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Nucleic Acids Research Advance Access originally published online on February 16, 2008
Nucleic Acids Research 2008 36(5):e31; doi:10.1093/nar/gkn052
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Nucleic Acids Research, 2008, Vol. 36, No. 5 e31
© 2008 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.

Methods Online

Facile SNP detection using bifunctional, cross-linking oligonucleotide probes

Xiaohua Peng and Marc M. Greenberg*

Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA

*To whom correspondence should be addressed. Tel: +410 516 8095; Fax: +410 516 8420; Email: mgreenberg{at}jhu.edu

Received January 4, 2008. Revised January 25, 2008. Accepted January 28, 2008.

A facile, sensitive method for detecting specific sequences of oligonucleotides was developed. Detection of DNA sequences with single nucleotide discrimination is achieved by combining the selectivity of hybridization with an efficient cross-linking reaction. Readily synthesized bifunctional oligonucleotide probes containing a modified pyrimidine that is capable of forming interstrand cross-links under mild oxidative conditions internally, and biotin at their 5'-termini were used to discriminate between 16-nt long sites in plasmid DNA that differ by a single nucleotide. The target sequence was detected via fluorescence spectroscopy by utilizing conjugates of avidin and horseradish peroxidase in a microtiter plate assay. The method is able to detect as little as 250 fmol of target without using PCR and exhibits single nucleotide discrimination that approaches 200:1. In principle, this method is capable of probing any target sequence containing a 2'-deoxyadenosine.


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Y.-W. Lin, H.-T. Ho, C.-C. Huang, and H.-T. Chang
Fluorescence detection of single nucleotide polymorphisms using a universal molecular beacon
Nucleic Acids Res., August 27, 2008; (2008) gkn537v1.
[Abstract] [Full Text] [PDF]


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