There are several way to introduce degenerate genetic code to an oligonucleotides. First, a mixed base using an addition of (N) to form degerate site. Second, the use of low but unequal hydrogen bonding to other bases such as 2'-deoxyInosine (dI) or 2'-deoxyNebularine (dN). The third option is the use of a universal base that does not hybridize significantly to the other four bases and makes up some of the duplex destabilization by acting as an intercalating agent. 3-Nitropyrrole 2'-deoxynucleoside (M) is the first example of a set of universal bases. Subsequently, 5-nitroindole was determined to be an effective universal base and to be superior to 3-nitropyrrole, based on duplex melting experiments. The modified bases designated P and K show considerable promise as degenerate bases. The pyrimidine derivative P, when introduced into oligonucleotides, base pairs with either A or G, while the purine derivative K base pairs with either C or T. A dP+dK mix also can serve as a mixed base with much less degeneracy than dA+dC+dG+dT (N).

Contact Bio-Synthesis for the synthesis of nitroindole oligo modification.

Product Information


Product Name:

5-Nitroindole-2'-deoxyriboside Oligonucleotide Modification


Wobble and Universal Bases

Chemical Formula:


Exact Mass:


Formula Weight:



Bio-Synthesis Inc. Oligo Structure



Delivery Format:


Shipping Conditions:

Room Temperature

Storage Conditions:

-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at -20°C) in a nuclease-free environment should be stable for years.