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Common 'caged' nucleic acid binders, which can be applied for temporal and spatial control of gene expression, are activated by high energy light (<450 nm). The light of this type is damaging to cells and is strongly absorbed by cellular components. Therefore, shifting the triggering light to the visible region (>550 nm) is highly desirable. Herein we report on a cyclic peptide nucleic acid (PNA), whose backbone contains a 9,10-dialkoxy-substituted anthracene linker. The sequence of this compound was selected to be complementary to a representative microRNA (miR-92). We demonstrated that the cyclic PNA does not bind complementary nucleic acids and is, correspondingly, 'caged'. Its uncaging can be conducted by its exposure to red light (635 nm) in the presence of pyropheophorbide-a. The latter process is mediated by singlet oxygen ((1)O2), which cleaves the 9,10-dialcoxyanthracene linker within the PNA with formation of a linear PNA, an efficient binder of the complementary ribonucleic acid. This is the first example of a red light-activated, 'caged' peptide nucleic acid., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Peptide nucleic acid (PNA) is a non-cyclic pseudopeptide-nucleic acid structural mimic with promising applications within diagnostics and drug discovery. This review focuses on metal complex derivatives of PNA. Metal ions and their complexes display unique physical and chemical properties and offer the opportunity to introduce new labels and probes for bioanalytical and diagnostic applications of PNA, but also to modulate or to introduce new (for example catalytic) functions and biological activities.

We have prepared cyclic peptide nucleic acids (PNAs). These compounds do not bind complementary nucleic acids. One carboxylic ester group was introduced in the backbone of the cyclic PNAs. This group is cleaved in the presence of Cu(2+) or coordinatively unsaturated Cu(2+) complexes. The cleavage products are linear PNAs. In contrast to the cyclic PNAs, they are efficient nucleic acid binders. The rate of formation of the linear PNAs is proportional to the concentration of the cleaving agents. Therefore, one may apply highly sensitive methods of detection of linear PNAs for determination of Cu(2+) concentration. In particular, we have demonstrated that both fluorescent spectroscopy in combination with molecular beacons and MALDI-TOF mass spectrometry are suitable for the detection of Cu(2+). A range of related divalent metal ions and Eu(3+), Ln(3+), Pr(3+), Ce(3+), and Zr(4+) do not interfere with Cu(2+) detection.

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.

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.

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.

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.

A series of conjugates of peptide nucleic acids (PNA) and Zr(IV) complexes was prepared. Their ability to hydrolyze DNA was tested using MALDI-TOF mass spectrometry and HPLC. The most efficient artificial restriction enzyme found, PNA conjugate with Zr(IV) complex of tris(hydroxymethyl)-aminomethane, cleaves DNA targets sequence selectively in close proximity to the Zr(IV) complex. It was demonstrated that cleavage products are substrates of terminal transferase.

Peptide nucleic acids (PNAs) are neutral DNA analogues, which bind single-stranded DNA (ssDNA) strongly and with high sequence specificity. However, binding efficiency is dependent on the purine content of the PNA strand. This property make more difficult application of PNA as hybridization probes in, e.g., PNA chips, since at a set temperature the hybridization of a fraction of the DNA targets to the PNA probes does not obey Watson-Crick binding rules. The polypurine PNAs, for example, bind the mismatch containing DNA targets stronger, than the pyrimidine rich PNAs their fully complementary targets. Herein we show that PNA-DNA binding efficiency can be finely tuned by the conjugation of derivatives of naphthalene diimide (NADI) to the N-terminus of PNA using polyamide linkers of different lengths. This approach can potentially be used for the design of PNA probes, which bind their DNA targets with similar affinity independently of the PNA sequence.

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.

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.

Conjugate Sn(IV)(pyropheophorbide a)dichloride–(peptide nucleic acid) catalyzes reduction of azobenzene derivatives in the presence of complementary nucleic acid (NA) upon irridiation with red light (660 nm). This is the first red light-induced NA-templated photoreduction. It is highly sensitive to single mismatches in the NA-template and can detect down to 5 nM NAs. [ABSTRACT FROM AUTHOR]

Abstract: 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 Zn2+. The magnitude of this effect could be controlled by a variation of the ligand. Upon binding Zn2+ 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 Zn2+ dependent stabilization takes place only if the ZnL complex has a higher total positive charge than the ligand. Linear correlation has been observed between Zn2+ induced stabilization of PNA/DNA duplexes and difference of charges of the ZnL complex and the ligand. [Copyright &y& Elsevier]