Cloning and sequencing

Cloning hairpins into VALIUM or WALIUM vectors

Prepared by Jian-Quan Ni, Matt Booker, Norbert Perrimon*

*Questions?  Contact Jian-Quan Ni at

For VALIUM10 (or WALIUM10)

Click here to download pdf

1. Oligo design

The TRiP oligos were designed using SnapDragon with the following criteria:

    1. Product size was set to 400 to 600 bp
    2. 19 bp predicted off-targets were avoided
    3. Only splice-form universal portions of each gene were selected for oligo design

2. PCR

Forward primer  20uM 0.5ul
Reverse primer  20uM 0.5ul
DNA Template (make sure to use genomic DNA or cDNA) 1ul
Taq polymerase mix (Promega, Cat No. M7122) 12.5ul
Add ddH2O to 25ul total volume

Once the PCR finishes (30 Cycles), load 10ul onto an agarose gel to verify the quality and quantity of the PCR product. If multiple bands are seen, cut out the relevant band and purify it.

3. TOPO Ligation

PCR product (there’s no need for purification) 1ul
pENTR/D-TOPO entry vector (Invitrogen, Cat.No. K240020) 1ul
Salt Solution (1.2M NaCl, 0.06M MgCl2) 1ul
Add ddH2O to 6ul total volume

Mix, incubate at room temperature for 10 min

4. Transformation

Transfer all ligation mix to 50ul TOP10 cells, place on ice for 30 min, heat shock, add SOC medium and incubate at 37°C for 50 min, then plate (Kan resistant).

5. Select clone, culture in LB medium (Kan resistant) and miniprep.

6. Sequence pENTR/D-TOPO entry vector to ensure the insertion and its orientation is correct; i.e., 3’ to 5’.

Oligo used for sequencing, M13-F: 5’-TTGTAAAACGACGGCCAGTC-3’

7. Recombination

45-85ng/ul pENTR/D-TOPO entry vector (from step 5) 0.3ul
200ng/ul VALIUM10 (or WALIUM10) 0.3ul
LR clonase (Invitrogen, Cat No. 11791-100) 0.8ul
Add ddH2O (or TE buffer, pH8.0) 4ul total volume

Mix, incubate at 25°C for 1 hr, and then add 1ul proteinase K (From LR clonase kit), further incubate at 37°C for 10 min to remove the recombinase.


Recombination product  5ul
TOP10 competent cells 50ul

Mix, incubate on ice 30 min, 42°C heat shock, add SOC medium, incubate at 37°C for 30 min, then plate (Amp resistant)

9. Select clone, culture in 5ml LB medium (Amp resistant) and miniprep At end elute with 100ul ddH2O.

10. Sequence hairpin construct to confirm the ftz intron is in the correct orientation (in our experience: 40-60% of the clones are correct).

Primer used for DNA sequencing, Hsp70F: 5'-CGCAGCTGAACAAGCTAAAC-3'

11. Precipitation (DNA from step 9)

DNA 90ul
3M NaAc, pH5.2 10ul
EtOH 500ul

Mix, -20°C for 1 hr

12. Centrifuge (15,000 rpm, 20 min), wash once with 70% EtOH, and dissolve in 40ul ddH2O

13. Construct is ready for injection

Note: The only difference between VALIUM10 and WALIUM10 is their selectable eye color marker; VALIUM10 uses Vermilion, WALIUM10 uses White.


Click here to download pdf

1. Oligo design:

Select a 21nucleotide sequence based on the algorithm of Vert et al. (2006). This oligo design eliminates off target effects starting at 16 nucleotides.

Based on a miR1 scaffold, for the top strand oligo, add ctagcagt to the 5’ end of the passenger strand DNA, add tagttatattcaagcata between the passenger strand DNA and the guide strand DNA, add gcg to the 3’ end of guide strand DNA, so the resulting oligo will be:


For the bottom strand oligo, add aattcgc to the 5’ end of the passenger strand DNA, add tatgcttgaatataacta between the passenger strand DNA and the guide strand DNA, add actg to the 3’ end of the guide strand DNA, so the resulting oligo will be:


2. Annealing the top and bottom strand oligos:

Add 10ul top strand oligo (10-20uM) and 10ul bottom strand oligo (10-20uM) into 80ul annealing buffer (10mM Tris-HCl, pH 7.5, 0.1M NaCl, 1mM EDTA).

Mix, incubate at 95ºC for 5 min, then slowly cool down to room temperature.

The resulting DNA fragment has overhangs for NheI and EcoRI.

3. Ligation:

Directly clone this DNA fragment into a VALIUM20 or VALIUM22 vector, which has been linearized by NheI and EcoRI.

6ul annealing product 2ul 10X ligation buffer

1ul T4 DNA ligase (1U/ul)

1ul  40ng/ul backbone (gel purified VALIUM20 or VALIUM22 cut with NheI and EcoRI)

Add ddH2O to 20ul total volume.

Mix, incubate at 16oC for 1 hour.

4. Transformation:

Add 10ul ligation product into 50ul TOP10 competent cells, following standard transformation protocol.

5. Colony selection:

PCR select the correct clone by appearance of a 350bp PCR product using the following PCR primers:


6. Sequencing:

Confirm the correct shRNA construct using the following sequencing primers:



7. DNA miniprep and injection.

Sequencing TRiP lines to test for the presence of a VALIUM insertion

For VALIUM1, the primers are:



For VALIUM10, the primers are:



For VALIUM20 and VALIUM21 the primers are:



For VALIUM22 the primers are: