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

Three-dimensional nanolithography guided by DNA modular epitaxy

Lithographic scaling of periodic three-dimensional patterns is critical for advancing scalable nanomanufacturing. Current state-of-the-art quadruple patterning or extreme-ultraviolet lithography produce a line pitch down to around 30 nm, which might be further scaled to sub-20 nm through complex post-fabrication processes. Herein, we report the use of three-dimensional (3D) DNA nanostructures to scale the line pitch down to 16.2 nm, around 50% smaller than state-of-the-art results. We use a DNA modular epitaxy approach to fabricate 3D DNA masks with prescribed structural parameters (geometry, pitch and critical dimensions) along a designer assembly pathway. Single-run reactive ion etching then transfers the DNA patterns to a Si substrate at a lateral critical dimension of 7 nm and a vertical critical dimension of 2 nm. The nanolithography guided by DNA modular epitaxy achieves a smaller pitch than the projected values for advanced technology nodes in field-effect transistors, and provides a potential complement to the existing lithographic tools for advanced 3D nanomanufacturing.

Porphyrins as Colorimetric and Photometric Biosensors in Modern Bioanalytical Systems

Advances in porphyrin chemistry have provided novel materials and exciting technologies for bioanalysis such as colorimetric sensor array (CSA), photo-electrochemical (PEC) biosensing, and nanocomposites as peroxidase mimetics for glucose detection. This review highlights selected recent advances in the construction of supramolecular assemblies based on the porphyrin macrocycle that provide recognition of various biologically important entities through the unique porphyrin properties associated with colorimetry, spectrophotometry, and photo-electrochemistry.

The Cucurbit[7]Uril-Based Supramolecular Chemistry for Reversible B/Z-DNA Transition

As a left-handed helical structure, Z-DNA is biologically active and it may be correlated with transcription and genome stability. Until recently, it remained a significant challenge to control the B/Z-DNA transition under physiological conditions. The current study represents the first to reversibly control B/Z-DNA transition using cucurbit[7]uril-based supramolecular approach. It is demonstrated that cucurbit[7]uril can encapsulate the central butanediamine moiety [HN(CH2)4NH] and reverses Z-DNA caused by spermine back to B-DNA. The subsequent treatment with 1-adamantanamine disassembles the cucurbit[7]uril/spermine complex and readily induces reconversion of B- into Z-DNA. The DNA conformational change is unequivocally demonstrated using different independent methods. Direct evidence for supramolecular interactions involved in DNA conformational changes is further provided. These findings can therefore open a new route to control DNA helical structure in a reversible way.

Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes

A novel π-extended Ni^II-porphyrin shows a high selectivity towards human telomeric G-quadruplexes.

Transition metal induced switch of fluorescence and absorption response of a Zn(ii)porphyrin–DNA conjugate to cysteine derivatives

We report a supramolecular zinc(ii)porphyrin–oligothymidine/metal ion complex as a dual highly sensitive optical probe of biothiols with switchable spectroscopic signals.

Unraveling the forming mechanism of hierarchical helices via self-assembly of an achiral supramolecular polymer brush

We propose a detailed structural transition of the hierarchical helix or superhelix of PVP–PDP from straightforward experimental evidence.

Chiroptical properties, binding affinity, and photostability of a conjugated zinc porphyrin dimer complexed with left-handed Z-DNA and right-handed B-DNA

We have studied the UV-vis absorption and chiroptical properties, binding affinity and photostability of a conjugated positively charged butadiyne-linked Zn(ii) porphyrin dimer bound to DNA sequence poly(dG-dC)2. Right-handed B-DNA, spermine-induced Z-DNA and Co(iii)-induced Z-DNA have been explored. Resonance light scattering (RLS) spectra showed formation of porphyrin aggregates in the presence of all DNA forms with the largest aggregates formed with B-DNA. The porphyrin dimer gave rise to induced bisignate circular dichroism (CD) signals in the presence of the left-handed Z-DNA conformations. On the other hand, the dimer stayed nearly chiroptically silent when complexed with the B-form of poly(dG-dC)2. Our results indicated that the conjugated Zn(ii) porphyrin dimer can be used as a sensor for the chiroptical detection of Z-DNA in the visible (400-500 nm) and near-infrared region of the electromagnetic spectrum (700-800 nm). The helicity of DNA had little effect on the dimer binding affinities. The photostability of the porphyrin dimer complexed with any form of DNA was higher than that of the free molecule. The porphyrin dimer bound to Z-DNA exhibited slower photobleaching than the B-DNA dimer complex.

Conformation-dependent DNA attraction

Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg(2+) ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg(2+) or Na(+), benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg(2+) bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.

B-Z transition of (dA-T)(n) duplexes induced by a spermine porphyrin-conjugate via an intermediate DNA conformation

The spermine conjugate of the cationic porphyrin ligand (1) selectively induced the B-Z transition of the [(dA-T)n]2 sequence at low salt concentrations. The [(dG-C)n]2 sequence was not transformed into the Z-form. The B-Z transition was induced via an intermediate DNA conformation, which was formed by the external binding and formation of an assembly of 1 onto B-DNA.

Chiroptical properties of anionic and cationic porphyrins and metalloporphyrins in complex with left-handed Z-DNA and right-handed B-DNA

We report the chiroptical signature and binding interactions of cationic (meso-tetrakis(4-N-methylptridyl)porphyrin, 2HT4) and anionic (meso-tetrakis(4-sulfonatophenyl)porphyrin, 2HTPPS) porphyrins and their zinc(II) and nickel(II) derivatives (ZnT4, ZnTPPS, NiT4, and NiTPPS) with right-handed B-form and two forms of left-handed Z-form of alternating guanine-cytosine polydeoxynucleotide poly(dG-dC)2. NiTPPS is able to spectroscopically discriminate between spermine-induced Z-DNA and Co(III)-induced Z-DNA via new induced circular dichroism signal in the visible region of the electromagnetic spectrum.

Highly sensitive and selective spectroscopic detection of mercury(II) in water by using pyridylporphyrin-DNA conjugates

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.

Sulfonated Ni(II)porphyrin improves the detection of Z-DNA in condensed and non-condensed BZB DNA sequences

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).

Chiroptical switches: applications in sensing and catalysis

Chiroptical switches have found application in the detection of a multitude of different analytes with a high level of sensitivity and in asymmetric catalysis to offer switchable stereoselectivity. A wide range of scaffolds have been employed that respond to metals, small molecules, anions and other analytes. Not only have chiroptical systems been used to detect the presence of analytes, but also other properties such as oxidation state and other physical phenomena that influence helicity and conformation of molecules and materials. Moreover, the tunable responses of many such chiroptical switches enable them to be used in the controlled production of either enantiomer or diastereomer at will in many important organic reactions from a single chiral catalyst through selective use of a low-cost inducer: Co-catalysts (guests), metal ions, counter ions or anions, redox agents or electrochemical potential, solvents, mechanical forces, temperature or electromagnetic radiation.

3,3'-diethylthiatricarbocyanine iodide: a highly sensitive chiroptical reporter of DNA helicity and sequence

Using UV-vis absorption and circular dichroism (CD) spectroscopies, we explored the binding interactions of 3,3′-diethylthiatricarbocyanine iodide (Cy7) with polynucleotides of different sequences and helicity. CD showed to be a very diagnostic tool giving different spectroscopic chiroptical signatures for all explored DNA sequences upon Cy7 binding. Cy7 was able to spectroscopically discriminate between the right handed B-DNA of poly(dG-dC)₂ and its left handed Z-DNA counterpart induced by spermine or Co(III)hexamine via nearly opposite induced circular dichroic signal.