Label-free fluorescent functional DNA sensors using unmodified DNA: A vacant site approach

Yu Xiang, Zidong Wang, Hang Xing, Ngo Yin Wong, Yi Lu

Research output: Contribution to journalArticlepeer-review


A general methodology to design label-free fluorescent functional DNA sensors using unmodified DNA via a vacant site approach is described. By extending one end of DNA with a loop, a vacant site that binds an extrinsic fluorophore, 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), could be created at a selected position in the DNA duplex region of DNAzymes or aptamers. When the vacant site binds ATMND, ATMNDs fluorescence is quenched. This fluorescence can be recovered when one strand of the duplex DNA is released through either metal ion-dependent cleavage by DNAzymes or analyte-dependent structural-switching by aptamers. Through this design, label-free fluorescent sensors for Pb2+, UO22+, Hg2+, and adenosine have been successfully developed. These sensors have high selectivity and sensitivity; detection limits as low as 3 nM, 8 nM, 30 nM, and 6 μM have been achieved for UO22+, Pb2+, Hg2+ and adenosine, respectively. Control experiments using vacant-site-free DNA duplexes and inactive variants of the functional DNAs indicate that the presence of the vacant site and the activity of the functional DNAs are essential for the performance of the proposed sensors. The vacant site approach demonstrated here can be used to design many other label-free fluorescent sensors to detect a wide range of analytes.

Original languageEnglish (US)
Pages (from-to)4122-4129
Number of pages8
JournalAnalytical Chemistry
Issue number10
StatePublished - May 15 2010

ASJC Scopus subject areas

  • Analytical Chemistry

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