Frank Wellmer
Meyerowitz lab,
Caltech Last
update: Feb. 2004
RNA amplification and labeling of RNA probes
This
protocol generates dye-labeled antisense RNA probes for microarray
hybridizations. In a first step polyA-RNA is amplified by in vitro transcription (according to Eberwine and
collaborators). During in vitro
transcription aminoallyl-UTP is incorporated into the newly synthesized RNA.
NHS-ester dyes are then directly coupled to the modified bases in a simple
chemical reaction.
METHOD:
Protect
all dye-containing solutions from light to prevent photo bleaching. We are
using total RNA purified on Qiagen RNeasy columns as starting material but
other RNA isolation methods may work as well.
1: Mix: Total
RNA 3-10
mg
Control
RNA (optional) x
ml
RNase-free
H2O to
12 ml
2: Incubate at 70ÁC for 10 min. Quick-chill on ice. Collect the contents
of the tube by quick centrifugation.
3: Add: 5X
First Strand Buffer 4
ml
0.1
M DTT 2
ml
dNTP-mix
(10 mM each) 1
ml
4: Incubate at 37ÁC for 2 min to equilibrate the temperature.
5: Add 1 ml of Superscript II and mix gently.
Final
volume of the 1st strand reaction: 20 ml
6: Incubate at 37ÁC for 1 hour. Put on ice.
7: Second strand synthesis.
Add: H2O 92
ml
5X
Second Strand Buffer 30
ml
dNTP-mix
(10 mM each) 3
ml
E.coli DNA Polymerase I 4
ml
E.coli RNase H 1
ml
8: Incubate at 16ÁC for 2 hours. Do not let the temperature rise above
16ÁC.
9: Add 10 ml of 0.5 M EDTA to stop the reaction.
1: Transfer reaction mix into a phase-lock gel tube
(spin tubes briefly before use to collect the gel on the bottom).
2: Add 160 ml of phenol:chloroform:isoamyl alcohol (25:24:1). Mix
thoroughly, but do not vortex. Spin 5 min at 14k rpm (12,000-16,000 x g).
3: Pipet off aqueous layer and place in a fresh tube.
4: Add an equal volume (~ 160 ml) of 5M NH4OAcetate.
5: Add 2.5x volumes of 100% EtOH (~ 800 ml). Add 1 µl of Linear Polyacrylamide. Mix and spin
for 5 min at 14k rpm, RT.
6: Remove supernatant carefully and wash pellet with 500
ml of 80% EtOH. Do not
vortex.
7: Spin for 5 min at 14k rpm.
8: Repeat the wash step.
9: Dry pellet in a speed-vac.
10: Resuspend pellet in 10 ml of RNase-free H2O.
Use
AmbionÍs Megascript T7 kit and aminoallyl-UTP. Set up reaction at room
temperature.
1: Mix the following:
RNase-free H2O 2.5
ml
ATP solution (75 mM) 2
ml
GTP
solution (75 mM) 2
ml
CTP
solution (75 mM) 2
ml
UTP
solution (75 mM) 1
ml
aa-UTP
solution (50 mM) 1.5
ml
10X
reaction buffer 2
ml
cDNA
from previous step 5
ml
FINAL
VOLUME: 20ml
2: Incubate the reaction at 37ÁC for 6 hours to overnight.
3: Clean up the RNA on a Qiagen RNeasy column:
-
Add 80 ml of RNase-free water
-
Add 350 ml of buffer RLT to the sample (add b-ME to buffer RLT before use; 10 ml b-ME / 1 ml buffer).
-
Add 250 ml 100% EtOH to the sample. Mix well by pipetting.
-
Transfer sample (700 ml) to an RNeasy mini spin column.
-
Centrifuge for 15 sec at
full speed.
-
Reload column with flow-through
and spin for 15 sec at full speed. This step may increase the RNA yield.
-
Transfer RNeasy column
to a new 2-ml collection tube (supplied in kit)
-
Add 500 ml of phosphate wash buffer. (DonÍt use QiagenÍs buffer RPE since it
contains Tris that might interfere with the labeling reaction). Centrifuge for
15 sec at 14 k (>8,000 x g), and discard flow-through
-
Pipet 500 ml of phosphate wash buffer onto the column. Centrifuge for 2 min at
maximum speed. Discard flow-through.
-
Centrifuge at full speed
for 1 min.
-
Transfer RNeasy column
into a 1.5 ml collection tube.
-
Add 30 ml of RNase-free water directly onto the RNeasy membrane.
-
Centrifuge for 1 min at
full speed.
-
Repeat elution step with
another 30 ml of water, into the same collection tube. Final
volume: 50-60 ml.
4: Run 2 ml of the RNA on a 1% agarose gel or run an aliquot on
a Bioanalyzer. Determine RNA concentration and calculate total yield. The
transcription reaction should result in at least 30-50 mg of RNA. Store RNA at Ü80oC until use.
Important: Make sure, to never over-dry the RNA in the following
steps. Precipitated RNA will appear as colored speckles on the membrane of the
RNeasy column after elution.
1: Dry down 5-10 mg of RNA in a
speed-vac to 3 ml.
2: Add 1 ml of 0.4 M Na2CO3
pH 8.5. Vortex vigorously to resuspend any precipitated RNA.
3: Add 4 ml of dye solution,
mix by vortexing and incubate for 1 h in the dark.
4: Add 92 ml of RNase-free
water and purify RNA on an RNeasy column as described above. Use buffer RPE for
the wash steps. Elute twice with 30 ml of RNase-free
water.
Check
the membrane for colored speckles (see above).
5: Measure dye incorporation and RNA recovery by
spectrophotometry: Dilute 4 ml of the eluate into 46 ml of water and analyze the sample in a spectrophotometer using a
micro-cuvette. For Cy3-containing samples measure the absorbance at 260 and 550
nm and for Cy5 at 260 and 650 nm. Calculate the dye incorporation as follows:
dye
molecules per 1000 nt= (Adye/A260)‡(9010 cm-1M-1/edye)‡1000
with
eCy3= 150,000
cm-1M-1 and eCy5= 250,000 cm-1M-1.
The
labeling reaction normally incorporates 25-50 dye molecules per 1000 nt.
1: Combine the labeled RNAs of a sample pair (~110 ml). Dry down RNA solution to 9 ml in a speed-vac. To
avoid over-drying, take the tubes out of the speed-vac a few time during the drying
procedure and vortex them thoroughly.
Add
1 ml of 10X fragmentation buffer (Ambion) and mix by
vortexing. Incubate at 70oC for exactly 10 min. Vortex the
tubes for a few seconds. Put tubes on ice and add 1 ml of stop buffer.
Note: This method generates RNA fragments <200 nt (peak at ~85 nt).
2: Add 20
ml of RNase-free water to the sample.
-
Pre-spin a Spin-50
column in a microcentrifuge at 1000 g
for 3 min. Empty collection tube.
-
Add 500 ml of RNase-free water to the column and spin column in a
microcentrifuge at 1000 g for 3
min.
-
Discard collection tube
and transfer column to an amber tube.
-
Load RNA sample onto the
center of the column. Spin column in a microcentrifuge at 1000 g for 3 min.
3: Continue with the hybridization protocol for RNA
probes.
Invitrogen:
E.coli Ribonuclease H (Cat. No. 18021071); 120 units, enough
for 60 rxns
E.coli DNA Polymerase I (Cat. No.18010025); 1000 units,
enough for 25 rxns
Superscript II (Cat.
No.18064071); 4x10,000 units, enough for 200 rxns
dNTP set (100 mM) (Cat. No.
10297018)
Ambion:
Megascript T7 kit (Cat. No.
1334), enough for 40 rxns
Fragmentation reagents (Cat.
No. 8740), enough for 200 rxns
Aminoallyl-UTP (Cat. No.
8437), enough for 33 rxns
Amersham:
Cy3 Mono-Reactive Dye Pack
(Cat. No. PA23001)
Cy5 Mono-Reactive Dye Pack
(Cat. No. PA25001)
Eppendorf:
Phase Lock Tubes, Gel Light
(200), 1.5 ml tubes (Cat. No. 0032 007.961)
Qiagen:
RNeasy Mini Kit (250) (Cat.
No. 74106)
Sigma:
Linear Polyacrylamide (Cat.
No. 5-6575)
USA Scientific:
Spin-50 Mini-Column (Cat. No.
1415-1602)
Various sources:
T7dT primer (PAGE purified):
5Í- TCT AGT CGA CGG CCA GTG
AAT TGT AAT ACG ACT CAC TAT AGG GCG TTT TTT TTT TTT TTT TTT TTN N-3Í
Phenol:chloroform:isoamyl
alcohol (25:24:1).
5x Second Strand Buffer
(store at -20ÁC):
100 mM Tris-HCl pH 6.9
450 mM KCl
23 mM MgCl2
50 mM (NH4)SO4
0.75 mM b-NAD+
0.1 M Na2CO3
pH 8.5:
Prepare fresh buffer every
3-4 weeks. Make up with RNase-free water.
Phosphate Wash Buffer:
Prepare: 1 M K2HPO4
and 1 M KH2PO4 solutions using RNase-free water.
Mix 9.5 ml of 1 M K2HPO4
and 0.5 ml of 1 M KH2PO4 to generate 1 M KPO4
pH 8.5 buffer.
For 100 ml of wash buffer
mix:
0.5
ml 1 M KPO4 pH 8.5
80 ml 100% ethanol
19.5 ml RNase-free water
Cy-dye
solutions (store at -20ÁC protected from light):
Resuspend the dried dye of
one vial in 73 ml of DMSO. Avoid repeated thawing of the dye
solutions.