Table 3.

Comparison of oligonucleotides and polynucleotides

	Oligonucleotides	Polynucleotides
Specificity	Higher. Single mismatch can be distinguished with or without competitor probes (depends on sequences and hybridization conditions).	Lower. The threshold for discrimination using polynucleotide probes has been reported to have 70–89% sequence identity.
Sensitivity	Lower. The number of molecules to be labeled is low (usually one or two).	Higher. Probes can be labeled with many molecules.
Design flexibility	Higher. Probes can be designed for a conserved region of a gene and also for a species-specific region.	Lower. Probe sequences depend on the template DNA.
Commercial availability	Yes. Fluorescently-, hapten-, and HRP-labeled probes can be purchased.	No. Probes need to be generated via in vitro transcription or PCR.
Permeability (nucleotides only)	Higher.	Lower.
Definition of Tm (Dissociation behavior)	Sequence-dependent. The point at which half the oligonucleotides are dissociated.	Base content-dependent. The point at which half the base pairs are dissociated.