Nucleic Acids Research Advance Access originally published online on October 24, 2007
Nucleic Acids Research 2007 35(21):7279-7287; doi:10.1093/nar/gkm771
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Nucleic Acids Research, 2007, Vol. 35, No. 21 7279-7287
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Chemistry |
Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem
Department of Chemistry and UF Genetics Institute, Shands Cancer Center, Center for Research at Bio/nano Interface and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
*To whom correspondence should be addressed. Tel/Fax: +352 846 2410; Email: tan{at}chem.ufl.edu
Received June 13, 2007. Revised September 12, 2007. Accepted September 13, 2007.
Hairpin nucleic acid probes have been highly useful in many areas, especially for intracellular and in vitro nucleic acid detection. The success of these probes can be attributed to the ease with which their conformational change upon target binding can be coupled to a variety of signal transduction mechanisms. However, false-positive signals arise from the opening of the hairpin due mainly to thermal fluctuations and stem invasions. Stem invasions occur when the stem interacts with its complementary sequence and are especially problematic in complex biological samples. To address the problem of stem invasions in hairpin probes, we have created a modified molecular beacon that incorporates unnatural enantiomeric L-DNA in the stem and natural D-DNA or 2'-O-Me-modified RNA in the loop. L-DNA has the same physical characteristics as D-DNA except that L-DNA cannot form stable duplexes with D-DNA. Here we show that incorporating L-DNA into the stem region of a molecular beacon reduces intra- and intermolecular stem invasions, increases the melting temperature, improves selectivity to its target, and leads to enhanced bio-stability. Our results suggest that L-DNA is useful for designing functional nucleic acid probes especially for biological applications.
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