Genotyping—From Genomic DNA to Genotype in a Single Tube

Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties

Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.

Stochastic DNA walker for electrochemical biosensing sensitized with gold nanocages@graphene nanoribbons

A target-driven stochastic DNA walking electrochemical biosensor sensitized with gold nanocages@graphene nanoribbons (Au NCs@GNRs) was explored for sensitive detection of target DNA. Benefited from the large surface area and excellent conductivity of Au NCs and GNRs, the proposed sensing platform not only improved the electron transfer kinetics involved in electrochemical reactions, but also enhanced the loading capability for stem-loop structural DNA segment (H). Upon the addition of target DNA, the hairpin structure of H was opened and H:target DNA duplex was formed based on toehold-mediated DNA strand displacement. In the presence of exonuclease III (Exo III), the H:target DNA duplex was digested. As a result, target DNA spontaneously dissociated from H:target DNA duplex and then hybridized with another H strand. Therefore, the continuous locomotion of target DNA unceasingly triggered new digestion process from near to far along the electrode surface, resulting in great signal amplification. The proposed strategy exhibited excellent detection performances for DNA analysis in complex matrix such as human serum, which illuminated the practical application field of the sensing platform.

Fluorescence turn-on hairpin-probe PCR

A new fluorescence turn-on type of PCR monitoring system (Hpro-PCR) using a hairpin probe and a primer having a tag sequence at the 5′ end with the fluorescent molecule 2,7-diamino-1,8-naphthyridine derivative (DANP) has been developed.

Sequence-Specific Incorporation of Enzyme-Nucleotide Chimera by DNA Polymerases

DNA polymerases select the right nucleotide for the growing polynucleotide chain based on the shape and geometry of the nascent nucleotide pairs and thereby ensure high DNA replication selectivity. High-fidelity DNA polymerases are believed to possess tight active sites that allow little deviation from the canonical structures. However, DNA polymerases are known to use nucleotides with small modifications as substrates, which is key for numerous core biotechnology applications. We show that even high-fidelity DNA polymerases are capable of efficiently using nucleotide chimera modified with a large protein like horseradish peroxidase as substrates for template-dependent DNA synthesis, despite this "cargo" being more than 100-fold larger than the natural substrates. We exploited this capability for the development of systems that enable naked-eye detection of DNA and RNA at single nucleotide resolution.

Cytosine-bulge-dependent fluorescence quenching for the real-time hairpin primer PCR

The progress of a polymerase chain reaction (PCR) was sensitively monitored based on the increase in fluorescence of N,N'-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine, which was covalently anchored on the cytosine bulge directly neighbouring the 5'-T_G-3'/5'-CCA-3' sequence in the hairpin tag at the 5' end of the PCR primer.

Ultrasensitive genotyping with target-specifically generated circular DNA templates and RNA FRET probes

A RNA FRET probe-based signal amplification strategy is designed for ultrasensitive detection of RCA products coupled with thermal cycle-based ligation.

Variants of a Thermus aquaticus DNA polymerase with increased selectivity for applications in allele- and methylation-specific amplification

The selectivity of DNA polymerases is crucial for many applications. For example, high discrimination between the extension of matched versus mismatched primer termini is desired for the detection of a single nucleotide variation at a particular locus within the genome. Here we describe the generation of thermostable mutants of the large fragment of Thermus aquaticus DNA polymerase (KlenTaq) with increased mismatch extension selectivity. In contrast to previously reported much less active KlenTaq mutants with mismatch discrimination abilities, many of the herein discovered mutants show conserved wild-type-like high activities. We demonstrate for one mutant containing the single amino acid exchange R660V the suitability for application in allele-specific amplifications directly from whole blood without prior sample purification. Also the suitability of the mutant for methylation specific amplification in the diagnostics of 5-methyl cytosines is demonstrated. Furthermore, the identified mutant supersedes other commercially available enzymes in human leukocyte antigen (HLA) analysis by sequence-specific primed polymerase chain reactions (PCRs).

A novel electrochemical aptasensor for highly sensitive detection of thrombin based on the autonomous assembly of hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme nanowires

In this work, a new signal amplified strategy was constructed based on isothermal exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR) generating the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme (HRP-mimicking DNAzyme) nanowires as signal output component for the sensitive detection of thrombin (TB). We employed EXPAR's ultra-high amplification efficiency to produce a large amount of two hairpin helper DNAs within a minutes. And then the resultant two hairpin helper DNAs could autonomously assemble the hemin/G-quadruplex HRP-mimicking DNAzymes nanowires as the redox-active reporter units on the electrode surface via hybridization chain reaction (HCR). The hemin/G-quadruplex structures simultaneously served as electron transfer medium and electrocatalyst to amplify the signal in the presence of H2O2. Specifically, only when the EXPAR reaction process has occurred, the HCR could be achieved and the hemin/G-quadruplex complexes could be formed on the surface of an electrode to give a detectable signal. The proposed strategy combines the amplification power of the EXPAR, HCR, and the inherent high sensitivity of the electrochemical detection. With such design, the proposed assay showed a good linear relationship within the range of 0.1 pM-50 nM with a detection limit of 33 fM (defined as S/N=3) for TB.

Development of an electrochemical method for Ochratoxin A detection based on aptamer and loop-mediated isothermal amplification

Loop-mediated isothermal amplification (LAMP) is an outstanding DNA amplification procedure, in which the reaction can accumulate 10(9) copies from less than 10 copies of input template within an hour. While the amplification reaction is extremely powerful, the quantitative detection of LAMP products is still analytically difficult. Besides, the type of targets that LAMP can detect is also less, which to some extent limited the application of LAMP. In this study, we are reporting for the first time an efficient and accurate detection system which employs the integration of LAMP, aptamer and the electrochemical method for the sensitive detection of Ochratoxin A (OTA). Aptamers were designed as the forward outer primer to trigger the LAMP reaction, and then the LAMP amplification products were combined with a redox active molecule methylene blue (MB) and analyzed by an electrode using differential pulse voltammograms (DPV). As the reaction progresses, the MB intercalated into double-stranded regions of LAMP amplicons reduces the free MB concentration. Hence, the peak current of reaction mixture decreased with the amplification because of the slow diffusion of MB-amplified DNA complex to the electrode surface. The peak height of the current was related to the input amount of the aptamers, providing a ready means to detection the concentration of OTA. With such design, the proposed assay showed a good linear relationship within the range of 0.001-50 nM with a detection limit of 0.3 pM (defined as S/N = 3) for OTA.

Oligonucleotide Labelling Using a Fluorogenic “Click” Reaction with a Hemicarboxonium Salt

Two fluorescent streptocyanine labelled oligonucleotides have been synthesized by a simple “click” reaction between a non-fluorescent hemicarboxonium salt and aminoalkyl functionalized thymidines within the oligonucleotide and their spectrophotometric properties have been studied.

Highly sensitive and selective chemiluminescent imaging for DNA detection by ligation-mediated rolling circle amplified synthesis of DNAzyme

A highly sensitive DNA biosensing method down to sub-femtomolar level with excellent selectivity was proposed by designing an amplified synthesis of horseradish peroxidase mimicking DNAzyme and introducing the amplified DNAzyme to chemiluminescent (CL) imaging. The amplified synthesis was achieved by combining a target DNA related ligase reaction with rolling circle amplification (RCA), which produced thousands of repeated sequences to bind hemin and form a mass of horseradish peroxidase-mimicing DNAzyme units. The amplification strategy greatly enhanced the CL emission of the luminol-H(2)O(2) system. The genotyping method displayed highly specific biochemistry in allele discrimination. The novel CL imaging strategy based on ligation-mediated RCA synthesis of DNAzyme showed high fidelity in discriminating single-base mismatch and efficiently facilitated signal amplification for sensitive target DNA detection. It could detect DNA ranging from 1×10(-15) M to 1×10(-11) M with a detection limit of 0.26 fM. The proposed approach provided a robust, cost-efficient, highly sensitive and specific platform for genetic target analysis in bioanalysis and clinic biomedical application.

Signal amplified strategy based on target-induced strand release coupling cleavage of nicking endonuclease for the ultrasensitive detection of ochratoxin A

In this work, a new signal amplified strategy based on target-induced strand release coupling cleavage of nicking endonuclease for the ultrasensitive detection of ochratoxin A (OTA) is reported. OTA aptamer (DNA1) and OTA aptamer complementary (DNA2) were immobilized onto a magnetic bead (MB). In the presence of OTA, DNA2 was dissociated and released from the MB. The released DNA2 then hybridized with DNA3, which was linked at the 5' terminus of the amplification template and can extend along the template in the presence of Phi 29 DNA polymerase. The formed double-stranded DNA was cleaved by nicking endonuclease Nb.BbvCI and produced a short single-stranded DNA. The cleaved DNA strand generated a new site by Phi 29 DNA polymerase and the process of extension and cleavage was cyclical. Thus, a amount of the short single-stranded DNA were produced. Using DNA and ABEI labeled carboxylic silica nanoparticles chemiluminescence (CL) probe, the short single-stranded DNA could be sensitively detected. The CL intensity (ΔI) versus the concentration of OTA was linear in the range from 1.0×10(-12) to 5.0×10(-8)g mL(-1). The detection limit was 3.0×10(-13)g mL(-1), and the RSD was 3.4% at 1.0×10(-10)g mL(-1) (n=7). The developed method has been applied to detect OTA in naturally contaminated wheat samples. Due to its simplicity, sensitivity and no need of specific recognition of aptamer for cleavage, this CL bioassay offers a promising approach for the detection of OTA and other biomolecules.

Genetic polymorphisms in homologous recombination repair genes in healthy Slovenian population and their influence on DNA damage

Background

Homologous recombination (HR) repair is an important mechanism involved in repairing double-strand breaks in DNA and for maintaining genomic stability. Polymorphisms in genes coding for enzymes involved in this pathway may influence the capacity for DNA repair. The aim of this study was to select tag single nucleotide polymorphisms (SNPs) in specific genes involved in HR repair, to determine their allele frequencies in a healthy Slovenian population and their influence on DNA damage detected with comet assay.

Materials and methods

In total 373 individuals were genotyped for nine tag SNPs in three genes: XRCC3 722C>T, XRCC3 -316A>G, RAD51 -98G>C, RAD51 -61G>T, RAD51 1522T>G, NBS1 553G>C, NBS1 1197A>G, NBS1 37117C>T and NBS1 3474A>C using competitive allele-specific amplification (KASPar assay). Comet assay was performed in a subgroup of 26 individuals to determine the influence of selected SNPs on DNA damage.

Results

We observed that age significantly affected genotype frequencies distribution of XRCC3 -316A>G (P = 0.039) in healthy male blood donors. XRCC3 722C>T (P = 0.005), RAD51 -61G>T (P = 0.023) and NBS1 553G>C (P = 0.008) had a statistically significant influence on DNA damage.

Conclusions

XRCC3 722C>T, RAD51 -61G>T and NBS1 553G>C polymorphisms significantly affect the repair of damaged DNA and may be of clinical importance as they are common in Slovenian population.

Dispersions based on noble metal nanoparticles-DNA conjugates

Many biomolecules have specific binding properties in the nanostructure formation; they are attractive materials for nanotechnology. One such promising construction material for growing a well-defined nanostructure is deoxyribonucleic acid, due to its π-electron hydrophobic core and predictable recognition attributed to the specificity of Watson-Crick base-pairing. Hydrogen bonding provides the specificity behind the matching of complementary pairs of single-stranded (ss) DNA to hybridize into a double strand (ds) of helical DNA. The double-helical structure of DNA is determined by a subtle balance of noncovalent interactions among the DNA building blocks. The most prominent role is played by the interactions between the DNA bases, where two binding motifs can be recognized: planar hydrogen bonding and vertical stacking. DNA-based nanotechnology has generated interest in a number of applications due to the specificity, programmability, and reproducibility of DNA interaction with noble metal nanoparticles. 5' and 3' thiol moieties are used to prepare composite DNAs, DNA-gold nanoparticle conjugates and nanostructures with a variety of nanoparticle-based DNA assays. Particularly, color changes induced by the association of nanometer-sized gold particles provide a basis of a simple yet highly selective method for detecting specific biological reactions between anchored ligand molecules and receptor molecules in the milieu. Colloidal noble metal nanoparticles, in particular, have found application in a variety of assay formats in which analyte binding is coupled to particle adsorption. The extreme sensitivity of the bandwidth, the peak height, and the position of the absorption (or scattering) maximum of surface plasmon resonance spectra to environmental changes have prompted the development of approaches directly monitor the DNA hybridization. The same features that make DNA an effective molecule for the storage of genetic information also render it useful as an engineering material for the construction of smart objects at the nanometer scale because of its ability to self organize into desired structures via the specific hybridization of complementary sequences. Biocompatibility between gold nanomaterials and biological scaffolding is crucial to the development of smart biomaterials. These DNA/metal colloids are interesting for their fundamental properties as well as for applications in nanomaterials science and nanobiotechnology.

One-pot synthesis of fluorescent oligonucleotide Ag nanoclusters for specific and sensitive detection of DNA

In this study, we prepared fluorescent, functional oligonucleotide-stabilized silver nanoclusters (FFDNA-Ag NCs) through one-pot synthesis and then employed them as probes for single nucleotide polymorphisms (SNPs). The FFDNA-Ag NCs were obtained through the NaBH(4)-mediated reduction of AgNO(3) in the presence of a DNA strand having the sequence 5'-C(12)-CCAGATACTCACCGG-3'. The specific DNA scaffold combines a fluorescent base motif (C(12)) and a specific sequence (CCAGATACTCACCGG) that recognizes a gene for fumarylacetoacetate hydrolase (FAH). The sensing mechanism of our new probe is based on the FFDNA-Ag NCs having different stabilities (fluorescence intensities) in solutions containing 150 mM NaCl in the absence and presence of perfect match DNA (DNA(pmt)). Under the optimal conditions (150 mM NaCl, 20 mM phosphate solution, pH 7.0), the fluorescence ratios of the FFDNA-Ag NC probes in the presence and absence of DNA(pmt), plotted against the concentration of DNA(pmt), was linear over the range 25-1000 nM (R(2)=0.98), with a limit of detection (S/N=3) of 14 nM. This cost-effective and simple FFDNA-Ag NC probe is sensitive and selective for SNPs of a gene for FAH.

Comparison of a nucleosidic vs non-nucleosidic postsynthetic "click" modification of DNA with base-labile fluorescent probes

The azides 1 and 2 bearing a phenoxazinium and a coumarin fluorophore, respectively, were applied in postsynthetic "click"-type bioconjugation and coupled to oligonucleotides modified with alkyne groups using two alternative approaches: (i) as a nucleotide modification at the 2'-position of uridine and (ii) as a nucleotide substitution using (S)-(-)-3-amino-1,2-propanediol as an acyclic linker between the phosphodiester bridges. The corresponding alkynylated phosporamidites 3 and 6 were used as DNA building blocks for the preparation of alkyne-bearing DNA duplexes. The base pairs adjacent to the site of modification and the base opposite to it were varied in the DNA sequences. The modified duplexes were investigated by UV/vis absorption spectroscopy (including melting temperatures) and fluorescence spectroscopy in order to study the different optical properties of the two chromophores and to evaluate their potential for bioanalytical applications. The sequence-selective fluorescence quenching of phenoxazinium 1 differs only slightly and does not depend on the type of modification, meaning whether it has been attached to the 2'-position of uridine or as DNA base surrogate using the acyclic glycol linker. The 2'-chromophore-modified uridine still recognizes adenine as the counterbase, and the duplexes exhibit a sufficient thermal stability that is comparable to that of unmodified duplexes. Thus, the application of the 2'-modification site of uridine is preferred in comparison to glycol-assisted DNA base surrogates. Accordingly, the coumarin dye azide 2 was attached only to the 2'-position of uridine. The significant Stokes shift of approximately 100 nm and the good quantum yields make the coumarin chromophore a powerful fluorescent label for nucleic acids.

Chemiluminescence DNA biosensor based on dual-amplification of thrombin and thiocyanuric acid-gold nanoparticle network

A sensitive DNA biosensor based on dual-amplification of thrombin and thiocyanuric acid-gold nanoparticle (TCA-AuNP) network is developed. First, the sandwich hybridization is formed by the capture probe immobilized on the surface of magnetic beads (MBs), the target DNA and the reporter probe loaded on PbS nanoparticles (PbS NPs). The PbS NPs contain two kinds of DNA sequences, one is the reporter probe complementary to the target DNA, and the other is the thrombin aptamer I. Through the specific recognition for thrombin, thrombin aptamer II labeled gold nanoparticles are linked to the sandwich complex, and further fabricate a network with TCA. AuNPs are released and dissolved into Au(3+), which catalyzes luminol chemiluminescence (CL) reaction. Due to the dual-amplification effects of thrombin-labeled PbS NPs and the TCA-AuNP network, a significant sensitivity enhancement of this DNA biosensor could be obtained, in the range of 2.0 x 10(-16) M to 3.5 x 10(-14) M, with a limit of detection (LOD) as low as 1.0 x 10(-16) M.

Copper-free "click" modification of DNA via nitrile oxide-norbornene 1,3-dipolar cycloaddition

Nitrile oxides react smoothly and rapidly with norbornene-modified DNA in a copper-free click reaction. The reaction allows high density functionalization of oligodeoxyribonucleotides (ODNs) with a large variety of molecules directly on solid supports and even in synthesizers without the need for an additional catalyst.

Fluorescent color readout of DNA hybridization with thiazole orange as an artificial DNA base

A fluorescent chameleon: A single thiazole orange (TO) dye, when used as an artificial DNA base shows the typical green emission, whereas the interstrand TO dimer exhibits an orange excimer-type emission inside duplex DNA (see picture).

Novel strategies for the site-specific covalent labelling of nucleic acids

To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.