yes it depends on application. in case of antisence oligonucleotides you use synthetic oligonucleotides and deliever to target cells and they selectively bound to the DNA during transcription or to mRNA after transcription. and block the message. in case of RNAi a vector is prepared that express short dsRNA molecules that then processed by the cells invivo and finally single standed RNA bound to the target and block the message. so Oligonucelotides are usually used for short term blocking the message but RNAi used for long term.
now a days mostly RNAi is used to knock down the genes.
Here is a paper discussing the difference between siRNA and two kinds of oligos, phosphorothioates (S-DNA) and Morpholinos.
Summerton J. Morpholino, siRNA, and S-DNA Compared: Impact of Structure and Mechanism of Action on Off-Target Effects and Sequence Specificity. Med Chem. 2007;7(7):651-660 [Only registered users see links. ]
There are two kinds of single-stranded antisense, those that trigger RNase-H activity to cleave the target RNA and those that do not trigger RNase-H and do not cleave their RNA targets.
Summerton J. Morpholino Antisense Oligomers: The Case for an RNase-H Independent Structural Type. Biochimica et Biophysica Acta 1999 1489: 141-158 [Only registered users see links. ]
Anionic oligos can electrostatically complex with delivery agents containing cationic guanidinium moieties, quenching their delivery activity. Uncharged oligos are better suited to delivery by guanidinium-rich delivery moieties such as arginine-rich peptides.
Moulton HM, Moulton JD. Arginine-rich cell-penetrating peptides with uncharged antisense oligomers. Drug Discov Today. 2004 Oct 15;9(20):870.
Morpholinos linked with guanidinium-based delivery moieties (Vivo-Morpholinos) can be delivered by injection into adult rodents, entering cells and then nuclei from the blood.
[Only registered users see links. ]
Also describing Vivo-Morpholinos:
Li YF, Morcos PA. [Only registered users see links. ] Bioconjug Chem. 2008 Jun 20. [Epub ahead of print]
While the Vivo-Morpholinos cannot be expressed by the cells, by administering periodic maintenance doses every few days a knockdown can be maintained over months (we've seen data for 12 weeks of knockdown so far).
As of yet, Vivo-Morpholinos have not been administered intrathecally. Vivo-Morpholinos became available for sale in early 2008.
Last edited by Jon Moulton; 07-02-2008 at 02:30 PM.
Reason: Add link
I have little information about antisense and siRNA.
about antisene synthesis some of them like PNA's have chemical synthesis and they are more stable in enviroment but they only make a barrier to expression but siRNA degrade the desired genes (mechanism).
in addition some antisense have their effects on DNA and some interact with mRNA but siRNA interact with the mRNA and so it interfere with the post transcription phase and like PNA do not interfere with the genes and chromosemes.
About their synthesis, most of the antisense have chemical synthesis and I think you should order your sequence of antisense but about the siRNA we have 3 main method to make our desire siRNA:
1- chemical synthesis ( you must order your sequence)
2- PCR based synthesis, it based on invitro transcription of the desired gene and expose your made mRNA with the recombinant DICER in invitro to make siRNA. ( if you want more information and the advantages of this method I can explain this method in detail.)
3- Vector based synthesis, that make your desired siRNA invivo.
about their application I think siRNA is a new method and have a high specific action and also act on the post transcription phase so have a more a advantages,