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Degenerate bases, in the context of modified bases, refers to their ability to form a reasonably stable base pair with more than one base, for example, with all pyrimidines (C and T) or purines (A and G). Examples of degenerate bases include deoxyinosine (dI) and 5-nitroindole, both of which can pair with all four naturally-occurring bases. Incorporation of degenerate base modifications is desirable in cases when either imprecise or random base-pairing is required, and the resulting “mis-matched” complements need to be stable. Examples include reverse-translation of known protein sequence for oligo design (oligos to be used as primers or probes), development of an in vitro or in vivo oligo probe able to hybridize to related but distinct genes (such as viral sub-strains or allelic variants—SNPs, indels, etc), in vitro site-directed mutagenesis and motif cloning (1).
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