Monitoring denaturation behaviour and comparative stability of DNA triple helices using oligonucleotide-gold nanoparticle conjugates

Detection of pyrimidine-rich DNA sequences based on the formation of parallel and antiparallel triplex DNA and fluorescent silver nanoclusters

In this work, the use of DNA-stabilized fluorescent silver nanoclusters for the detection of target pyrimidine-rich DNA sequences by formation of parallel and antiparallel triplex structures is studied by molecular fluorescence spectroscopy. In the case of parallel triplexes, the probe DNA fragments are Watson-Crick stabilized hairpins, and whereas in the case of antiparallel triplexes, the probe fragments are reverse-Hoogsteen clamps. In all cases, the formation of the triplex structures has been assessed by means of polyacrylamide gel electrophoresis, circular dichroism, and molecular fluorescence spectroscopies, as well as multivariate data analysis methods. The results have shown that it is possible the detection of pyrimidine-rich sequences with an acceptable selectivity by using the approach based on the formation of antiparallel triplex structures.

Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence-Specific Detection of Double-Stranded DNA

In this study the position of the thiazole orange derivative in triplex-forming oligonucleotides (TFOs) is varied and the fluorescence of the resulting complexes with DNA duplexes, single-stranded DNAs and RNAs are evaluated. Under similar conditions single attachment of the TO-dye to 2'-O-propargyl nucleotides in the TFOs (assembly dependent fluorescence enhancing nucleic acids, AFENA) led to probes with low fluorescent intensity in the single-stranded state with fluorescence quantum yield (Φ_F ) of 0.9 %-1.5 %. Significant increase in fluorescence intensity was detected after formation of DNA triplexes (Φ_F =23.5 %-34.9 %). Under similar conditions, Watson-Crick-type duplexes formed by the probes with single stranded (ss) RNA and ssDNA showed lower fluorescence intensities. Bugle insertions of twisted intercalating nucleic acid (TINA) monomers were shown to improve the fluorescent characteristics of GT/GA-containing antiparallel AFENA-TFOs. Self-aggregation of TFOs caused by guanosines was eliminated by TINA insertion which also promoted DNA triplex formation at pH 7.2. Importantly these AFENA-TINA-TFOs can bind to the duplex in the presence of complementary RNA at 37 °C.

Assembly of liposomes controlled by triple helix formation

Attachment of DNA to the surface of different solid nanoparticles (e.g., gold and silica nanoparticles) is well established, and a number of DNA-modified solid nanoparticle systems have been applied to thermal denaturation analysis of oligonucleotides. We report herein the noncovalent immobilization of oligonucleotides on the surface of soft nanoparticles (i.e., liposomes) and the subsequent controlled assembly by DNA triple helix formation. The noncovalent approach avoids tedious surface chemistry and necessary purification procedures and can simplify and extend the available methodology for the otherwise difficult thermal denaturation analysis of complex triple helical DNA assemblies. The approach is based on lipid modified triplex forming oligonucleotides (TFOs) which control the assembly of liposomes in solution in the presence of single- or double-stranded DNA targets. The thermal denaturation analysis is monitored by ultraviolet spectroscopy at submicromolar concentrations and compared to regular thermal denaturation assays in the absence of liposomes. We report on triplex forming oligonucleotides (TFOs) based on DNA and locked nucleic acid (LNA)/DNA hybrid building blocks and different target sequences (G or C-rich) to explore the applicability of the method for different triple helical assembly modes. We demonstrate advantages and limitations of the approach and show the reversible and reproducible formation of liposome aggregates during thermal denaturation cycles. Nanoparticle tracking analysis (NTA) and dynamic light scattering (DLS) show independently from ultraviolet spectroscopy experiments the formation of liposome aggregates.

Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides

Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine.

Triplex-stabilizing properties of parallel clamps carrying LNA derivatives at the Hoogsteen strand

DNA Parallel clamps with a polypurine strand linked to a polypyrimidine Hoogsteen strand containing locked nucleic acids bind their corresponding polypyrimidine targets with high affinity.

Interaction of isoquinoline alkaloids with an RNA triplex: structural and thermodynamic studies of berberine, palmatine, and coralyne binding to poly(U).poly(A)(*)poly(U)

The interaction of two natural protoberberine alkaloids berberine and palmatine and the synthetic derivative coralyne with the RNA triplex poly(U).poly(A)(*)poly(U) was studied using various biophysical and calorimetric techniques. All the three alkaloids bind noncooperatively to the triplex. The affinity of berberine and palmatine was in the order of 10(5) M(-1), while that of coralyne was one order higher as inferred from spectroscopic studies. The alkaloids stabilized the Hoogsteen base-paired third strand of the triplex without affecting the stability of the duplex. Fluorescence quenching and viscosity studies gave convincing evidence for the partial intercalation of berberine and palmatine and a true intercalative binding of coralyne to the triplex. This was further supported from the significant polarization of the emission spectra of the complex and the energy transfer from the base triplets to the alkaloids. Circular dichroic studies suggested that the conformation of the triplex was perturbed significantly by the binding of the alkaloids, being more by coralyne compared to berberine and palmatine and also evidenced by the generation of strong induced optical activity in the bound coralyne molecules. Isothermal titration calorimetric studies revealed that the binding to the triplex was favored by a predominantly large negative enthalpy change (DeltaH degrees = -5.42 kcal/mol) with small favorable entropy contribution (TDeltaS degrees = 2.02 kcal/mol) in berberine, favored by almost equal negative enthalpy (DeltaH degrees = -3.93 kcal/mol) and entropy changes (TDeltaS degrees = 3.89 kcal/mol) in palmatine and driven by predominant entropy contributions (DeltaH degrees = -1.84 and TDeltaS degrees = 7.44 kcal/mol) in coralyne. These results advance our knowledge on the binding of small molecule isoquinoline alkaloids that are specific binders of RNA structures, particularly triplexes.

LNA functionalized gold nanoparticles as probes for double stranded DNA through triplex formation

Nanoparticle modified LNA probes have been used for colorimetric identification of double stranded DNA via parallel triplex formation, eliminating the need for prior denaturation of the target duplex.

Synthesis and triplex-forming properties of cyclic oligonucleotides with (G,A)-antiparallel strands

Cyclic oligonucleotides carrying an oligopurine Watson-Crick sequence linked to the corresponding (G,A)- and (G,T)-antiparallel strands were prepared by nonenzymatic template-assisted cyclization of phosphorylated precursors. Cyclization was attempted using 3'-phosphate and 5'-phosphate linear precursors with carbodiimide or BrCN activation. The best results were obtained with the 5'-phosphorylated precursors and carbodiimide activation. Cyclic oligonucleotides bind polypyrimidine target sequence by formation of antiparallel triplexes. We have used UV and circular dichroism (CD) spectroscopy to analyze triplexes formed by cyclic oligonucleotides carrying G and A in the reverse-Hoogsteen strand. The relative stability of the triplexes formed by cyclic and linear oligonucleotides with a common polypyrimidine target was determined by melting experiments. The most-stable triplexes were formed by the cyclic oligonucleotide, followed by the unphosphorylated and phosphorylated oligonucleotide precursors, and, finally, the corresponding hairpin. Although the differences in binding affinity between cyclic oligonucleotides and their corresponding linear precursors are small, the use of cyclic oligonucleotides offers a clear advantage over conventional duplex recognition.

Efficient manipulation of nanoparticle-bound DNA via restriction endonuclease

As a programmable biopolymer, DNA has shown great potential in the fabrication and construction of nanometer-scale assemblies and devices. In this report, we described a strategy for efficient manipulation of gold nanoparticle-bound DNA using restriction endonuclease. The digestion efficiency of this restriction enzyme was studied by varying the surface coverage of stabilizer, the size of nanoparticles, as well as the distance between the nanoparticle surface and the enzyme-cutting site of particle-bound DNA. We found that the surface coverage of stabilizer is crucial for achieving high digestion efficiency. In addition, this stabilizer surface coverage can be tailored by varying the ion strength of the system. Based on the results of polyacrylamide gel electrophoresis and fluorescent study, a high digestion efficiency of 90+% for particle-bound DNA was achieved for the first time. This restriction enzyme manipulation can be considered as an additional level of control of the particle-bound DNA and is expected to be applied to manipulate more complicated nanostructures assembled by DNA.

Chains, dimers, and sandwiches: melting behavior of DNA nanoassemblies

We have studied, in experiment and theory, the melting behavior of DNA nanoassemblies of perylenediimide-bis-oligonucleotides (PON), in which two short oligonucleotide chains (16- or 24-mers) are attached to the extremities of a spacer molecule. By varying both the sequence orientation (exchange of 3' and 5' ends neighboring the spacer) and the oligomer composition of the solutions, nanoassemblies of different complexity can be generated. Our results show a subtle dependence of the melting behavior on the supramolecular arrangement of the DNA-based assemblies.