scholarly journals Molecular design of artificial restriction enzymes.

1997 ◽  
Vol 37 (3) ◽  
pp. 126-129
Author(s):  
Makoto KOMIYAMA ◽  
Kazunari MATSUMURA
Keyword(s):  
Molecular Design ◽  
Restriction Enzymes ◽  
Artificial Restriction

Programmable DNA-Guided Artificial Restriction Enzymes

2017 ◽  
Vol 6 (5) ◽  
pp. 752-757 ◽  
Author(s):  
Behnam Enghiad ◽  
Huimin Zhao
Keyword(s):  
Restriction Enzymes ◽  
Artificial Restriction

scholarly journals PlasmidMaker: a Versatile, Automated, and High Throughput End-to-End Platform for Plasmid Construction

2022 ◽  
Author(s):  
Behnam Enghiad ◽  
Pu Xue ◽  
Nilmani Singh ◽  
Aashutosh Girish Boob ◽  
Chengyou Shi ◽  
...  
Keyword(s):  
High Throughput ◽  
Pyrococcus Furiosus ◽  
Restriction Enzymes ◽  
Dna Assembly ◽  
Assembly Method ◽  
Free Construction ◽  
Artificial Restriction ◽  
End To End ◽  
Plasmid Design ◽  
User Friendly

Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high-throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments within 3 days. PlasmidMaker should greatly expand the potential of synthetic biology.

Thermodynamics of the interaction between the spike protein of severe acute respiratory syndrome- coronavirus-2 and the receptor of human angiotensin converting enzyme 2. Effects of possible ligands

2020 ◽  
Author(s):  
Cristina Garcia-Iriepa ◽  
Cecilia Hognon ◽  
Antonio Francés-Monerris ◽  
Isabel Iriepa ◽  
Tom Miclot ◽  
...  
Keyword(s):  
Angiotensin Converting Enzyme ◽  
Molecular Mechanisms ◽  
Molecular Design ◽  
Binding Free Energy ◽  
Transmembrane Protein ◽  
Spike Protein ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Rational Molecular Design ◽  
Rational Evaluation

<div><p>Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 180,000 deaths all over the world, still lacking a medical treatment despite the concerns of the whole scientific community. Human Angiotensin-Converting Enzyme 2 (ACE2) was recently recognized as the transmembrane protein serving as SARS-CoV-2 entry point into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the complex and of the effects of possible ligands. Moreover, binding free energy between ACE2 and the active Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein is evaluated quantitatively, assessing the molecular mechanisms at the basis of the recognition and the ligand-induced decreased affinity. These results boost the knowledge on the molecular grounds of the SARS-CoV-2 infection and allow to suggest rationales useful for the subsequent rational molecular design to treat severe COVID-19 cases.</p></div>

Restriction of Access to Dark State: A New Mechanistic Model for Heteroatom-Containing AIE Systems

2019 ◽  
Author(s):  
Yujie Tu ◽  
Junkai Liu ◽  
Haoke Zhang ◽  
Qian Peng ◽  
Jacky W. Y. Lam ◽  
...  
Keyword(s):  
Excited States ◽  
Radiative Decay ◽  
Molecular Design ◽  
Mechanistic Model ◽  
Zinc Ion ◽  
Easy Access ◽  
Triplet States ◽  
Dark State ◽  
Ion Probe ◽  
Π State

Aggregation-induced emission (AIE) is an unusual photophysical phenomenon and provides an effective and advantageous strategy for the design of highly emissive materials in versatile applications such as sensing, imaging, and theragnosis. "Restriction of intramolecular motion" is the well-recognized working mechanism of AIE and have guided the molecular design of most AIE materials. However, it sometimes fails to be workable to some heteroatom-containing systems. Herein, in this work, we take more than one excited state into account and specify a mechanism –"restriction of access to dark state (RADS)" – to explain the AIE effect of heteroatom-containing molecules. An anthracene-based zinc ion probe named APA is chosen as the model compound, whose weak fluorescence in solution is ascribed to the easy access from the bright (π,π*) state to the closelying dark (n,π*) state caused by the strong vibronic coupling of the two excited states. By either metal complexation or aggregation, the dark state is less accessible due to the restriction of the molecular motion leading to the dark state and elevation of the dark state energy, thus the emission of the bright state is restored. RADS is found to be powerful in elucidating the photophysics of AIE materials with excited states which favor non-radiative decay, including overlap-forbidden states such as (n,π*) and CT states, spin-forbidden triplet states, which commonly exist in heteroatom-containing molecules.

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