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Single-labeled pyridylporphyrin-DNA conjugates are reported as highly sensitive and selective spectroscopic sensors for mercury(II) ions in water. The effects of chemical structure (thymine versus adenine), number of nucleotides (monomer versus octamer), and porphyrin metalation (Zn versus free base) on the sensitivity and selectivity of mercury(II) detection are explored. The results indicated that pyridylporphyrin rather than the nucleobase plays a crucial role in mercury(II) sensing, because porphyrin conjugates with both adenosine and thymidine exhibited excellent mercury(II) detection. Mercury(II) recognition was shown in emission quenching, as well as in a redshift of the porphyrin Soret band absorption. The limit of detection (LOD, 3σ/slope) of zinc(II) pyridylporphyrin-5'-oligodeoxythymidine (ZnPorT8) obtained by fluorescence quenching was calculated to be 21.14 nM. Other metal cations (Zn(2+), Cd(2+), Pb(2+), Mn(2+), Ca(2+), Ni(2+), Mg(2+), Fe(2+), Cu(2+), and Na(+)) did not interfere with the emission and absorption sensing of mercury(II). Free-base porphyrin-oligothymine conjugate 2HPorT8 displayed similar sensitivity to ZnPorT8 but different selectivity. The results also implied that the sensing properties of porphyrin-deoxythymidine conjugates could potentially be tuned by porphyrin metalation., (Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

We report a very selective and sensitive spectroscopic detection of Z-DNA embedded in B-DNA in condensed as well as non-condensed DNA using anionic Ni(II) meso-tetrakis(4-sulphonatophenyl)porphyrin, NiTPPS. A combination of micromolar concentrations of Ni(II) and spermine(4+) allowed us to prepare left-handed Z-DNA in short oligonucleotides without DNA condensation. A strong induced circular dichroism (ICD) signal was observed in the visible absorption region when NiTPPS was added to BZ DNA (Z-DNA fragment located at the end of a B-DNA tract with one B/Z DNA junction) and BZB DNA (Z-DNA sequence embedded in B-DNA having two B/Z DNA junctions). Almost no ICD signal was detected when NiTPPS was added to B-DNA. NiTPPS showed different binding modes with condensed and non-condensed Z-DNAs and allowed the distinction between condensed Z-DNA (positive bisignate CD couplet) and non-condensed Z-DNA (negative bisignate CD couplet)., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Here, we report a highly sensitive and specific chiroptical detection method of condensed left-handed Z-DNA in the presence of canonical right-handed B-DNA. The selective formation of a left-handed cytosine-guanine oligonucleotide (CG ODN) in the presence of a right-handed adenine-thymine oligonucleotide (AT ODN) was induced by millimolar concentrations of NiCl(2) and confirmed by electronic circular dichroism. The nickel(II) induced B- to Z-DNA transition of the CG ODN was accompanied by the concurrent condensation of the Ni(II)-Z-DNA, as confirmed by resonance light scattering, transmission spectroscopy, and centrifugation. The selective condensation of the CG ODN allowed its separation from the AT ODN using centrifugation. No structural changes were observed for the AT ODN upon addition of Ni(II). Anionic nickel(II) meso-tetra(4-sulfonatophenyl) porphyrin (NiTPPS) spectroscopically detected the left-handed Z-DNA in the Z-DNA/B-DNA mixture via a strong exciton coupled circular dichroism (ECCD) signal induced in the porphyrin Soret band absorption region. The bisignate ECCD signal originates from the assembly of achiral porphyrins into helical arrays by intermolecular interactions with the condensed Z-DNA scaffold. No induced CD signal was observed for the Ni(II)-B-DNA-NiTPPS complex. Hence, an unambiguous spectroscopic recognition of Ni(II) induced condensed Z-DNA in the presence of B-DNA is possible. The sensitivity of this chiroptical method was as low as 5% of the Z-DNA (4.4 μmol base pair concentration) in the presence of 95% B-DNA (80 μmol). Thus, NiTPPS is a highly sensitive probe for applications in biosensing via the CD signal amplification., (© 2011 American Chemical Society)

Abstract: The left-handed Z-DNA form of the short unmodified alternating guanine–cytosine oligonucleotides, 5′-(dGdC)24 and 5′-(dGdC)18, was selectively detected under physiological ionic strength and pH conditions using the anionic nickel(II) porphyrin, NiTPPS. No spectroscopic signal was observed for NiTPPS with any right-handed oligonucleotides under identical conditions. The 48mer 5′-(dGdC)24 Z-form was detected at concentrations as low as 100nM. The binding of NiTPPS to the B- and Z-oligonucleotides was studied quantitatively by UV–vis absorption and circular dichroism spectroscopies. NiTPPS was found to be a universal DNA binder, with binding affinity and geometry depending on the ionic composition of the solution, rather than on the DNA helical twist. This is the first example of a successful spectroscopic detection of the Z-DNA of short unmodified oligonucleotides under physiological pH and ionic strength conditions. [Copyright &y& Elsevier]