. They can be used in gene�c therapies and basic biomedical research.

pri-miRNAdatabase

Scoring:1.Structure2.Same first nucleotides of siRNA and miRNA sequence3.Endogenous pri-miRNA product homogeneity (isomirs)

Output:2-3 sh-miRs with best scoring results ordered from the best onepdf with 2D structureweb link to miRbase site of pri-miRNA, which flanking sequences where used

'name': name, 'flanks3_s': flanks3_s, 'flanks3_a': flanks3_a, 'flanks5_s': flanks5_s, 'flanks5_a': flanks5_a, 'loop_s': loop_s, 'loop_a': loop_a, 'miRNA_s': miRNA_s, 'miRNA_a': miRNA_a, 'miRNA_length': miRNA_length, 'miRNA_min': miRNA_min, 'miRNA_max': miRNA_max, 'miRNA_end_5': miRNA_end_5, 'miRNA_end_3': miRNA_end_3, 'structure': structure, 'homogeneity': homogeneity, 'miRBase_link': miRBase_link

155 pri-miRNA

AG

G

C

UU

G

C

UG

U

A

G

G

C

U

G

U

A

U

G

C

U

G

U

U

U

G

U

A

U

U

C

A

G

C

C

C

A

U

A

G

C

G

C

U

U

U

U

G

CC U

C

C

A

A

C

UG

G

C

G

C

U

A

U

G

G

C

G

A

A

U

A

C

A

A

A

C

A

G

U

G

U

A

UGA

UG

C

C

U

GU

U

A

CU

A

G

C

A

U

U

C

A

C

A

U

G

GA

A

C

A

AAU

U

GC

U

G

C

C

G

U

G

G

G

A

GGAUGA

CA

A

A

G

A 5’3’

20

40

60

80

100

120

140

AG G

C

UU

G

C

UG

U

A

G

G

C

U

G

U

A

U

G

C

U

G

U

U

A

A

U

G

C

U

A

A

U

C

G

U

G

A

U

A

G

G

G

G

U

U

U

U

G

CC U

C

C

A

AC

UG

A

C

U

C

C

U

A

C

A

U

A

U

U

A

G

C

A

U

U

A

A

C

A

G

U

G

U

A

UGA

UG

C

C

U

G

U

U

A

CU

A

G

C

A

U

U

C

A

C

A

U

G

G

A

A

C

A

AAU

U

GC

U

G

C

C

G

U

G

G

G

A

GGAUG

AC

A

A

A

G

A 5’

3’

20

40

60

80

100

120

140

Drosha cut

sh-miR designer

Dicer cut

tool for construction of RNA interference reagents: sh-miRs

sh-miRNA with siRNA targeted on luciferase transcriptin 155 pri-miRNA flansking sequence