5-Nitroindole - 1 modification

Universal bases can be used instead of degenerate bases, and have the advantage that the hybridisation probe is not diluted by the non-pairing components of the degeneracy. In this case, the base analogue does not hybridise significantly to the other four bases and makes up for some of the duplex destabilisation by acting as a light intercalating agent. Our available universal nucleosides are 3-nitropyrrole 2’-deoxynucleoside, 5-nitroindole and, finally, P and K nucleoside analogues that are able to hybridise efficiently with respectively both purine (A-G) or pyrimidine (C-T). It is usually not recommended to introduce universal bases in template strands (e.g. PCR primers), as DNA polymerases may dissociate from the template when encoutering these bases.

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