Difference between revisions of "Designing and Preparing dsRNA"
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==Preparing dsRNA== | ==Preparing dsRNA== | ||
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===Template Preparation=== | ===Template Preparation=== | ||
*set up a 250 uL PCR reaction | *set up a 250 uL PCR reaction | ||
| − | ** | + | **25 uL 10X KOD buffer |
| − | ** | + | **25 uL dNTPs |
| − | ** | + | **50 uL Primers (sense and antisense combined and diluted to 1 uM. 2 uL of each primer plus 196 uL of water) |
| + | **15 uL MgCl (this can be adjusted to optimize PCR conditions) | ||
**Template (previously prepared PCR product or 1 uL of cDNA) | **Template (previously prepared PCR product or 1 uL of cDNA) | ||
**2 uL KOD polymerase | **2 uL KOD polymerase | ||
| − | **Water | + | **132uL Water (bring up to 250 uL) |
**Run using TD-KOD program | **Run using TD-KOD program | ||
*transfer PCR product to a clean tube. Add 25 uL of 3M NaAcetate (pH 5.2) and 500 uL ice cold ethanol (stored at -20). | *transfer PCR product to a clean tube. Add 25 uL of 3M NaAcetate (pH 5.2) and 500 uL ice cold ethanol (stored at -20). | ||
| Line 39: | Line 38: | ||
*Dilute RNA 10x in loading dye | *Dilute RNA 10x in loading dye | ||
*Load 1 and 3 uL of diluted RNA, plus 4 or 8 uL of 1 kB Plus DNA Ladder | *Load 1 and 3 uL of diluted RNA, plus 4 or 8 uL of 1 kB Plus DNA Ladder | ||
| − | *Using ImageJ, quantify ladder and dsRNA bands and calculate concentration. Check that the dilutions are close to 3x apart in signal intensity. | + | *Using ImageJ, quantify ladder and dsRNA bands and calculate concentration. See [[Using ImageJ to Quantify Bands]]. Check that the dilutions are close to 3x apart in signal intensity. |
*Label RNA with concentration and store at -20 | *Label RNA with concentration and store at -20 | ||
| + | |||
| + | *see PMID 18388942, PMID 18265350 , PMID 11752672 and http://www.flyrnai.org/DRSC-PRS.html | ||
Latest revision as of 14:31, 1 October 2009
Ordering dsRNA Primers
- If available, choose primers from Harvard DSRC site http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl
- Add T7 RNA Polymerase sites to the 5' of each primer (TAATACGACTCACTATAGG)
- Record primer and amplicon (DSRC)
Preparing dsRNA
Template Preparation
- set up a 250 uL PCR reaction
- 25 uL 10X KOD buffer
- 25 uL dNTPs
- 50 uL Primers (sense and antisense combined and diluted to 1 uM. 2 uL of each primer plus 196 uL of water)
- 15 uL MgCl (this can be adjusted to optimize PCR conditions)
- Template (previously prepared PCR product or 1 uL of cDNA)
- 2 uL KOD polymerase
- 132uL Water (bring up to 250 uL)
- Run using TD-KOD program
- transfer PCR product to a clean tube. Add 25 uL of 3M NaAcetate (pH 5.2) and 500 uL ice cold ethanol (stored at -20).
- Incubate on ice for >20 min.
- Centrifuge 5 min at 4C on high in eppendorf centrifuge.
- Carefully aspirate supernatant. Add 1 mL 70% ethanol and centrifuge again.
- Aspirate supernatant and let pellet air dry.
- Resuspend in 20 uL EB and measure concentration by nanodrop.
RNA Synthesis
- Prepare RNA synthesis reaction (RiboMAX Large Scale RNA Preparation Kit):
- 20 uL T7 Buffer
- 30 uL rNTPs (prepare by combining equal volmes of rNTP together)
- 10 uL Enzyme mix
- 10 ug PCR product
- water to bring volume up to 100 uL
- Place in PCR machine and incubate overnight at 37C (37 hold program)
Quantify RNA
- Dilute RNA 10x in loading dye
- Load 1 and 3 uL of diluted RNA, plus 4 or 8 uL of 1 kB Plus DNA Ladder
- Using ImageJ, quantify ladder and dsRNA bands and calculate concentration. See Using ImageJ to Quantify Bands. Check that the dilutions are close to 3x apart in signal intensity.
- Label RNA with concentration and store at -20
