A superior G-quadruplex DNAzyme through functionalized modification of the hemin cofactor

2020 ◽  
Vol 56 (16) ◽  
pp. 2427-2430
Author(s):  
Yan Liu ◽  
Peidong Lai ◽  
Jingru Wang ◽  
Xiwen Xing ◽  
Liang Xu

Chemical modifications of the hemin structure through introducing new functionalities are proposed to enhance the catalytic efficiency of the hemin/G-quadruplex DNAzyme.

2021 ◽  
Vol 217 ◽  
pp. 107649 ◽  
Author(s):  
Claudia Riccardi ◽  
Ettore Napolitano ◽  
Chiara Platella ◽  
Domenica Musumeci ◽  
Daniela Montesarchio

Amylase ◽  
2020 ◽  
Vol 4 (1) ◽  
pp. 11-23
Author(s):  
Dhanya Gangadharan ◽  
Anu Jose ◽  
K. Madhavan Nampoothiri

Abstractα-Amylases from a huge number of sources have been isolated and characterised but very few of them meet the demands of the industries. The industrial processes take place under conditions hostile to biocatalysts thus increasing the industrial demand for a highly stable enzyme in good titre level. Improved understanding of biomolecular aspects of α-amylases has led to the advanced understanding of their catalytic nature. Enzymes with high stability are obtained from extremophiles. Extensive studies have demonstrated the importance of regulating expression and catalytic efficiency of nonextremophiles through genetic engineering, directed evolution and chemical modifications. The inability to culture most microorganisms in the environment by standard methods has also led to the focus on the development of metagenomics for getting improved biocatalytic functions. The present review aims to compile the studies reported by researchers in manipulating nonextremophiles and improving stability through directed evolution, metagenomics and protein engineering.


Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4620
Author(s):  
Vibhav Valsangkar ◽  
Sweta Vangaveti ◽  
Goh Woon Lee ◽  
Walid M. Fahssi ◽  
Waqas S. Awan ◽  
...  

The thrombin binding aptamer (TBA) is a promising nucleic acid-based anticoagulant. We studied the effects of chemical modifications, such as dendrimer Trebler and NHS carboxy group, on TBA with respect to its structures and thrombin binding affinity. The two dendrimer modifications were incorporated into the TBA at the 5′ end and the NHS carboxy group was added into the thymine residues in the thrombin binding site of the TBA G-quadruplex (at T4, T13 and both T4/T13) using solid phase oligonucleotide synthesis. Circular dichroism (CD) spectroscopy confirmed that all of these modified TBA variants fold into a stable G-quadruplex. The binding affinity of TBA variants with thrombin was measured by surface plasmon resonance (SPR). The binding patterns and equilibrium dissociation constants (KD) of the modified TBAs are very similar to that of the native TBA. Molecular dynamics simulations studies indicate that the additional interactions or stability enhancement introduced by the modifications are minimized either by the disruption of TBA–thrombin interactions or destabilization elsewhere in the aptamer, providing a rational explanation for our experimental data. Overall, this study identifies potential positions on the TBA that can be modified without adversely affecting its structure and thrombin binding preference, which could be useful in the design and development of more functional TBA analogues.


2021 ◽  
Vol 14 (12) ◽  
pp. 1326
Author(s):  
Weronika Kotkowiak ◽  
Zofia Jahnz-Wechmann ◽  
Anna Pasternak

Aptamers constitute an answer for the growing need for targeted therapy development. One of the most well-known representatives of this group of compounds is thrombin binding aptamers (TBA) targeted towards thrombin. The TBA inhibitory activity is determined by its spatial arrangement, which consists of two G-tetrads linked by two shorter TT loops and one longer TGT loop and folds into a unimolecular, antiparallel G-quadruplex structure. Interesting properties of the aptamer can be further improved via the introduction of a number of chemical modifications. Herein, a comprehensive analysis of the influence of pyrrolo-2’-deoxycytidine (Py-dC) and its derivatives on TBA physicochemical and biological properties has been presented. The studies have shown that the presence of modified residues at the T7 position of the TGT loop has only minor effects on TBA thermodynamic stability without affecting its folding topology. All analyzed oligomers exhibit anticoagulant properties, but only aptamer modified with a decyl derivative of Py-dC was able to inhibit thrombin activity more efficiently than unmodified, parental compounds. Importantly, the same compound also possessed the potential to effectively restrain HeLa cell line growth.


Catalysts ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 613 ◽  
Author(s):  
Raphael I. Adeoye ◽  
Dunsin S. Osalaye ◽  
Theresia K. Ralebitso-Senior ◽  
Amanda Boddis ◽  
Amanda J. Reid ◽  
...  

G-quadruplex DNAzymes are short DNA aptamers with repeating G4 quartets bound in a non-covalent complex with hemin. These G4/Hemin structures exhibit versatile peroxidase-like catalytic activity with a wide range of potential applications in biosensing and biotechnology. Current efforts are aimed at gaining a better understanding of the molecular mechanism of DNAzyme catalysis as well as devising strategies for improving their catalytic efficiency. Multimerisation of discrete units of G-quadruplexes to form multivalent DNAzyes is an emerging design strategy aimed at enhancing the peroxidase activities of DNAzymes. While this approach holds promise of generating more active multivalent G-quadruplex DNAzymes, few examples have been studied and it is not clear what factors determine the enhancement of catalytic activities of multimeric DNAzymes. In this study, we report the design and characterisation of multimers of five G-quadruplex sequences (AS1411, Bcl-2, c-MYC, PS5.M and PS2.M). Our results show that multimerisation of G-quadruplexes that form parallel structure (AS1411, Bcl-2, c-MYC) leads to significant rate enhancements characteristic of cooperative and/or synergistic interactions between the monomeric units. In contrast, multimerisation of DNA sequences that form non-parallel structures (PS5.M and PS2.M) did not exhibit similar levels of synergistic increase in activities. These results show that design of multivalent G4/Hemin structures could lead to a new set of versatile and efficient DNAzymes with enhanced capacity to catalyse peroxidase-mimic reactions.


1994 ◽  
Vol 72 (06) ◽  
pp. 862-868 ◽  
Author(s):  
Frederick A Ofosu ◽  
J C Lormeau ◽  
Sharon Craven ◽  
Lori Dewar ◽  
Noorildan Anvari

SummaryFactor V activation is a critical step preceding prothrombinase formation. This study determined the contributions of factor Xa and thrombin, which activate purified factor V with similar catalytic efficiency, to plasma factor V activation during coagulation. Prothrombin activation began without a lag phase after a suspension of coagulant phospholipids, CaCl2, and factor Xa was added to factor X-depleted plasma. Hirudin, a potent thrombin inhibitor, abrogated prothrombin activation initiated with 0.5 and 1.0 nM factor Xa, but not with 5 nM factor Xa. In contrast, hirudin did not abrogate prothrombin activation in plasmas pre-incubated with 0.5,1.0 or 5 nM α-thrombin for 10 s followed by the coagulant suspension containing 0.5 nM factor Xa. Thus, thrombin activates plasma factor V more efficiently than factor Xa. At concentrations which doubled the clotting time of contact-activated normal plasma, heparin and three low Mr heparins also abrogated prothrombin activation initiated with 0.5 nM factor Xa, but not with 5 nM factor Xa. If factor V in the factor X-depleted plasma was activated (by pre-incubation with 10 nM a-thrombin for 60 s) before adding 0.5,1.0, or 5 nM factor Xa, neither hirudin nor the heparins altered the rates of prothrombin activation. Thus, none of the five anticoagulants inactivates prothrombinase. When 5 or 10 pM relipidated r-human tissue factor and CaCl2 were added to normal plasma, heparin and the three low Mr heparins delayed the onset of prothrombin activation until the concentration of factor Xa generated exceeded 1 nM, and they subsequently inhibited prothrombin activation to the same extent. Thus, hirudin, heparin and low Mr heparins suppress prothrombin activation solely by inhibiting prothrombinase formation.


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