Difference between revisions of "Team:SSHS-Shenzhen/Experiments"
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Based on the Phyllotreta striolata transcriptome sequence data provided by Professor Weichang Yu, we selected our target mRNAs, which are the mRNAs of Arginine Kinase, Glutathione S-Transferase and Aldose Reductase. These three genes encode important enzymes that are involved in metabolic pathways. The mRNA sequences for arginine kinase (Fig. 1-1), Glutathione S-Transferase(Fig. 1-2), and Aldose Reductase(Fig. 1-3) were obtained. | Based on the Phyllotreta striolata transcriptome sequence data provided by Professor Weichang Yu, we selected our target mRNAs, which are the mRNAs of Arginine Kinase, Glutathione S-Transferase and Aldose Reductase. These three genes encode important enzymes that are involved in metabolic pathways. The mRNA sequences for arginine kinase (Fig. 1-1), Glutathione S-Transferase(Fig. 1-2), and Aldose Reductase(Fig. 1-3) were obtained. | ||
| + | </p> | ||
| + | |||
| + | <h2> | ||
| + | 2. siRNA and shRNA design | ||
| + | </h2> | ||
| + | <p id="para"> | ||
| + | Based on the Phyllotreta striolata transcriptome sequence data provided by Professor Weichang Yu, we selected our target mRNAs, which are the mRNAs of Arginine Kinase, Glutathione S-Transferase and Aldose Reductase. These three genes encode important enzymes that are involved in metabolic pathways. The mRNA sequences for arginine kinase (Fig. 1-1), Glutathione S-Transferase(Fig. 1-2), and Aldose Reductase(Fig. 1-3) were obtained. | ||
| + | Based on the mRNA sequences, we designed 7 double strand siRNAs and 7 corresponding single strand shRNAs. Factors that affect in vitro transcription efficiency, such as the requirement of a ‘GG’ or ‘GA’ dinucleotide at the start of the transcript; and factors that affect RNAi efficiency, such as distance of target region to transcription start site, nucleotide composition, absence of secondary structures in the target site, and siRNA and the presence of asymmetry and energy valley within the siRNA; were considered during siRNA/shRNA designing. | ||
| + | <br><br> | ||
| + | These criteria include:<br><br> | ||
| + | Target site criteria: <br> | ||
| + | Not being in the first 75 bases from the start codon <br> | ||
| + | Not being in the intron.<br><br> | ||
| + | Nucleotide content of siRNA: <br> | ||
| + | GC content of ~50% GC content. <br> | ||
| + | UU overhangs in 3′-end (increase siRNA stability)<br> | ||
| + | Weak base pairing at 5′-end of the antisense strand (presence of A/U) <br> | ||
| + | Strong base pairing at 5′-end of the sense strand (presence of G/C) <br> | ||
| + | 5′-end of the antisense strand start with C (Insect agoraute2 prefers 5’ C)<br> | ||
| + | Based on these criteria, siRNAs that may target the Phyllotreta striolata genes were designed (Table 2-1).<br> | ||
| + | |||
</p> | </p> | ||
Revision as of 19:38, 23 September 2018
Experimental summary
Short interfering RNAs (siRNAs) and their corresponding shRNAs were designed based on the mRNA sequences of their target genes. siRNAs were synthesized by a bio-company, shRNAs were produced by in vitro transcription. The efficiency of both siRNAs and shRNAs in mediating RNAi in Phyllotreta striolata were examined. Experimental results show that both siRNAs and shRNA could successfully silence their target genes, which was demonstrated by the survival rate decrease after siRNA or shRNA treatment. Results also show that GC percentage of the total siRNA/shRNA, the 5’ end of the siRNA/shRNA, the 3’ end of the siRNA/shRNA affect the RNAi efficiency.
In addition, we tested the attraction effect of sucrose and lemon yellow on P. S. Results show that sucrose plus lemon yellow has the best attraction effect.
Objectives
The objective of our project is to trigger the RNAi mechanism in Phyllotreta striolata, which could lead to the death of the beetle, by topical application of exogenous shRNA/siRNAs.
1. Target mRNA selection
Based on the Phyllotreta striolata transcriptome sequence data provided by Professor Weichang Yu, we selected our target mRNAs, which are the mRNAs of Arginine Kinase, Glutathione S-Transferase and Aldose Reductase. These three genes encode important enzymes that are involved in metabolic pathways. The mRNA sequences for arginine kinase (Fig. 1-1), Glutathione S-Transferase(Fig. 1-2), and Aldose Reductase(Fig. 1-3) were obtained.
2. siRNA and shRNA design
Based on the Phyllotreta striolata transcriptome sequence data provided by Professor Weichang Yu, we selected our target mRNAs, which are the mRNAs of Arginine Kinase, Glutathione S-Transferase and Aldose Reductase. These three genes encode important enzymes that are involved in metabolic pathways. The mRNA sequences for arginine kinase (Fig. 1-1), Glutathione S-Transferase(Fig. 1-2), and Aldose Reductase(Fig. 1-3) were obtained.
Based on the mRNA sequences, we designed 7 double strand siRNAs and 7 corresponding single strand shRNAs. Factors that affect in vitro transcription efficiency, such as the requirement of a ‘GG’ or ‘GA’ dinucleotide at the start of the transcript; and factors that affect RNAi efficiency, such as distance of target region to transcription start site, nucleotide composition, absence of secondary structures in the target site, and siRNA and the presence of asymmetry and energy valley within the siRNA; were considered during siRNA/shRNA designing.
These criteria include:
Target site criteria:
Not being in the first 75 bases from the start codon
Not being in the intron.
Nucleotide content of siRNA:
GC content of ~50% GC content.
UU overhangs in 3′-end (increase siRNA stability)
Weak base pairing at 5′-end of the antisense strand (presence of A/U)
Strong base pairing at 5′-end of the sense strand (presence of G/C)
5′-end of the antisense strand start with C (Insect agoraute2 prefers 5’ C)
Based on these criteria, siRNAs that may target the Phyllotreta striolata genes were designed (Table 2-1).