5-Nitroindole

5-Nitroindole is a hydrophobic aromatic compound, and can be used as a universal base analog in oligonucleotides. Incorporation of universal bases into oligos is desirable in cases when either imprecise or random base-pairing is required, and the resulting “mis-matched” complements need to be stable. 5-Nitroindole does not discriminate between the four natural nucleotide bases in duplex formation. Substitution of this chemical as a universal base is less destabilizing towards the ends of oligos than towards the center. Substitutions at, or within eight bases of, the 3’-end produce primers that generally are ineffective at priming.