Split DNA enzyme for visual single nucleotide polymorphism typing

Fluorescent sensor for monitoring structural changes of G-quadruplexes and detection of potassium ion

G-rich sequences with the potential for quadruplex formation are common in genomic DNA. Considering that the biological functions of G-quadruplexes may well depend on their structures, the development of a sensitive structural probe for distinguishing different types of quadruplexes has received great attention. Crystal violet (CV) is a triphenylmethane dye, which can stack onto the two external G-quartets of a G-quadruplex. The ability of CV to discriminate G-quadruplexes from duplex and single-stranded DNAs has been reported by us. Herein, the ability of CV to discriminate parallel from antiparallel structures of a G-quadruplex was studied. The binding of CV to an antiparallel G-quadruplex can make its fluorescence intensity increase to a high level because of the protection of bound CV from the solvent by quadruplex end loops. The presence of side loops in parallel G-quadruplexes cannot provide bound CV such protection, causing the fluorescence intensity of CV/G-quadruplex mixture to be obviously weaker when the G-quadruplex adopts a parallel structure than that when the G-quadruplex adopts an antiparallel structure. Therefore, CV can be developed as a sensitive fluorescent biosensor for the discrimination of antiparallel G-quadruplexes from parallel G-quadruplexes and for monitoring the structural interconversion of G-quadruplexes. In addition, considering that some G-rich DNA sequences can adopt different G-quadruplex structures under Na(+) or K(+) ion conditions, a novel, cheap and simple K(+) ion detection method was developed. This method displays a high K(+) ion selectivity against Na(+) ion, the change of 200 mM in Na(+) ion concentration only causes a similar fluorescent signal change to 0.3 mM K(+) ion.

Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: a paradigm for DNA sensors and aptasensors

The activation of a DNAzyme cascade by the cooperative self-assembly of multicomponent nucleic acid structures is suggested as a method for the amplified sensing of DNA, or the specific substrates of aptamers. According to one configuration, the DNA analyte 1 is detected by two tailored nucleic acids 2 and 3 that form a multicomponent supramolecular structure with a ribonucleobase-containing quasi-circular DNA 4, but only upon the concomitant hybridization with 1. The resulting supramolecular nucleic acid structure includes the Mg(2+)-dependent DNAzyme that cleaves the ribonucleobase site of 4. The cleavage of the quasi-circular DNA 4 results in the fragmentation of the supramolecular structure and the release of two horseradish peroxidase (HRP) mimicking units that were incorporated in the blocked quasi-circular DNA 4. The HRP-mimicking DNAzyme catalyzed the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS(2-)) by H(2)O(2) to ABTS(*-), and the product provided the colorimetric readout signal for the analyzed DNA. The method enabled the analysis of DNA with a detection limit of 1 x 10(-12) M. Similarly, an analogous DNAzyme cascade was activated by the low-molecular-weight substrates, adenosine triphosphate (ATP) or cocaine. This was induced by the self-assembly of nucleic acids that included fragments of the respective aptamers and the Mg(2+)-dependent DNAzyme. Furthermore, nucleic acids consisting of fragments of the aptamers against ATP or cocaine and fragments of the HRP-mimicking DNAzyme self-assemble, in the presence of the respective substrates, to the active DNAzyme structure that catalyzes the oxidation of ABTS(2-) by H(2)O(2) to form the colored product ABTS(*-). The resulting product provided the readout signal for the recognition events. The cooperative interaction in the formation of the supramolecular nucleic acid assemblies and the activation of the DNAzymes are discussed.

Split hybridisation probes for electrochemical typing of single-nucleotide polymorphisms

This paper describes the development of a highly selective single-nucleotide polymorphisms (SNPs) typing method based on the use of split hybridisation probes and demonstrates the concept through the electrochemical analysis of single-base mutations in actual patient samples. The requirement that two probes hybridised adjacent to one another to allow for stabilisation (via base-stacking) and binding of the allele-specific oligonucleotide (ASO), imparted highly stringent selectivity criteria to the assay. Simple rules for tuning the characteristics of such stacking/ASO probe pairs and achieve full mismatch discrimination at ambient conditions (with no need to strictly control the temperature) are provided. All genotyping experiments were indeed performed at room temperature, using the planar surface of disposable probe-modified gold electrodes as the genosensing platform. The ability to detect nanomolar amounts of a synthetic target even within a vast excess of single-base substituted sequences gave strong evidence of the specificity of the split probes assay. Proving the general validity of this genotyping approach, application of the analytical pathway was further demonstrated for clinical targets (amplified from the human TP53 gene) whose mutational site was poorly accessible, being part of a thermodynamically stable hairpin. In combination with use of auxiliary oligonucleotides (which restored the availability of each pre-defined hybridisation site), the assay demonstrated the ability to fully discriminate single-base mutations with detection limits in the high picomolar range (total analysis time: 60 min). Our specific probe design, hybridisation and signal transduction paths make the analytical process remarkably simple, relatively low cost and, thus, well suited for low throughput analysis of clinically relevant samples.

Rational design of an optical adenosine sensor by conjugating a DNA aptamer with split DNAzyme halves

Split halves of a hemin-binding DNAzyme have been assembled with an anti-adenosine aptamer to build a homogeneous allosteric sensor for adenosine with high selectivity and sensitivity.

Fluorescence detection of single nucleotide polymorphisms using a universal molecular beacon

We present a simple and novel assay—employing a universal molecular beacon (MB) in the presence of Hg²⁺—for the detection of single nucleotide polymorphisms (SNPs) based on Hg²⁺–DNA complexes inducing a conformational change in the MB. The MB (T₇-MB) contains a 19-mer loop and a stem of a pair of seven thymidine (T) bases, a carboxyfluorescein (FAM) unit at the 5′-end, and a 4-([4-(dimethylamino)phenyl]azo)benzoic acid (DABCYL) unit at the 3′-end. Upon formation of Hg²⁺–T₇-MB complexes through T–Hg²⁺–T bonding, the conformation of T₇-MB changes from a random coil to a folded structure, leading to a decreased distance between the FAM and DABCYL units and, hence, increased efficiency of fluorescence resonance energy transfer (FRET) between the FAM and DABCYL units, resulting in decreased fluorescence intensity of the MB. In the presence of complementary DNA, double-stranded DNA complexes form (instead of the Hg²⁺–T₇-MB complexes), with FRET between the FAM and DABCYL units occurring to a lesser extent than in the folded structure. Under the optimal conditions (20 nM T₇-MB, 20 mM NaCl, 1.0 μM Hg²⁺, 5.0 mM phosphate buffer solution, pH 7.4), the linear plot of the fluorescence intensity against the concentration of perfectly matched DNA was linear over the range 2–30 nM (R² = 0.991), with a limit of detection of 0.5 nM at a signal-to-noise ratio of 3. This new probe provides higher selectivity toward DNA than that exhibited by conventional MBs.

Template-directed formation of luminescent lanthanide complexes: versatile tools for colorimetric identification of single nucleotide polymorphism

We present the facile technique of colorimetric SNP (single nucleotide polymorphism) analysis through DNA-templated cooperative complexation between a luminescent lanthanide ion (Ln(III): Tb(III) or Eu(III)) and two ODN (oligodeoxyribonucleotide) conjugates carrying a metal chelator. Families of complexane-type chelators and heterocyclic aromatic ligands were covalently attached to ODNs to form conjugates for application as capture and sensitizer probes. The sequences of the conjugates were designed so as to form a ternary tandem duplex with the target, where their auxiliary units face each other, providing a microenvironment to accommodate Ln(III). Only the combination of EDTA (ethylenediaminetetraacetic acid) conjugates and phen (1,10-phenanthroline) conjugates provided significant emissions with quantum yields of 3.3% and 1.5% for Tb(III) and Eu(III), respectively, in the presence of the target. Biallelic polymorphism in the TPMT (thiopurine S-methyltransferase) gene, wt/wt (G/G), mut/mut (C/C), and wt/mut (G/C), were distinguished as emissions in green, red, and yellow, respectively; the colors were identified even by the naked eye.