Literature DB >> 31686495

A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells.

João Pedro Fonseca1, Alain R Bonny1, G Renuka Kumar2, Andrew H Ng3, Jason Town1, Qiu Chang Wu4, Elham Aslankoohi1, Susan Y Chen1, Galen Dods1, Patrick Harrigan1, Lindsey C Osimiri1,5, Amy L Kistler2, Hana El-Samad1,2.   

Abstract

The ability to rapidly assemble and prototype cellular circuits is vital for biological research and its applications in biotechnology and medicine. Current methods for the assembly of mammalian DNA circuits are laborious, slow, and expensive. Here we present the Mammalian ToolKit (MTK), a Golden Gate-based cloning toolkit for fast, reproducible, and versatile assembly of large DNA vectors and their implementation in mammalian models. The MTK consists of a curated library of characterized, modular parts that can be assembled into transcriptional units and further weaved into complex circuits. We showcase the capabilities of the MTK by using it to generate single-integration landing pads, create and deliver libraries of protein variants and sgRNAs, and iterate through dCas9-based prototype circuits. As a biological proof of concept, we demonstrate how the MTK can speed the generation of noninfectious viral circuits to enable rapid testing of pharmacological inhibitors of emerging viruses that pose a major threat to human health.

Entities:  

Keywords:  library generation; modular cloning; virology

Mesh:

Substances:

Year:  2019        PMID: 31686495     DOI: 10.1021/acssynbio.9b00322

Source DB:  PubMed          Journal:  ACS Synth Biol        ISSN: 2161-5063            Impact factor:   5.110


  12 in total

Review 1.  Engineering Closed-Loop, Autoregulatory Gene Circuits for Osteoarthritis Cell-Based Therapies.

Authors:  Rhima M Coleman
Journal:  Curr Rheumatol Rep       Date:  2022-04-11       Impact factor: 4.592

2.  Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling.

Authors:  João Pedro Fonseca; Elham Aslankoohi; Andrew H Ng; Michael Chevalier
Journal:  PLoS Comput Biol       Date:  2022-03-30       Impact factor: 4.475

3.  FRAGLER: A Fragment Recycler Application Enabling Rapid and Scalable Modular DNA Assembly.

Authors:  David Öling; Olivier Lan-Chow-Wing; Andrea Martella; Samuel Gilberto; Jordi Chi; Emily Cooper; Tora Edström; Bo Peng; Dean Sumner; Fredrik Karlsson; Petr Volkov; Carl I Webster; Robert Roth
Journal:  ACS Synth Biol       Date:  2022-07-07       Impact factor: 5.249

4.  De novo design of tyrosine and serine kinase-driven protein switches.

Authors:  Nicholas B Woodall; Zara Weinberg; Jesslyn Park; Florian Busch; Richard S Johnson; Mikayla J Feldbauer; Michael Murphy; Maggie Ahlrichs; Issa Yousif; Michael J MacCoss; Vicki H Wysocki; Hana El-Samad; David Baker
Journal:  Nat Struct Mol Biol       Date:  2021-09-13       Impact factor: 18.361

5.  Assembly of Genetic Circuits with the Mammalian ToolKit.

Authors:  João P Fonseca; Alain R Bonny; Jason Town; Hana El-Samad
Journal:  Bio Protoc       Date:  2020-03-05

6.  Versatile Labeling and Detection of Endogenous Proteins Using Tag-Assisted Split Enzyme Complementation.

Authors:  Suraj Makhija; David Brown; Rachel M Rudlaff; Julia K Doh; Struan Bourke; Yina Wang; Shuqin Zhou; Rasmi Cheloor-Kovilakam; Bo Huang
Journal:  ACS Chem Biol       Date:  2021-03-18       Impact factor: 5.100

7.  Universal loop assembly: open, efficient and cross-kingdom DNA fabrication.

Authors:  Bernardo Pollak; Tamara Matute; Isaac Nuñez; Ariel Cerda; Constanza Lopez; Valentina Vargas; Anton Kan; Vincent Bielinski; Peter von Dassow; Chris L Dupont; Fernán Federici
Journal:  Synth Biol (Oxf)       Date:  2020-02-05

8.  Orthogonal control of mean and variability of endogenous genes in a human cell line.

Authors:  Alain R Bonny; João Pedro Fonseca; Jesslyn E Park; Hana El-Samad
Journal:  Nat Commun       Date:  2021-01-12       Impact factor: 14.919

9.  Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein.

Authors:  Zara Y Weinberg; Claire E Hilburger; Matthew Kim; Longxing Cao; Mir Khalid; Sarah Elmes; Devan Diwanji; Evelyn Hernandez; Jocelyne Lopez; Kaitlin Schaefer; Amber M Smith; Fengbo Zhou; G Renuka Kumar; Melanie Ott; David Baker; Hana El-Samad
Journal:  bioRxiv       Date:  2021-04-20

10.  Independent control of mean and noise by convolution of gene expression distributions.

Authors:  Karl P Gerhardt; Satyajit D Rao; Evan J Olson; Oleg A Igoshin; Jeffrey J Tabor
Journal:  Nat Commun       Date:  2021-11-29       Impact factor: 14.919

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