The design of primers is frequently complicated by the degeneracy of the genetic code. Three strategies are now available to confront this problem. In the first, a mixed base addition (N) is used to form the degenerate site. This approach is best if the number of degenerate sites is small. A second option is the use of 2'-deoxyInosine or 2'-deoxyNebularine which exhibit low, but unequal, hydrogen bonding to the other four bases. The third option is the use of a universal nucleoside. In this strategy, the base analog does not hybridize significantly to the other four bases and makes up some of the duplex destabilization by acting as an intercalating agent.
A 3' chain terminator is an oligo modification to block ligation at the 3' terminus or to prevent polymerase extension from the 3' terminus. Similarly, In situations where ligation must be blocked at the 5' terminus, a 5' blocker may be used.
Glen Research offers a variety of phosphoramidites and supports for research in duplex effects.