Conjugation of hemin to G-quadruplex forming oligonucleotide using click chemistry

Functionalised Cofactor Mimics for Interactome Discovery and Beyond

Cofactors are required for almost half of all enzyme reactions, but their functions and binding partners are not fully understood even after decades of research. Functionalised cofactor mimics that bind in place of the unmodified cofactor can provide answers, as well as expand the scope of cofactor activity. Through chemical proteomics approaches such as activity-based protein profiling, the interactome and localisation of the native cofactor in its physiological environment can be deciphered and previously uncharacterised proteins annotated. Furthermore, cofactors that supply functional groups to substrate biomolecules can be hijacked by mimics to site-specifically label targets and unravel the complex biology of post-translational protein modification. The diverse activity of cofactors has inspired the design of mimics for use as inhibitors, antibiotic therapeutics, and chemo- and biosensors, and cofactor conjugates have enabled the generation of novel enzymes and artificial DNAzymes.

Sequence Effect on the Activity of DNAzyme with Covalently Attached Hemin and Their Potential Bioanalytical Application

In this work we investigated the effect of a DNA oligonucleotide sequence on the activity of a DNAzyme with covalently attached hemin. For this purpose, we synthesized seven DNA-hemin conjugates. All DNA-hemin conjugates as well as DNA/hemin complexes were characterized using circular dichroism, determination of melting temperatures and pKa of hemin. We observed that hemin conjugation in most cases led to the formation of parallel G-quadruplexes in the presence of potassium and increased thermal stability of all studied systems. Although the activity of DNA-hemin conjugates depended on the sequence used, the highest activity was observed for the DNA-hemin conjugate based on a human telomeric sequence. We used this DNAzyme for development of "sandwich" assay for detection of DNA sequence. For this assay, we used electric chip which could conduct electricity after silver deposition catalyzed by DNAzyme. This method was proved to be selective towards DNA oligonucleotides with mismatches and could be used for the detection of the target. To prove the versatility of our DNAzyme probe we also performed experiments with streptavidin-coated microplates. Our research proved that DNAzyme with covalently attached hemin can be used successfully in the development of heterogeneous assays.

Enhancement of Activity for Peroxidase-Mimicking DNAzyme by Covalent Attachment of Hemin to G-Quadruplex-Forming Oligonucleotide Using Click Chemistry

Peroxidase-mimicking DNAzymes are used in the development of new bioanalytical assays due to their advantages like thermal stability, simple synthesis and purification, and ability to hybridize with the complementary strand of nucleic acid. Here, we describe the method of covalent attachment of hemin to DNA oligonucleotide using click chemistry that allows good yield (60-70%) of the final conjugate product. The activity of obtained DNAzymes is monitored using chromogenic and fluorogenic substrates.

The proximity of the G-quadruplex to hemin impacts the intrinsic DNAzyme activity in mitochondria

The DNAzyme activity of G-quadruplex/hemin in mitochondria has not been characterized. Herein, we report an unexpected difference in the DNAzyme activity between in vitro assays and in mitochondria. Molecular dynamic simulations illustrate how the interaction of the G-quadruplex with hemin may modulate the DNAzyme activity. These results might facilitate a better understanding of the catalytic mechanism of the DNAzyme and help the rational design of stable and active DNAzymes suitable for intracellular catalysis.

Azides and Porphyrinoids: Synthetic Approaches and Applications. Part 1-Azides, Porphyrins and Corroles

Azides and porphyrinoids (such as porphyrin and corrole macrocycles) can give rise to new derivatives with significant biological properties and as new materials' components. Significant synthetic approaches have been studied. A wide range of products (e.g., microporous organic networks, rotaxane and dendritic motifs, dendrimers as liquid crystals, as blood substitutes for transfusions and many others) can now be available and used for several medicinal and industrial purposes.

Advances in optical assays for detecting telomerase activity

Telomerase uses its RNA as template and its protein unit as reverse transcriptase to synthesize TTAGGG repeats at the ends of the eukaryotic chromosome to maintain the lengths of telomeres. Telomerase activity up-regulates in about 85% of human tumors compared with somatic cells, which indicates that telomerase is a tumor biomarker. Reliable assay of telomerase activity is thus essential in diagnosis and management of malignant tumors. In this review, recent developed optical assays are summarized based on the readout signal, including chemiluminescence assay, colorimetric assay, and fluorescence assay.

An Ultrasensitive Colorimetric Strategy for Detection of Cadmium Based on the Peroxidase-like Activity of G-Quadruplex-Cd(II) Specific Aptamer

We rationally designed an ultrasensitive and label-free sensing platform for determination of cadmium (Cd). The sensing platform contains G-quadruplex-Cd(II) specific aptamer (GCDSA) constructed by incorporating G-rich sequence at the end of 5' and the critical domain of the Cd-4 aptamer. GCDSA designed act as both a special recognition sequence for Cd²⁺ and a signal DNAzyme. In absence of Cd²⁺, GCDSA may mainly exist in a random coil sequence. Upon addition of Cd²⁺, GCDSA could probably be induced to fold into a G-quadruplex structure. The generation of plentiful active G-quadruplex interacts with hemin to form a peroxidase-like DNAzyme, leading to increased absorbance signal of the sensing system. ΔA was directly proportional to the two segments of concentrations for Cd²⁺, with the detection of limit of 0.15 nM. The proposed method avoids the labeled oligonucleotides and allows directly quantitative analysis of the samples by cheap instruments, with an excellent dynamic range.

Comparison of Characteristics and DNAzyme Activity of G4⁻Hemin Conjugates Obtained via Two Hemin Attachment Methods

Two conjugation methods using different linkers were applied for the investigation of the spectral characteristics and activity of G-quadruplex (G4)–hemin conjugates. For this purpose, two G-quadruplex-forming DNA sequences were selected, and then conjugated to a hemin molecule via either amine coupling or a click reaction. The products obtained via these two methods differed in their chemistry and the length of the linker between the DNA and hemin molecules. Spectral characteristics revealed that both methods produced conjugates that were more thermally stable than G4/hemin complexes. Despite similar spectral characteristics, the conjugates obtained via these two methods differed in their DNAzyme activity. G4–hemin conjugates obtained through amine coupling exhibited higher activity than conjugates obtained through a click reaction. This was potentially due to the length and chemistry of the linker, which was 30 atoms long following the click reaction, but only six atoms long following amine coupling. A longer connector favors higher flexibility, and hence, reduces the binding of hemin with G4. The aromatic groups present in the linker obtained through the click reaction can also disturb the G4–hemin interaction. However, the conjugation of G4 DNA to hemin via the click reaction was connected to a higher yield, and did not require any sophisticated synthesis equipment.

Dataset on characterization of hemin-azide derivative and DNA oligonucleotide-hemin conjugate

In this article newly synthesized azide derivative of hemin and DNA-hemin conjugate are characterized. Hemin-azide was purified using HPLC and characterized using elemental analysis, IR and NMR. The DNA-hemin conjugate was obtained via click chemistry [1] and click reaction was carried out using traditional Cu-catalyzed and Cu-free approaches. The final product was successfully obtained using Cu-free cycloaddition. The identity of product was confirmed using Maldi TOF spectrometry. Obtained hemin-DNA conjugate exhibited peroxidase-like activity.