Chemodosimeter for Cu(II) detection based on cyclic peptide nucleic acids.
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Copper↗
Biomedical subjects
Andriy Mokhir
Publications and source records attributed to Andriy Mokhir.
Metal complex catalysis on a double stranded DNA template.
The reaction of ester hydrolysis catalysed by a DNA duplex in a sequence specific fashion has been developed, which is the fastest and most high yielding in comparison with the known reactions of this type.
Base Sequence↗
Zn2+ dependent DNA binders based on terminally modified peptide nucleic acids.
Two ligand-intercalator-peptide nucleic acid conjugates (L-NADI-PNAs) have been synthesized. Affinity of these conjugates to their complementary DNAs was found to be affected by Zn(2+). The magnitude of this effect could be controlled by a variation of the ligand. Upon binding Zn(2+) the L-NADI-PNAs form positively charged ZnL complexes, which interact with the negatively charged DNA backbone. This electrostatic interaction stabilizes PNA/DNA duplexes. It has been found that Zn(2+) dependent stabilization takes place only if the ZnL complex has a higher total positive charge than the ligand. Linear correlation has been observed between Zn(2+) induced stabilization of PNA/DNA duplexes and difference of charges of the ZnL complex and the ligand.
DNA↗
Fluorescent sensor for Cu2+ with a tunable emission wavelength.
A concept of fluorescent metal ion sensing with an easily tunable emission wavelength is presented and its principle demonstrated by detection of Cu(2+). A fluorescein dye was chemically modified with a metal chelating group and then attached to the terminus of ss-DNA. This was combined with a complementary ss-DNA modified with another fluorescent dye (ATTO 590), emitting at a longer wavelength. In the assembled duplex, fluorescence resonance energy transfer (FRET) between the fluorescein donor (excited at 470 nm) and the ATTO 590 acceptor (emitting at 624 nm) is observed. Proper positioning within the rigid DNA double helix prevents intramolecular contact quenching of the two dyes. Coordination of paramagnetic Cu(2+) ions by the chelating unit of the sensor results in direct fluorescence quenching of the fluorescein dye and indirect (by loss of FRET) quenching of the ATTO 590 emission at 624 nm. As a result, emission of the acceptor dye can be used for monitoring of the concentration of Cu(2+), with a 20 nM detection limit. The emission wavelength is readily tuned by replacement of ATTO-DNA by other commercially available DNA-acceptor dye conjugates. Fluorescent metal ion sensors emitting at >600 nm are very rare. The possibility of tuning the emission wavelength is important with respect to the optimization of this sensor type for application to biological samples, which usually show broad autofluorescence at <550 nm.
Binding Sites↗
Templated metal catalysis for single nucleotide specific DNA sequence detection.
A catalytic DNA-templated reaction of hydrolysis of an ester group in an N-modified peptide nucleic acid, which is activated by a Cu2+ complex-PNA, has been discovered and optimized. Both the ester-containing PNA and the metal complex PNA bind neighboring sites on a template DNA. This brings the reacting groups (the ester and the Cu2+ complex) in proximity to each other and accelerates the hydrolysis of the ester approximately 500 times in comparison with its hydrolysis in the absence of the template. The hydrolysis reaction provides >10(2)-fold kinetic discrimination between DNAs that are different from each other at a single nucleotide position. Natural enzyme T4 DNA ligase is slightly less selective. On the basis of this reaction a fully homogeneous and sensitive assay for sequence-specific DNA detection has been developed (10 fmol DNA). Identification of one of four DNAs (variation at one position) can be done in a single experiment. Since the Cu2+ ion is tightly bound in an associate containing the ester PNA, the metal complex PNA, and the template DNA, application of this method in buffers containing other Cu2+-binding ligands, e.g., PCR buffer and physiological buffer, is possible.
Base Sequence↗
Double discrimination by binding and reactivity in fluorescent metal ion detection.
Metal ion detection using a fluorescent dye containing reactive ester groups allows discrimination on the basis of the hydrolytic reactivities of metal ions, which display the same qualitative fluorescence response on binding only.
Journal Article↗
Hybridization dependent cleavage of internally modified disulfide-peptide nucleic acids.
Selectivity of the cleavage of single stranded over hybridized forms of internally modified disulfide-peptide nucleic acids (PNA) has been optimized using a series of phosphines and thiols, which have different sizes and charges. For the most selective cleaver found (tris-(carboxyethyl)-phosphine), reactivity of single stranded PNA is 33 times higher than that of the PNA-DNA duplex. Selectivity of single stranded disulfide-PNA cleavage has been explained in terms of electrostatic interaction between the substrate and the cleaver.
DNA↗
Synthesis and DNA binding properties of dioxime-peptide nucleic acids.
Peptide nucleic acids (PNAs) C- or N-modified with dioxime ligands were prepared by solid-phase synthesis using iron(II)-clathrochelates as protected dioxime building blocks. These PNA bind complementary DNA sequence specifically, though with much reduced affinity in comparison with nonmodified PNA. The dioxime-PNA conjugates bind Cu2+ and Ni2+ at microM concentration.
Base Sequence↗
Zn2+-dependent peptide nucleic acids probes.
Binding of bis-picolylamine-naphthalene diimide-peptide nucleic acid conjugates to complementary DNA is strongly dependent upon Zn2+; ultimately, hybridization is switched ON in the presence muM Zn2+.
Journal Article↗
DNA-templated metal catalysis.
Hydrolysis of an ester substrate by a CuII complex catalyst, both attached to oligo-peptide nucleic acids (PNA), is accelerated up to 485-fold in the presence of a complementary DNA template. The approach combines the sequence selectivity of DNA-templated reactions with signal amplification by multiple turnover and the versatility of metal catalysis.
Catalysis↗
Synthesis and DNA binding properties of terminally modified peptide nucleic acids.
PNAs with terminal modifications of varying structure and charge were synthesized and their binding to DNA was studied. A variation in thermal stability of 19. 8 degrees C has been observed between the least and the most stable PNA-DNA duplexes. The most stable duplex melts 7.7 degrees C higher than the duplex of the corresponding non-modified PNA and complementary DNA. It has been shown that sequence fidelity of the PNA conjugate having the highest DNA affinity is significantly better than that of non-modified PNA. The results obtained can be used for the design of PNA probes, whose binding to DNA is sequence independent.
Chemical Phenomena↗
Peptide nucleic acid-metal complex conjugates: facile modulation of PNA-DNA duplex stability.
Conjugates of peptide nucleic acids (PNA) and metal binding ligands were prepared using solid-phase synthesis. Stability of duplexes of bis-picolylamine-PNA conjugates and DNA was found to be modulated by equimolar concentrations of bioavailable metal ions: Ni(2+), Zn(2+)>Cu(2+). Sequence specificity of PNA was not compromised in the presence of these metal ions.
Base Pair Mismatch↗