Faculty Opinions recommendation of A ligation-independent cloning method using nicking DNA endonuclease.

Author(s):  
Scott Silverman
BioTechniques ◽  
2010 ◽  
Vol 49 (5) ◽  
pp. 817-821 ◽  
Author(s):  
Jie Yang ◽  
Zhihong Zhang ◽  
Xin Zhang ◽  
Qingming Luo

2012 ◽  
Vol 78 (15) ◽  
pp. 5440-5443 ◽  
Author(s):  
Jae-Yeon Jeong ◽  
Hyung-Soon Yim ◽  
Ji-Young Ryu ◽  
Hyun Sook Lee ◽  
Jung-Hyun Lee ◽  
...  

ABSTRACTWe developed one-step sequence- and ligation-independent cloning (SLIC) as a simple, cost-effective, time-saving, and versatile cloning method. Highly efficient and directional cloning can be achieved by direct bacterial transformation 2.5 min after mixing any linearized vector, an insert(s) prepared by PCR, and T4 DNA polymerase in a tube at room temperature.


2007 ◽  
Vol 35 (6) ◽  
pp. e45-e45 ◽  
Author(s):  
N. S. Berrow ◽  
D. Alderton ◽  
S. Sainsbury ◽  
J. Nettleship ◽  
R. Assenberg ◽  
...  

2020 ◽  
Author(s):  
Shreya Ghosh ◽  
Anam Ejaz ◽  
Lucas Repeta ◽  
Stewart Shuman

Abstract Pseudomonas putida MPE exemplifies a novel clade of manganese-dependent single-strand DNA endonuclease within the binuclear metallophosphoesterase superfamily. MPE is encoded within a widely conserved DNA repair operon. Via structure-guided mutagenesis, we identify His113 and His81 as essential for DNA nuclease activity, albeit inessential for hydrolysis of bis-p-nitrophenylphosphate. We propose that His113 contacts the scissile phosphodiester and serves as a general acid catalyst to expel the OH leaving group of the product strand. We find that MPE cleaves the 3′ and 5′ single-strands of tailed duplex DNAs and that MPE can sense and incise duplexes at sites of short mismatch bulges and opposite a nick. We show that MPE is an ambidextrous phosphodiesterase capable of hydrolyzing the ssDNA backbone in either orientation to generate a mixture of 3′-OH and 3′-PO4 cleavage products. The directionality of phosphodiester hydrolysis is dictated by the orientation of the water nucleophile vis-à-vis the OH leaving group, which must be near apical for the reaction to proceed. We propose that the MPE active site and metal-bound water nucleophile are invariant and the enzyme can bind the ssDNA productively in opposite orientations.


2021 ◽  
Author(s):  
Dung Thanh Dang ◽  
Le Tuan Anh Nguyen ◽  
Tuom Tinh Thi Truong ◽  
Hoang Duc Nguyen ◽  
Anh Tuân Phan

A G-quadruplex-specific DNA endonuclease was constructed by fusing a RHAU G-quadruplex recognition domain with a Fok1 cleavage domain, providing a useful tool for detection of G-quadruplex structures.


Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1254 ◽  
Author(s):  
Xi Chen ◽  
Dong Chen ◽  
Linyuan Huang ◽  
Xiaoling Chen ◽  
Mei Zhou ◽  
...  

The peptides from the ranacyclin family share similar active disulphide loop with plant-derived Bowman–Birk type inhibitors, some of which have the dual activities of trypsin inhibition and antimicrobial. Herein, a novel Bowman–Birk type trypsin inhibitor of the ranacyclin family was identified from the skin secretion of broad-folded frog (Sylvirana latouchii) by molecular cloning method and named as SL-BBI. After chemical synthesis, it was proved to be a potent inhibitor of trypsin with a Ki value of 230.5 nM and showed weak antimicrobial activity against tested microorganisms. Modified analogue K-SL maintains the original inhibitory activity with a Ki value of 77.27 nM while enhancing the antimicrobial activity. After the substitution of active P1 site to phenylalanine and P2′ site to isoleucine, F-SL regenerated its inhibitory activity on chymotrypsin with a Ki value of 309.3 nM and exhibited antiproliferative effects on PC-3, MCF-7 and a series of non-small cell lung cancer cell lines without cell membrane damage. The affinity of F-SL for the β subunits in the yeast 20S proteasome showed by molecular docking simulations enriched the understanding of the possible action mode of Bowman–Birk type inhibitors. Further mechanistic studies have shown that F-SL can activate caspase 3/7 in H157 cells and induce apoptosis, which means it has the potential to become an anticancer agent.


1986 ◽  
Vol 94 (1-2) ◽  
pp. 201-208 ◽  
Author(s):  
Slawomir Kosinski ◽  
Ulrich Hämmerling

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