Nucleoapzymes: catalyst-aptamer conjugates as enzyme-mimicking structures

2019 ◽  
Vol 3 (5) ◽  
pp. 493-499 ◽  
Author(s):  
Verena Wulf ◽  
Itamar Willner
Keyword(s):  
Nucleic Acid ◽  
Variable Structure ◽  
Structural Diversity ◽  
Research Field ◽  
Dynamic Simulations ◽  
Catalytic Function ◽  
Enzyme Mimicking ◽  
G Quadruplex ◽  
Catalytic Sites ◽  
Hydrolysis Of

The conjugation of catalytic sites to sequence-specific, ligand-binding nucleic acid aptamers yields functional catalytic ensembles mimicking the catalytic/binding properties of native enzymes. These catalyst-aptamer conjugates termed ‘nucleoapzymes’ reveal structural diversity, and thus, vary in their catalytic activity, due to the different modes of conjugation of the catalytic units to the nucleic acid aptamer scaffold. The concept of nucleoapzymes is introduced with the assembly of a set of catalysts consisting of the hemin/G-quadruplex DNAzyme (hGQ) conjugated to the dopamine aptamer. The nucleoapzymes catalyze the oxidation of dopamine by H2O2 to yield aminochrome. The catalytic processes are controlled by the structures of the nucleoapzymes, and chiroselective oxidation of l-DOPA and d-DOPA by the nucleoapzymes is demonstrated. In addition, the conjugation of a Fe(III)-terpyridine complex to the dopamine aptamer and of a bis-Zn(II)-pyridyl-salen-type complex to the ATP-aptamer yields hybrid nucleoapzymes (conjugates where the catalytic site is not a biomolecule) that catalyze the oxidation of dopamine to aminochrome by H2O2 and the hydrolysis of ATP to ADP, respectively. Variable, structure-controlled catalytic activities of the different nucleoapzymes are demonstrated. Molecular dynamic simulations are applied to rationalize the structure-catalytic function relationships of the different nucleoapzymes. The challenges and perspectives of the research field are discussed.

scholarly journals GUANINEHEXOSIDE OBTAINED ON HYDROLYSIS OF THYMUS NUCLEIC ACID

1912 ◽  
Vol 12 (3) ◽  
pp. 377-379
Author(s):  
P.A. Levene ◽  
W.A. Jacobs
Keyword(s):  
Nucleic Acid ◽  
Hydrolysis Of

scholarly journals Overlapping but distinct: a new model for G-quadruplex biochemical specificity

2021 ◽  
Author(s):  
Martin Volek ◽  
Sofia Kolesnikova ◽  
Katerina Svehlova ◽  
Pavel Srb ◽  
Ráchel Sgallová ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Drug Design ◽  
Solution Structure ◽  
Biochemical Data ◽  
Biological Regulation ◽  
New Model ◽  
G Quadruplex ◽  
Range Of Functions ◽  
Nucleic Acid Structures ◽  
Sequence Requirements

Abstract G-quadruplexes are noncanonical nucleic acid structures formed by stacked guanine tetrads. They are capable of a range of functions and thought to play widespread biological roles. This diversity raises an important question: what determines the biochemical specificity of G-quadruplex structures? The answer is particularly important from the perspective of biological regulation because genomes can contain hundreds of thousands of G-quadruplexes with a range of functions. Here we analyze the specificity of each sequence in a 496-member library of variants of a reference G-quadruplex with respect to five functions. Our analysis shows that the sequence requirements of G-quadruplexes with these functions are different from one another, with some mutations altering biochemical specificity by orders of magnitude. Mutations in tetrads have larger effects than mutations in loops, and changes in specificity are correlated with changes in multimeric state. To complement our biochemical data we determined the solution structure of a monomeric G-quadruplex from the library. The stacked and accessible tetrads rationalize why monomers tend to promote a model peroxidase reaction and generate fluorescence. Our experiments support a model in which the sequence requirements of G-quadruplexes with different functions are overlapping but distinct. This has implications for biological regulation, bioinformatics, and drug design.

Enzymatic Hydrolysis of PET: Structural Diversity and Kinetic Properties of Cutinases from Thermobifida

2014 ◽  
Vol 31 ◽  
pp. S88
Author(s):  
Altijana Hromic ◽  
Doris Ribitsch ◽  
Andrzej Lyskowski ◽  
Georg Steinkellner ◽  
Helmut Schwab ◽  
...  
Keyword(s):  
Enzymatic Hydrolysis ◽  
Structural Diversity ◽  
Kinetic Properties ◽  
Hydrolysis Of

Using the structural diversity of siderophore biosynthesis genes for intra-and interspecific differentiation of pathogenic yersinia

2021 ◽  
pp. 50-56
Author(s):  
Daria Aleksandrovna Kuznetsova ◽  
Aleksey Leonidovich Trukhachev ◽  
Violetta Aleksandrovna Rykova ◽  
Olga Nikolaevna Podladchikova
Keyword(s):  
Tandem Repeats ◽  
Variable Structure ◽  
Structural Diversity ◽  
Variable Number ◽  
Differential Diagnostics ◽  
Pcr Analysis ◽  
Unknown Variable ◽  
Siderophore Biosynthesis ◽  
Pathogenic Yersinia

The paper analyzes the siderophore biosynthesis genes that are located in the ysu and ynp loci of only Y. pestis and Y. pseudotuberculosis, have variable structure between different strains of both species and contain previously unknown variable number tandem repeats (VNTR). The purpose of the study was to assess the possibility of using these VNTR as genetic markers for intra-and interspecific differentiation of pathogenic Yersinia. Based on the novel VNTR-markers, three pairs of primers (ysu-interF/R, ilp1F/R и ilp2F/R) were designed and used for the in silico and in vitro PCR analysis of various Y.pestis and Y. pseudotuberculosis strains. All studied Y. pestis strains of the main subspecies (ssp pestis), unlike the strains of non-main subspecies and Y. pseudotuberculosis, did not give amplicon with ilp1F/R primers, since the area between them contains an IS100 element. To identify the strains of the main subspecies, the fourth pair of primers ilp1F-is100R was designed, allowing the most dangerous ssp pestis strains to be distinguished from the not dangerous non-main ssp strains. Y. pseudotuberculosis strains were characterized by a significant variety of amplicons with three pairs of primers, and which made it possible to carry out intraspecies strain genotyping. At the same time, for those strains whose serotype is known, the correlation between the serogroup and the genotype of the strains was observed. Analysis of the 1 serotype strains representing most sequenced Y. pseudotuberculosis strains allowed us to separate two gene groups differing from the rest of 1 serotype gene groups. The first one included the serotype 1a strains isolated from people in Europe, which are known to have the greatest pathogenetic potential. The other one was formed by serotype 1b strains isolated from people in Siberia and Primorye, which are characterized by the high epidemic potential. Thus, four pairs of primers designed in this study can be used to develop additional tests for the identification and differential diagnostics of the most dangerous Y. pestis ssp pestis and Y. pseudotuberculosis serotype 1a and 1b strains.

scholarly journals Structural and Catalytic Characterization of TsBGL, a β-Glucosidase From Thermofilum sp. ex4484_79

2021 ◽  
Vol 12 ◽  
Author(s):  
Anke Chen ◽  
Dan Wang ◽  
Rui Ji ◽  
Jixi Li ◽  
Shaohua Gu ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Specific Activity ◽  
Maximum Activity ◽  
Homologous Proteins ◽  
Glycosidic Bonds ◽  
Catalytic Sites ◽  
Potential Applications ◽  
Beta Glucosidase ◽  
Hydrolysis Of

Beta-glucosidase is an enzyme that catalyzes the hydrolysis of the glycosidic bonds of cellobiose, resulting in the production of glucose, which is an important step for the effective utilization of cellulose. In the present study, a thermostable β-glucosidase was isolated and purified from the Thermoprotei Thermofilum sp. ex4484_79 and subjected to enzymatic and structural characterization. The purified β-glucosidase (TsBGL) exhibited maximum activity at 90°C and pH 5.0 and displayed maximum specific activity of 139.2μmol/min/mgzne against p-nitrophenyl β-D-glucopyranoside (pNPGlc) and 24.3μmol/min/mgzen against cellobiose. Furthermore, TsBGL exhibited a relatively high thermostability, retaining 84 and 47% of its activity after incubation at 85°C for 1.5h and 90°C for 1.5h, respectively. The crystal structure of TsBGL was resolved at a resolution of 2.14Å, which revealed a classical (α/β)8-barrel catalytic domain. A structural comparison of TsBGL with other homologous proteins revealed that its catalytic sites included Glu210 and Glu414. We provide the molecular structure of TsBGL and the possibility of improving its characteristics for potential applications in industries.

scholarly journals Oxadiazole/Pyridine-Based Ligands: A Structural Tuning for Enhancing G-Quadruplex Binding

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2162 ◽  
Author(s):  
Filippo Doria ◽  
Valentina Pirota ◽  
Michele Petenzi ◽  
Marie-Paule Teulade-Fichou ◽  
Daniela Verga ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Structural Transition ◽  
Binding Mode ◽  
Telomeric Sequence ◽  
Recognition Element ◽  
New Family ◽  
G Quadruplex ◽  
Preferential Binding ◽  
High Cytotoxicity ◽  
Nucleic Acid Structures

Non-macrocyclic heteroaryls represent a valuable class of ligands for nucleic acid recognition. In this regard, non-macrocyclic pyridyl polyoxazoles and polyoxadiazoles were recently identified as selective G-quadruplex stabilizing compounds with high cytotoxicity and promising anticancer activity. Herein, we describe the synthesis of a new family of heteroaryls containing oxadiazole and pyridine moieties targeting DNA G-quadruplexes. To perform a structure–activity analysis identifying determinants of activity and selectivity, we followed a convergent synthetic pathway to modulate the nature and number of the heterocycles (1,3-oxazole vs. 1,2,4-oxadiazole and pyridine vs. benzene). Each ligand was evaluated towards secondary nucleic acid structures, which have been chosen as a prototype to mimic cancer-associated G-quadruplex structures (e.g., the human telomeric sequence, c-myc and c-kit promoters). Interestingly, heptapyridyl-oxadiazole compounds showed preferential binding towards the telomeric sequence (22AG) in competitive conditions vs. duplex DNA. In addition, G4-FID assays suggest a different binding mode from the classical stacking on the external G-quartet. Additionally, CD titrations in the presence of the two most promising compounds for affinity, TOxAzaPy and TOxAzaPhen, display a structural transition of 22AG in K-rich buffer. This investigation suggests that the pyridyl-oxadiazole motif is a promising recognition element for G-quadruplexes, combining seven heteroaryls in a single binding unit.

Effect of Cytokinins on the Expansion and Metabolism of Excised Cucumber Cotyledons

1980 ◽  
Vol 7 (3) ◽  
pp. 227
Author(s):  
C Tsui ◽  
Tao Guo-qing ◽  
Chen Hui-ying ◽  
Son Yan-ru ◽  
Lian Han-ping ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Soluble Sugars ◽  
Dry Weight ◽  
Acid Synthesis ◽  
Cell Number ◽  
Cucumis Sativus L ◽  
Biochemical Processes ◽  
Dna And Rna ◽  
Lag Period ◽  
Hydrolysis Of

Expansion of excised cucumber (Cucumis sativus L.) cotyledons was stimulated by treatment with cytokinin, and commenced after a lag period of about 4 h. Expansion induced by benzyladenine (BA) was due mainly to increase of fresh weight, but cell number increased slightly. Hydrolysis of protein and lipid was stimulated by BA, and soluble sugars increased simultaneously. However, there was no significant change in the dry weight of cotyledons during the period of expansion. It is assumed that the transformation of lipid to sugar in the cotyledon is stimulated by BA. The respiration of cotyledons was evidently stimulated by BA and was entirely inhibited by respiratory inhibitors, e.g. NaN,, malonate and dinitrophenol. Inhibitors of protein and nucleic acid synthesis, such as chloramphenicol and actinomycin D, inhibited only the BA-induced expansion. They had no effect on the expansion of controls. These results suggest that different biochemical processes are involved in the expansion of cotyledons induced by BA and in controls. The former is related not only to respiration but also to the synthesis of protein and nucleic acid. BA increased DNA and RNA content per cotyledon. The increase of total RNA is due mainly to the increase of 25 S and 18 S rRNA.

scholarly journals Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe

2019 ◽  
Vol 47 (12) ◽  
pp. 6059-6072 ◽  
Author(s):  
Ashok Nuthanakanti ◽  
Ishtiyaq Ahmed ◽  
Saddam Y Khatik ◽  
Kayarat Saikrishnan ◽  
Seergazhi G Srivatsan
Keyword(s):  
Nucleic Acid ◽  
Ligand Binding ◽  
Real Time ◽  
Telomeric Dna ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Class ◽  
Loop Region ◽  
Dna Repeat ◽  
G Quadruplex

Abstract Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2′-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.

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