A novel borax-specific ssDNA aptamer screened by high-throughput SELEX and its colorimetric assay with aggregation of AuNPs

2021 ◽  
Vol 101 ◽  
pp. 103947
Author(s):  
Le Jing ◽  
Mingwei Qin ◽  
Xiaomeng Zhang ◽  
Yuzhu Song ◽  
Jinyang Zhang ◽  
...  
2018 ◽  
Vol 84 (16) ◽  
Author(s):  
Wei Zhou ◽  
Rui Huang ◽  
Zhiguang Zhu ◽  
Yi-Heng P. Job Zhang

ABSTRACT Thermostability and specific activity of enzymes are two of the most important properties for industrial biocatalysts. Here, we developed a petri dish-based double-layer high-throughput screening (HTS) strategy for rapid identification of desired mutants of polyphosphate glucokinase (PPGK) from a thermophilic actinobacterium, Thermobifida fusca YX, with both enhanced thermostability and activity. Escherichia coli colonies representing a PPGK mutant library were grown on the first-layer Phytagel-based plates, which can remain solid for 1 h, even at heat treatment temperatures of more than 100°C. The second layer that was poured on the first layer contained agarose, substrates, glucose 6-phosphate dehydrogenase (G6PDH), the redox dye tetranitroblue tetrazolium (TNBT), and phenazine methosulfate. G6PDH was able to oxidize the product from the PPGK-catalyzed reaction and generate NADH, which can be easily examined by a TNBT-based colorimetric assay. The best mutant obtained after four rounds of directed evolution had a 7,200-fold longer half-life at 55°C, 19.8°C higher midpoint of unfolding temperature (Tm), and a nearly 3-fold enhancement in specific activities compared to those of the wild-type PPGK. The best mutant was used to produce 9.98 g/liter myo-inositol from 10 g/liter glucose, with a theoretical yield of 99.8%, along with two other hyperthermophilic enzymes at 70°C. This PPGK mutant featuring both great thermostability and high activity would be useful for ATP-free production of glucose 6-phosphate or its derived products.IMPORTANCE Polyphosphate glucokinase (PPGK) is an enzyme that transfers a terminal phosphate group from polyphosphate to glucose, producing glucose 6-phosphate. A petri dish-based double-layer high-throughput screening strategy was developed by using ultrathermostable Phytagel as the first layer instead of agar or agarose, followed by a redox dye-based assay for rapid identification of ultrathermostable PPGK mutants. The best mutant featuring both great thermostability and high activity could produce glucose 6-phosphate from glucose and polyphosphate without in vitro ATP regeneration.


2020 ◽  
Vol 26 (47) ◽  
pp. 10719-10723 ◽  
Author(s):  
Shaochi Wang ◽  
Alexandra P. Breslawec ◽  
Crystal Li ◽  
Myles B. Poulin

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 245-245
Author(s):  
Christine M. Palermo ◽  
William C. Wimley ◽  
Charles S. Hemenway

Abstract Despite ongoing success in the treatment of childhood acute lymphoblastic leukemia (ALL), patients harboring translocations involving the genetic locus 11q23 continue to have a poor prognosis. The majority of 11q23 translocations result in the formation of a functional fusion protein consisting of the N-terminus of MLL fused to the C-terminal portion of one of more than 30 fusion partners. This translocation results in a functional chimeric protein critical for leukemogenesis. Recently, our lab has identified an interaction between two common MLL fusion partners, AF4 and AF9. Through a series of mapping experiments we identified a small region of human AF4 to be sufficient for its interaction with AF9. Based on these studies, a synthetic peptide (PFWT) that mimics the AF9 binding site on AF4 was developed. Treatment of leukemia cells that express the MLL-AF4 protein with PFWT results in apoptosis with no observable affects on CD34+ hematopoietic stem cells, suggesting the AF9-AF4 interaction is a promising chemotherapeutic target. To improve upon the therapeutic potential of PFWT, we developed a high-throughput enzyme-linked colorimetric assay to identify peptidomimetics that block the AF9-AF4 interaction. A combinatorial peptide library was synthesized in which each position of the 10-mer sequence was substituted with either the α- or corresponding β-amino acid. β-Amino acids which are similar to α-amino acids but contain an additional carbon in their backbone were chosen because of their resistance to proteases (210= 1024 possible unique sequences). To date, 30 of the peptides screened compare favorably with PFWT for disrupting the AF4-AF9 interaction. Sequencing of the peptides by MS/MS revealed substitutions at the N- and C-terminal ends are well tolerated. In addition, peptides can incorporate as many as three β-amino acids and still retain biological activity. These data are important for establishing a sequence with improved pharmacokinetic properties as compared to PFWT and serve as the first step in our design towards an optimal peptide sequence for drug development. They also validate the utility of a high-throughput assay system for drug screening. Future studies for the identified peptides include determining their biological half-lives, AF9 binding affinities, and ability to induce apoptosis in leukemia cells.


2015 ◽  
Vol 20 (6) ◽  
pp. 801-809 ◽  
Author(s):  
Kyle J. Seamon ◽  
James T. Stivers

Sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1) is a recently discovered enzyme that plays a central role in nucleotide metabolism and innate immunity. SAMHD1 has deoxyribonucleoside triphosphate (dNTP) triphosphohydrolase activity that depletes the dNTP substrates required for DNA synthesis in cells. The involvement of SAMHD1 in biological processes as varied as viral restriction, endogenous retroelement control, cancer, and modulation of anticancer/antiviral nucleoside drug efficacy makes it a valuable target for the development of small-molecule inhibitors. We report a high-throughput colorimetric assay for SAMHD1 dNTP hydrolase activity that takes advantage of Escherichia coli inorganic pyrophosphatase to convert PPPi to 3 Pi. The assay was validated by screening a library of 2653 clinically used compounds. Fifteen primary hits were obtained (0.57% hit rate); 80% of these were confirmed in a direct secondary assay for dNTP hydrolysis. The zinc salt of the antibiotic cephalosporin C was a potent inhibitor of SAMHD1 with an IC50 of 1.1 ± 0.1 µM, and this inhibition was largely attributable to the presence of zinc. The assay also screened a targeted library of nucleosides and their analogs, revealing that the antiviral drug acycloguanosine (acyclovir) is an inhibitor possessing excellent properties for future fragment-based drug development efforts.


2016 ◽  
Vol 182 (1) ◽  
pp. 142-154 ◽  
Author(s):  
Manoj Kumar Yadav ◽  
Vijay Kumar ◽  
Bijender Singh ◽  
Santosh Kumar Tiwari

2015 ◽  
Vol 109 ◽  
pp. 140-148 ◽  
Author(s):  
Magda C. Semedo ◽  
Amin Karmali ◽  
Luís Fonseca

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