Relations between the loop transposition of DNA G-quadruplex and the catalytic function of DNAzyme

G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol

Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin's peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair.

The noncovalent dimerization of a G-quadruplex/hemin DNAzyme improves its biocatalytic properties

While many protein enzymes exert their functions through multimerization, which improves both selectivity and activity, this has not yet been demonstrated for other naturally occurring catalysts. Here, we report a multimerization effect applied to catalytic DNAs (or DNAzymes) and demonstrate that the enzymatic efficiency of G-quadruplexes (GQs) in interaction with the hemin cofactor is remarkably enhanced by homodimerization. The resulting non-covalent dimeric GQ-DNAzyme system provides hemin with a structurally defined active site in which both the cofactor (hemin) and the oxidant (H2O2) are activated. This new biocatalytic system efficiently performs peroxidase- and peroxygenase-type biotransformations of a broad range of substrates, thus providing new perspectives for biotechnological application of GQs.

Investigation and improvement of catalytic activity of G-quadruplex/hemin DNAzymes using designed terminal G-tetrads with deoxyadenosine caps

It is generally acknowledged that G-quadruplexes (G4s) acquire peroxidase activity upon interaction with hemin. Hemin has been demonstrated to bind selectively to the 3′-terminal G-tetrad of parallel G4s via end-stacking; however, the relationships between different terminal G-tetrads and the catalytic functions of G4/hemin DNAzymes are not fully understood. Herein, the oligonucleotide d(AGGGGA) and its three analogues, d(AG^BrG^BrGGA), d(AG^BrGGG^BrA) and d(AG^BrGG^BrGA) (G^Br indicates 8-bromo-2′-deoxyguanosine), were designed. These oligonucleotides form three parallel G4s and one antiparallel G4 without loop regions. The scaffolds had terminal G-tetrads that were either anti-deoxyguanosines (anti-dGs) or syn-deoxyguanosines (syn-dGs) at different proportions. The results showed that the parallel G4 DNAzymes exhibited 2 to 5-fold higher peroxidase activities than the antiparallel G4 DNAzyme, which is due to the absence of the 3′-terminal G-tetrad in the antiparallel G4. Furthermore, the 3′-terminal G-tetrad consisting of four anti-dGs in parallel G4s was more energetically favorable and thus more preferable for hemin stacking compared with that consisting of four syn-dGs. We further investigated the influence of 3′ and 5′ deoxyadenosine (dA) caps on the enzymatic performance by adding 3′-3′ or 5′-5′ phosphodiester bonds to AG₄A. Our data demonstrated that 3′ dA caps are versatile residues in promoting the interaction of G4s with hemin. Thus, by increasing the number of 3′ dA caps, the DNAzyme of 3′A5′-5′GG3′-3′GG5′-5′A3′ with two 5′-terminal G-tetrads can exhibit significantly high catalytic activity, which is comparable to that of 5′A3′-3′GG5′-5′GG3′-3′A5′ with two 3′-terminal G-tetrads. This study may provide insights into the catalytic mechanism of G4-based DNAzymes and strategies for promoting their catalytic activities.

Investigation of the peroxidase activities of G4/hemin DNAzymes using designed terminal G-tetrads by eliminating the steric effect of loop regions.

Heme•G-Quadruplex DNAzymes: Conditions for Maximizing Their Peroxidase Activity

Catalytic DNAs (DNAzymes) with peroxidase-like activity have great potential in bioanalytical chemistry [1], owing to numerous advantages that DNA enzymes offer over conventional protein enzymes, including structural simplicity, low cost, thermal stability, and straightforward handling and preparation. Maximizing the efficiency of the peroxidase activity of such DNAzymes is a subject in need of review. In this chapter, we discuss the optimal experimental conditions for the peroxidase activity of these DNAzymes and describe general procedures for their utilization.

An oxidatively damaged G-quadruplex/hemin DNAzyme

Oxidative damage of guanine to 8-oxoguanine triggers a partial and variable loss of G-quadruplex/hemin DNAzyme activity and provides clues to the mechanistic origins of DNAzyme deactivation, which originates from an interplay between decreased G-quadruplex stability, lower hemin affinity and a modification of the nature of hemin binding sites.

Loop permutation affects the topology and stability of G-quadruplexes

G-quadruplexes are unusual DNA and RNA secondary structures ubiquitous in a variety of organisms including vertebrates, plants, viruses and bacteria. The folding topology and stability of intramolecular G-quadruplexes are determined to a large extent by their loops. Loop permutation is defined as swapping two or three of these regions so that intramolecular G-quadruplexes only differ in the sequential order of their loops. Over the past two decades, both length and base composition of loops have been studied extensively, but a systematic study on the effect of loop permutation has been missing. In the present work, 99 sequences from 21 groups with different loop permutations were tested. To our surprise, both conformation and thermal stability are greatly dependent on loop permutation. Loop permutation actually matters as much as loop length and base composition on G-quadruplex folding, with effects on T_m as high as 17°C. Sequences containing a longer central loop have a high propensity to adopt a stable non-parallel topology. Conversely, sequences containing a short central loop tend to form a parallel topology of lower stability. In addition, over half of interrogated sequences were found in the genomes of diverse organisms, implicating their potential regulatory roles in the genome or as therapeutic targets. This study illustrates the structural roles of loops in G-quadruplex folding and should help to establish rules to predict the folding pattern and stability of G-quadruplexes.

Fluorescence Spectroscopic Insight into the Supramolecular Interactions in DNA-Based Enantioselective Sulfoxidation

Interactions of copper(II)-bipyridine cofactors and thioanisole substrate with human telomeric G-quadruplex DNA were studied by UV/Vis absorption, circular dichroism, and fluorescence quenching titration. Three copper(II)-bipyridine complexes are equivalently anchored to the G-quadruplex scaffold at all five fluorescently labeled sites. Thioanisole interacts with the DNA architecture at both the second loop and 3' terminus in the absence or presence of copper(II)-bipyridine complexes. These nonspecificities in the weak interactions of Cu^II complexes and thioanisole with G-quadruplex might explain why DNA only affords a modest enantioselectivity in the oxidation of thioanisole. These findings provide insights toward the construction of highly enantioselective DNA-based catalysts.

A topological transition from bimolecular quadruplex to G-triplex/tri-G-quadruplex exhibited by truncated double repeats of human telomere

Human telomeric G-rich sequences can fold back into various conformations depending upon the salt (Na⁺ or K⁺) at physiological pH. On the basis of results obtained by native PAGE electrophoresis, circular dichroism, and UV-melting experiments, we report here that truncated sequences of human telomere (d-GGGTTAGGG; GM9, d-AGGGTTAGGG; GM10, d-TAGGGTTAGGG; GM11) adopt a varied range of quadruplex conformations as a function of the cation present. By correlating CD and gel electrophoresis experiments; it was concluded that the GM9 oligonucleotide can self-associate to form a tetramer quadruplex (antiparallel; AP) in Na⁺ solution and a mixture of G-triplex (AP) or tri-G-quadruplex (parallel; P) along with a tetramer G-quadruplex structure (AP) in K⁺. The GM10 oligonucleotide formed a bimolecular G-quadruplex in both Na⁺ and K⁺ solutions, while GM11 associated to form a bimolecular G-quadruplex (AP) structure in Na⁺ solution and a mixture of bimolecular G-quadruplex (AP) and bimolecular G-quadruplex (P) along with parallel G-triplex or antiparallel tri-G-quadruplex in K⁺. All the UV-melting profiles, thermal difference spectra, and CD melting curves suggested the formation of a variety of G-quadruplex conformations by the DNA sequences studied in Na⁺ and K⁺ ions. Hypothetical models for different conformations adopted by these DNA molecules have also been proposed, which may further enhance our knowledge about the divergent topologies of guanine quadruplexes.

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.