Chain Terminators

In situations where ligation must be blocked at the 5’ terminus, 5’-OMe-dT may be used.  5’-OMe modification of a strand of siRNA using 5’-OMe-T can control guide strand selection and targeting specificity.1   5’-Amino-dT terminates an oligonucleotide with a 5’-amino group which may be used for attaching a peptide or a PNA sequence.  To avoid polymerase extension at the 3’ terminus, 2’,3’-dideoxynucleoside and 3’-deoxynucleoside CPGs have proved to be effective.  2’,3’- Phosphoramidites are designed to be used with the 5’-phosphoramidites and supports.  Since these phosphoramidites have no DMT group, they are not compatible with purification by the DMT-on technique.  Ion exchange HPLC or PAGE should be used to purify these dideoxy terminated oligos to ensure that shorter sequences (containing 3’-OH) groups are removed.  (3’-Termination can also be effected using a 3’-3’ linkage formed using 5’-supports, or 3’-spacer C3 CPG.)  

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