Literature DB >> 26758940

An innovative platform for quick and flexible joining of assorted DNA fragments.

Henrique Cestari De Paoli1, Gerald A Tuskan1, Xiaohan Yang1.   

Abstract

Successful synthetic biology efforts rely on conceptual and experimental designs in combination with testing of multi-gene constructs. Despite recent progresses, several limitations still hinder the ability to flexibly assemble and collectively share different types of DNA segments. Here, we describe an advanced system for joining DNA fragments from a universal library that automatically maintains open reading frames (ORFs) and does not require linkers, adaptors, sequence homology, amplification or mutation (domestication) of fragments in order to work properly. This system, which is enhanced by a unique buffer formulation, provides unforeseen capabilities for testing, and sharing, complex multi-gene circuitry assembled from different DNA fragments.

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Year:  2016        PMID: 26758940      PMCID: PMC4725820          DOI: 10.1038/srep19278

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  39 in total

Review 1.  Synthetic biology: an emerging engineering discipline.

Authors:  Allen A Cheng; Timothy K Lu
Journal:  Annu Rev Biomed Eng       Date:  2012-05-07       Impact factor: 9.590

2.  Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing.

Authors:  Yangbin Gao; Yunde Zhao
Journal:  J Integr Plant Biol       Date:  2014-03-06       Impact factor: 7.061

Review 3.  Tweaking biological switches through a better understanding of bistability behavior.

Authors:  Anushree Chatterjee; Yiannis N Kaznessis; Wei-Shou Hu
Journal:  Curr Opin Biotechnol       Date:  2008-10-01       Impact factor: 9.740

Review 4.  The N-end rule pathway and regulation by proteolysis.

Authors:  Alexander Varshavsky
Journal:  Protein Sci       Date:  2011-08       Impact factor: 6.725

5.  Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

Authors:  Nicola J Patron; Diego Orzaez; Sylvestre Marillonnet; Heribert Warzecha; Colette Matthewman; Mark Youles; Oleg Raitskin; Aymeric Leveau; Gemma Farré; Christian Rogers; Alison Smith; Julian Hibberd; Alex A R Webb; James Locke; Sebastian Schornack; Jim Ajioka; David C Baulcombe; Cyril Zipfel; Sophien Kamoun; Jonathan D G Jones; Hannah Kuhn; Silke Robatzek; H Peter Van Esse; Dale Sanders; Giles Oldroyd; Cathie Martin; Rob Field; Sarah O'Connor; Samantha Fox; Brande Wulff; Ben Miller; Andy Breakspear; Guru Radhakrishnan; Pierre-Marc Delaux; Dominique Loqué; Antonio Granell; Alain Tissier; Patrick Shih; Thomas P Brutnell; W Paul Quick; Heiko Rischer; Paul D Fraser; Asaph Aharoni; Christine Raines; Paul F South; Jean-Michel Ané; Björn R Hamberger; Jane Langdale; Jens Stougaard; Harro Bouwmeester; Michael Udvardi; James A H Murray; Vardis Ntoukakis; Patrick Schäfer; Katherine Denby; Keith J Edwards; Anne Osbourn; Jim Haseloff
Journal:  New Phytol       Date:  2015-07-14       Impact factor: 10.151

6.  j5 DNA assembly design automation software.

Authors:  Nathan J Hillson; Rafael D Rosengarten; Jay D Keasling
Journal:  ACS Synth Biol       Date:  2011-12-20       Impact factor: 5.110

Review 7.  A brief history of synthetic biology.

Authors:  D Ewen Cameron; Caleb J Bashor; James J Collins
Journal:  Nat Rev Microbiol       Date:  2014-04-01       Impact factor: 60.633

8.  Interactive assembly algorithms for molecular cloning.

Authors:  Evan Appleton; Jenhan Tao; Traci Haddock; Douglas Densmore
Journal:  Nat Methods       Date:  2014-04-28       Impact factor: 28.547

9.  The small, versatile pPZP family of Agrobacterium binary vectors for plant transformation.

Authors:  P Hajdukiewicz; Z Svab; P Maliga
Journal:  Plant Mol Biol       Date:  1994-09       Impact factor: 4.076

10.  A modular cloning system for standardized assembly of multigene constructs.

Authors:  Ernst Weber; Carola Engler; Ramona Gruetzner; Stefan Werner; Sylvestre Marillonnet
Journal:  PLoS One       Date:  2011-02-18       Impact factor: 3.240

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  6 in total

1.  Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots.

Authors:  David I Walsh; Marilene Pavan; Luis Ortiz; Scott Wick; Johanna Bobrow; Nicholas J Guido; Sarah Leinicke; Dany Fu; Shreya Pandit; Lucy Qin; Peter A Carr; Douglas Densmore
Journal:  SLAS Technol       Date:  2019-02-15       Impact factor: 3.047

2.  Editorial: Plant Molecular Farming: Fast, Scalable, Cheap, Sustainable.

Authors:  Domenico De Martinis; Edward P Rybicki; Kazuhito Fujiyama; Rosella Franconi; Eugenio Benvenuto
Journal:  Front Plant Sci       Date:  2016-08-03       Impact factor: 5.753

3.  GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data.

Authors:  Marta Vazquez-Vilar; Alfredo Quijano-Rubio; Asun Fernandez-Del-Carmen; Alejandro Sarrion-Perdigones; Rocio Ochoa-Fernandez; Peio Ziarsolo; José Blanca; Antonio Granell; Diego Orzaez
Journal:  Nucleic Acids Res       Date:  2017-02-28       Impact factor: 16.971

4.  MetClo: methylase-assisted hierarchical DNA assembly using a single type IIS restriction enzyme.

Authors:  Da Lin; Christopher A O'Callaghan
Journal:  Nucleic Acids Res       Date:  2018-11-02       Impact factor: 16.971

5.  A high-throughput transient expression system for rice.

Authors:  Mike T Page; Martin A J Parry; Elizabete Carmo-Silva
Journal:  Plant Cell Environ       Date:  2019-04-02       Impact factor: 7.228

6.  The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.

Authors:  Xiaohan Yang; Rongbin Hu; Hengfu Yin; Jerry Jenkins; Shengqiang Shu; Haibao Tang; Degao Liu; Deborah A Weighill; Won Cheol Yim; Jungmin Ha; Karolina Heyduk; David M Goodstein; Hao-Bo Guo; Robert C Moseley; Elisabeth Fitzek; Sara Jawdy; Zhihao Zhang; Meng Xie; James Hartwell; Jane Grimwood; Paul E Abraham; Ritesh Mewalal; Juan D Beltrán; Susanna F Boxall; Louisa V Dever; Kaitlin J Palla; Rebecca Albion; Travis Garcia; Jesse A Mayer; Sung Don Lim; Ching Man Wai; Paul Peluso; Robert Van Buren; Henrique Cestari De Paoli; Anne M Borland; Hong Guo; Jin-Gui Chen; Wellington Muchero; Yanbin Yin; Daniel A Jacobson; Timothy J Tschaplinski; Robert L Hettich; Ray Ming; Klaus Winter; James H Leebens-Mack; J Andrew C Smith; John C Cushman; Jeremy Schmutz; Gerald A Tuskan
Journal:  Nat Commun       Date:  2017-12-01       Impact factor: 14.919

  6 in total

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