Ultrasensitive and Selective Colorimetric DNA Detection by Nicking Endonuclease Assisted Nanoparticle Amplification

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

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, ATMND's 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 Pb(2+), UO(2)(2+), Hg(2+), 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 microM have been achieved for UO(2)(2+), Pb(2+), Hg(2+) 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.

Multiplex single-nucleotide polymorphism typing by nanoparticle-coupled DNA-templated reactions

A novel chip-based detection approach for single-nucleotide polymorphism (SNP) typing based on nanoparticle-coupled DNA-templated ligation reactions is reported. In contrast to conventional methods or recently developed techniques, this approach does not need costly instrumentation and complex stringency washing processes and offers both rapid multiplex SNP detection capability and ultrahigh sensitivity. The ability of the approach to quickly identify the precise location of the single-base mismatch may provide a time-efficient method for high-throughput multiplex SNP genotyping.

Synthesis and thermally reversible assembly of DNA-gold nanoparticle cluster conjugates

We describe the facile synthesis of stable gold nanoparticle clusters densely functionalized with DNA (DNA-AuNP clusters) using dithiothreitol and monothiol DNA and their thermally reversible assembly properties. The size of the clusters exhibits a very narrow distribution and can be easily controlled by adjusting the stoichiometry of dithiothreitol and DNA, leading to a variety of colors due to the surface plasmon resonance of the AuNP clusters. Importantly, the DNA-AuNP clusters exhibit highly cooperative melting properties with distinctive and diverse color changes depending on their size. The selective and sensitive colorimetric detection of target sequences was demonstrated based upon the unique properties of the DNA-AuNP clusters.

pH-stimulated concurrent mechanical activation of two DNA "tweezers". A "SET-RESET" logic gate system

A DNA tweezer consisting of C-rich arms is kept in the "closed" form by hybridization of the arms with a nucleic acid cross-linker. At acidic pH (pH = 5.2), the arms are stabilized through the formation of the i-motif, C-quadruplex structures, releasing the cross-linking nucleic acid and transforming the tweezer to its "opened" state. At neutral pH (pH = 7.2), the C-quadruplex structures are dissociated, resulting in the capturing of the cross-linking nucleic acid and the closure of the tweezer. By the reversible treatment of the tweezer at pH = 5.2 and at pH = 7.2, the tweezer system is cycled between the open and closed states, respectively, followed by a FRET process between a fluorophore-quencher pair that labels the tweezer. Also the concurrent activation of two DNA tweezers by pH stimuli is described. The pH-induced opening of one tweezer (tweezer A) by the formation of C-quadruplex (pH = 5.2) and the release of the cross-linking nucleic acid result in the closure of a second tweezer (tweezer B) by the hybridization of the released strand with the arms of tweezer B. The dissociation of the C-quadruplex structures (pH = 7.2) results in the favored translocation of the cross-linking nucleic acid from tweezer B to A. By the cycling of the pH of the system between pH = 5.2 and pH = 7.2, the concurrent opening and closure of the two tweezers are accomplished. The two tweezers system performs a SET-RESET logic gate operation, where the pH stimuli act as inputs.