Can an entire 110bp shRNA sequence be synthesized with the XhoI/EcoRI sites to be cloned into pSM2, pSMP, LMP, TMP or pTRIPZ?
Yes, it can. If you are going to have the whole hairpin sequence synthesized (instead of just the 97-mer and then using primers separately to add XhoI and EcoRI as outlined in the Paddison paper) there are two things that you need to be aware of:
1) With an oligo that long, the error rate can be higher for synthesis. Check the error rate of the company that you use. We have used IDT in the past for this kind of application (called ultramers).
2) You can have the sequence synthesized with the restriction site overhangs (so that you don’t have to restriction digest the oligo). You can either ask the synthesis company to phosphorylate the 5' end or you can purchase a kit from NEB to phosphorylate the ends your self with polynucleotide kinase. They will ship the oligo to you in two tubes (one for each strand) and then provide a protocol for melting and annealing the two together so that you can clone it into the vector backbone.
** Please note the TMP/LMP vectors have been discontinued