Subject: | Molecular Beacons |
Presenter: | Dan Tulpan |
Paper: | " Hybridization kinetics and thermodynamics of molecular beacons " |
  | by Tsourkas et al. |
Abstract |
Hybridization kinetics and thermodynamics of molecular beacons
Molecular beacons are increasingly being used in many applications involving
nucleic acid detection and quantification. The stem.loop structure of
molecular beacons provides a competing reaction for probe.target hybridization
that serves to increase probe specificity, which is particularly useful when
single-base discrimination is desired. To fully realize the potential of
molecular beacons, it is necessary to optimize their structure. Here we report
a systematic study of the thermodynamic and kinetic parameters that describe
the molecular beacon structure.function relationship. Both probe and stem
lengths are shown to have a significant impact on the binding specificity and
hybridization kinetic rates of molecular beacons. Specifically, molecular
beacons with longer stem lengths have an improved ability to discriminate
between targets over a broader range of temperatures. However, this is
accompanied by a decrease in the rate of molecular beacon.target hybridization.
Molecular beacons with longer probe lengths tend to have lower dissociation
constants, increased kinetic rate constants, and decreased specificity.
Molecular beacons with very short stems have a lower signal-to-background ratio
than molecular beacons with longer stems. These features have significant
implications for the design of molecular beacons for various applications.
Reference:
Tsourkas et al., "Hybridization kinetics and thermodynamics of
molecular beacons", NAR 2003, 31(4): 1319-1330.
The paper is available at http://nar.oupjournals.org/cgi/reprint/31/4/1319
Other interesting papers on the topic can be found at:
http://www.molecular-beacons.org
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