Is it best to order 5' thiol modifed oligonucleotide in thiol protected form?
The decision to order protected form of a 5' thiol modified oligonucleotide relies on the experiment. In most applications, the thiol will be reduced prior to usage to ensure the unwanted dimers are cleaved. Cross link thiol modified oligonucleotide with a maleimide reactive group, the reduction can actually be done in situ. In that case, there is very little difference. A protected thiol modified oligonucleotide is easier to purify, but it is very difficult to keep it on completely intact.
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08/20/2013