Effect of Distance from Catalytic Synergy Group to Iron Porphyrin Center on Activity of G-Quadruplex/Hemin DNAzyme

Dehui Qiu,Yongqiang Cheng,Yuan Liu,Jiangyan Zhang,Jingang Mo,Xiaobo Zhang

doi:10.3390/molecules25153425

Dehui Qiu, Yongqiang Cheng + Show 4 more

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https://doi.org/10.3390/molecules25153425

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Abstract

G-quadruplex/Hemin (G4/Hemin) complex has been widely used in biocatalysis and analytical applications. Meanwhile, compared with natural proteinous enzyme, its low catalytic activity is still limiting its applications. Even though several methods have been developed to enhance the peroxidation efficiency, the important core of the G4 design based enhancement mechanism is still indistinct. Here, we focus the mechanism study on the two most important microdomains: the iron porphyrin center and the catalytic synergy group within the 3′ flanking. These microdomains not only provide the pocket for the combination of substrate, but also offer the axial coordination for the accelerated formation of Compound I (catalytic intermediate). In order to obtain a more suitable space layout to further accelerate the catalytic process, we have used the bases within the 3′ flanking to precisely regulate the distance between microdomains. Finally, the position-dependent effect on catalytic enhancement is observed. When dC is positioned at the second-position of 3′ flanking, the newly obtained DNAzyme achieves an order of magnitude improvement compared to parent G4/Hemin in catalytic activity. The results highlight the influence of the distance between the catalytic synergy group and iron porphyrin center on the activity of DNAzyme, and provide insightful information for the design of highly active DNAzymes.

Highlights

Some exogenous catalytic synergy agents, such as adenosine triphosphate (ATP) [22,23], DOTA-templated synthetic G-quartet (DOTASQ) [24], nitrogenous buffers [6], and spermine [25], have been used as efficient additives to boost the catalytic activity of G4/Hemin
(-NH2 ) of the dA or dC have been considered as important candidates for improving the catalytic activity of DNAzyme (Supplementary Figure S1A,B, marked with red) [28]
All the results presented here show that the peroxidase-mimicking DNAzyme activity can be regulated by the 30 end flanking sequences with a position-dependent effect

Summary

Introduction

G-quadruplex (G4) is a four-stranded nucleic acid structure formed by stacked guanine tetrads [1,2,3]and it can combine with Hemin (G4/Hemin) to mimic peroxidase for catalyzing redox reaction [4,5,6].Compared with protein peroxidases, G4/Hemin possesses several significant advantages, including high cost-efficiency ratio, excellent adaptability to harsh conditions, and chemical modification potential [7,8,9].As a promising DNAzyme, G4/Hemin DNAzyme can efficiently catalyze H2 O2 -mediated oxidation with several substrates including 2,20 -azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) [5], 3,30 ,5,50 -tetramethylbenzidine sulfate (TMB) [10], luminol [11], nicotinamide adenine dinucleotideMolecules 2020, 25, 3425; doi:10.3390/molecules25153425 www.mdpi.com/journal/molecules (NADH) [12], and dopamine [13]. Some exogenous catalytic synergy agents, such as adenosine triphosphate (ATP) [22,23], DOTA-templated synthetic G-quartet (DOTASQ) [24], nitrogenous buffers [6], and spermine [25], have been used as efficient additives to boost the catalytic activity of G4/Hemin. These exciting results only appear along with extremely high concentrations of above additives, which is very unfriendly for related applications, especially in vivo experiments

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