Chiroptical detection of condensed nickel(II)-Z-DNA in the presence of the B-DNA via porphyrin exciton coupled circular dichroism

Abstract

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.

Chart 1

Structure of nickel(II) meso-tetra(4-sulfonatophenyl) porphyrin, NiTPPS, and DNA sequences used in this study.

Figure 1

Schematic representation of the selective formation, condensation and detection of the left-handed Z-DNA in the presence of the right-handed B-DNA using NiTTPS chiroptical probe. Chiral NiTPPS assemblies formed on the Z-DNA give rise to the exciton coupled CD signal.

Figure 2

a) RLS spectra of the CG 48mer 5'-(dGdC)₂₄ (blue curve), AT 48mer 5'-(dAdT)₂₄ (green curve), and the mixture of the CG 48mer + AT 48mer (red curve) upon addition of 50 mM NiCl₂. b) Normalized intensity of the CD signal at 250 nm (black circles) and RLS signal at 490 nm (blue squares) of the CG 48mer 5'-(dGdC)₂₄ as a function of NiCl₂ concentration. Condition: [5'-(dGdC)₂₄] = 80 μM, [5'-(dAdT)₂₄] = 80 μM, Na-cacodylate buffer (1 mM, pH = 7.0).

Figure 3

a) CD spectra of the mixture of the CG 48mer and the AT 48mer in the absence (blue curve, B+B DNA) and presence (black curve, Z+B DNA) of 50 mM NiCl₂. b) CD spectra of Z-form of the 48mer 5'-(dGdC)₂₄ induced in the presence of B-form of the 48mer 5'-(dAdT)₂₄ with 50 mM NiCl₂ obtained by subtraction of B-DNA CD signal (green curve). Condition: [5'-(dGdC)₂₄] = 80 μM, [5'-(dAdT)₂₄] = 80 μM, 50 mM NiCl₂, Na-cacodylate buffer (1 mM, pH = 7.0).

Figure 4

CD spectra (a) and UV-vis absorption spectra (b) of the upper half of the solution obtained upon centrifugation (black curve) and a freshly prepared solution of 48mer 5'-(dAdT)₂₄ in the presence of 50 mM NiCl₂ (green curve). Condition: [5'-(dGdC)₂₄] = 80 μM, [5'-(dAdT)₂₄] = 80 μM, 50 mM NiCl₂, Na-cacodylate buffer (1 mM, pH = 7.0), centrifugation: 14500 rpm, 30 min.

Figure 5

CD spectra of the mixture of Z-form of the 48mer 5′-(dGdC)₂₄ and B-form of 48mer 5′-(dAdT)₂₄ titrated with NiTPPS. Inset: intensity of the ECCD as a function of NiTPPS concentration. Condition: [5′-(dGdC)₂₄] = 80 μM, [5′-(dAdT)₂₄] = 80 μM, 50 mM NiCl₂, Na-cacodylate buffer (1 mM, pH = 7.0).

Figure 6

RLS spectra of the NiTPPS added to a) the B-form AT 48mer 5′-(dAdT)₂₄, b) the Z-form CG 48mer 5′-(dGdC)₂₄, and c) the 1:1 Z+B DNA mixture in the presence of 50 mM NiCl₂. Inset: increased in intensity of the RLS at 490 nm as a function of NiTPPS concentration. Condition: [5′-(dGdC)₂₄] = 80 μM, [5′-(dAdT)₂₄] = 80 μM, Na-cacodylate buffer (1 mM, pH = 7.0).

Figure 7

UV-vis absorption spectra of NiTPPS added to the Z-form of the 48mer 5′-(dGdC)₂₄ (blue curve), to the B-form of 48mer 5′-(dAdT)₂₄ (green curve), to the B+Z DNA mixture (1:1, red curve) consisted of CG 48mer and AT 48mer. Inset: Soret band absorption wavelength as a function of NiTPPS concentration. Condition: [5′-(dGdC)₂₄] = 80 μM, [5′-(dAdT)₂₄] = 80 μM, 50 mM NiCl₂, Nacacodylate buffer (1 mM, pH = 7.0), method A.

Figure 8

a) CD spectra of the 5:95 mixture of Z-form 48mer 5′-(dGdC)₂₄ and B-form 48mer 5′-(dAdT)₂₄ (black curve) and the CD spectrum of the Z-form obtained by subtraction from the CD spectrum of Z+B DNA mixture (red curve). b) ECCD observed upon titration of NiTPPS into the 5:95 mixture of Z-form 48mer 5′-(dGdC)₂₄ and B-form of 48mer 5'-(dAdT)₂₄. Condition: [5′-(dGdC)₂₄] = 4.4 μM, [5′-(dAdT)₂₄] = 80 μM, 50 mM NiCl₂, Na-cacodylate buffer (1 mM, pH = 7.0).