Molecular beacons (MBs) are stem-loop DNA probes used for identifying and reporting the presence and localization of nucleic acid targets in vitro and in vivo via target dependent dequenching of fluorescence. To avoid the participation of stem nucleotides in target binding, which can lead to false positive results we have replaced the stem part of MBs by homo-DNA, which recognizes itself but does not recognize natural nucleic acids. Such hybrid MBs show cooperative hairpin to coil transitions in the absence of a DNA target, indicating stable homo-DNA base-pair formation in the hairpin form. Furthermore our results show that the homo-adenylate stem is excluded from DNA target binding which leads to a significant increase in target binding selectivity.

This work was carried out in the group of Prof. Christian Leumann.

References:

• C. Crey-Desbiolles, D.-R. Ahn, C. J. Leumann;
  "Molecular beacons with a homo-DNA stem: improving target selectivity"
  Nucleic Acids Res., 33, e77/1-7, (2005); doi:10.1093/nar/gni076.