Porphyrin metalation catalyzed by DNAzymes and nanozymes

Yang, Hualin; Zhou, Yu; Liu, Juewen

doi:10.1039/d1qi00105a

Cited by 21 publications

(9 citation statements)

References 124 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As there exist numerous metalloporphyrins (i.e., Fe-PPIX, Mg-PPIX and Zn-PPIX), the structures of these metalloporphyrins differ depending on their associated central metal ions, which might lead to a variable rate at which protons replace metal ions to form PPIX monomers (Fleischer, 1970;Yang et al, 2021). Besides, metalloporphyrins are also unstable according to their associated ions, likely following an order of stability as the following: medium-sized metals (like Fe 2+ , Cu 2+ , Zn 2+ ) > large sized metals (Hg 2+ , Pb 2+ , Cd 2+ ) > alkali metals (Na + , K + , Li + ) (Yang et al, 2021). For example, Cu 2+ is more stable as a soft Lewis acid once tightly bound to porphyrin rings, which can only be desorbed or destructed under drastic conditions (Yang et al, 2021).…”

Section: The Ppix Dynamics From the Freshwater To Saline Watersmentioning

confidence: 99%

“…Besides, metalloporphyrins are also unstable according to their associated ions, likely following an order of stability as the following: medium-sized metals (like Fe 2+ , Cu 2+ , Zn 2+ ) > large sized metals (Hg 2+ , Pb 2+ , Cd 2+ ) > alkali metals (Na + , K + , Li + ) (Yang et al, 2021). For example, Cu 2+ is more stable as a soft Lewis acid once tightly bound to porphyrin rings, which can only be desorbed or destructed under drastic conditions (Yang et al, 2021). The metalloporphyrins with large metals and alkali metals could be more easily transformed into the corresponding free porphyrin molecules in dilute acids (Barnes and Dorough, 1950;Yang et al, 2021).…”

Section: The Ppix Dynamics From the Freshwater To Saline Watersmentioning

confidence: 99%

“…For example, Cu 2+ is more stable as a soft Lewis acid once tightly bound to porphyrin rings, which can only be desorbed or destructed under drastic conditions (Yang et al, 2021). The metalloporphyrins with large metals and alkali metals could be more easily transformed into the corresponding free porphyrin molecules in dilute acids (Barnes and Dorough, 1950;Yang et al, 2021).…”

Section: The Ppix Dynamics From the Freshwater To Saline Watersmentioning

confidence: 99%

See 2 more Smart Citations

A new technique of quantifying protoporphyrin IX in microbial cells in seawater

Yue

Zhong

et al. 2022

Front. Mar. Sci.

View full text Add to dashboard Cite

Protoporphyrin IX (PPIX), a fundamental precursor in the synthesis of heme and chlorophyll, plays a vital role in the biological metabolism and biogeochemical cycling in the ocean. PPIX has previously been identified in humans, animals, and plants, while so far as we know, there is no measurements until now regarding its contents in microbes, and especially in marine phytoplankton and bacteria. Here, for the first time, we reported a method of determining PPIX in marine microbial cells via acetone extraction followed by reversed phase high-performance liquid chromatography quantification, in which acetone-acetonitrile/water-formic acid buffer was used as a gradient elution solvent. The method was optimized with the detection limit of 3.8 ± 1.0 pM, and recovery rate of 97.5 ± 1.9%. The structure of the extracted PPIX was further confirmed using tandem mass spectrometry as positively associated with specific protonated molecules [M + H]+. The method was then successfully applied in the determination of PPIX in microbial cells in the water samples collected from a median-sized subtropical estuary (the Jiulong River Estuary, China). The results showed that PPIX existed widely and ranged from 20 – 170 ng/L in cells in the water samples. In the whole estuary, cellular PPIX generally decreased linearly with increasing salinity. A positive correlation of PPIX with particulate organic matter in the estuary suggested of sediment suspension and dissolution as its possible source. In addition, a general hyperbolic fitting pattern was observed for PPIX against dissolved inorganic nitrogen, PO43−, and the bacterial abundance (104 – 106 cells/mL) in the estuary. Such results indicated that PPIX played a crucial role in linking nutrients and the microbial productivity. In summary, we developed a new technique of quantifying cellular PPIX in water samples and confirmed the wide existence of cellular PPIX in natural waters. The data from Jiulong River estuary further suggest that the contents of cellular PPIX be enhanced with the nutrient supply from riverine inputs and sediment suspensions, which thereafter dictate the productivity of phytoplankton and bacteria in coastal waters.

show abstract

Section: The Ppix Dynamics From the Freshwater To Saline Watersmentioning

confidence: 99%

Section: The Ppix Dynamics From the Freshwater To Saline Watersmentioning

confidence: 99%

Section: The Ppix Dynamics From the Freshwater To Saline Watersmentioning

confidence: 99%

See 1 more Smart Citation

A new technique of quantifying protoporphyrin IX in microbial cells in seawater

Yue

Zhong

et al. 2022

Front. Mar. Sci.

View full text Add to dashboard Cite

show abstract

“…Development of the new bioanalytical methods is often achieved using DNAzymes [1,2]. These catalytically active DNA molecules can catalyze such reactions such as DNA and RNA ligation or cleavage, DNA phosphorylation, porphyrin metalation, or peroxidase reaction [3][4][5]. In many bioassays G-quadruplex/hemin DNAzyme with peroxidase activity is used for the analytical signal generation [6].…”

Section: Introductionmentioning

confidence: 99%

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

Kosman

Żukowski

Csáki

et al. 2022

Sensors

View full text Add to dashboard Cite

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.

show abstract

“…Many methods have been developed by controlling the formation or destruction of the G‐quadruplex. [ 31–34 ] In addition, SG I is a common commercial dsDNA dye; once it binds to dsDNA, a strong fluorescence increase can be triggered. [ 35,36 ] In our proposed method, the fluorescent pairs of G‐quadruplex/NMM and dsDNA/SG I were utilized to develop a novel Hg 2+ biosensor.…”

Section: Introductionmentioning

confidence: 99%

A label‐free ratiometric method to detect Hg²⁺ based on structural change of DNA

Peng

Liu

et al. 2021

Luminescence

Self Cite

View full text Add to dashboard Cite

In this work, a simple ratiometric method has been designed to detect Hg2+ based on the structural change between double‐stranded DNA (dsDNA) and its G‐quadruplex structure. When Hg2+ was added, the designed G‐quadruplex structure could change into the corresponding dsDNA by forming the T–Hg2+–T mismatch. This kind of variation resulted in a decrease in the fluorescence of the G‐quadruplex/N‐methyl mesoporphyrin IX (NMM) complex and an increase in the fluorescence from the dsDNA/SYBR Green I (SG I) pair. The secondary excitation wavelength of SG I was used to excite NMM and SG I simultaneously. The titration experiment indicated that the new method had a linear response within 0.7–2.5 μM Hg2+ with a limit of detection of 9.3 nM. Because using the T–Hg2+–T mismatch to recognize Hg2+ was very specific, the selectivity of the new method was also satisfactory. The recoveries ranged from 92.8% to 110.2% suggested that this new method could achieve a potential application for Hg2+ detection in real environmental samples.

show abstract

Porphyrin metalation catalyzed by DNAzymes and nanozymes

Abstract: In this review, DNA and nanomaterial based catalysts for porphyrin metalation reactions are summarized, including the selection of DNAzymes, choice of nanomaterials, their catalytic mechanisms, and applications of the reactions.

Cited by 21 publications

References 124 publications

A new technique of quantifying protoporphyrin IX in microbial cells in seawater

A new technique of quantifying protoporphyrin IX in microbial cells in seawater

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

A label‐free ratiometric method to detect Hg²⁺ based on structural change of DNA

Contact Info

Product

Resources

About

Porphyrin metalation catalyzed by DNAzymes and nanozymes

Abstract: In this review, DNA and nanomaterial based catalysts for porphyrin metalation reactions are summarized, including the selection of DNAzymes, choice of nanomaterials, their catalytic mechanisms, and applications of the reactions.

Cited by 21 publications

References 124 publications

A new technique of quantifying protoporphyrin IX in microbial cells in seawater

A new technique of quantifying protoporphyrin IX in microbial cells in seawater

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

A label‐free ratiometric method to detect Hg2+ based on structural change of DNA

Contact Info

Product

Resources

About

A label‐free ratiometric method to detect Hg²⁺ based on structural change of DNA