An arrangement of DNA or RNA bases in which the bases lie on top of each other.
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Stabilizer oligonucleotides are necessary to promote opening of the secondary structures of DNA templates and for the base-stacking format.
Seven of the sequence variants were located either at the 5' terminus (P250R, S252W, F276V, C342R, S347C) or at the 3' terminus (A344P, P253R) of the probe, because a base-stacking interaction with an adjacent stabilizer oligonucleotide permitted a more stable probe-to-template interaction in this format.
Design of capture and reporter oligos incorporates a base-stacking technology.
These include [T.sub.m], which was maximized for the target and minimized for the nontarget; base-stacking energy; GC content; and secondary structure of the reporters.