Literature DB >> 26081612

Bricks and blueprints: methods and standards for DNA assembly.

Arturo Casini1, Marko Storch1, Geoffrey S Baldwin1, Tom Ellis2.   

Abstract

DNA assembly is a key part of constructing gene expression systems and even whole chromosomes. In the past decade, a plethora of powerful new DNA assembly methods - including Gibson Assembly, Golden Gate and ligase cycling reaction (LCR) - have been developed. In this Innovation article, we discuss these methods as well as standards such as the modular cloning (MoClo) system, GoldenBraid, modular overlap-directed assembly with linkers (MODAL) and PaperClip, which have been developed to facilitate a streamlined assembly workflow, to aid the exchange of material between research groups and to create modular reusable DNA parts.

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Year:  2015        PMID: 26081612     DOI: 10.1038/nrm4014

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  75 in total

1.  BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology.

Authors:  Marko Storch; Arturo Casini; Ben Mackrow; Toni Fleming; Harry Trewhitt; Tom Ellis; Geoff S Baldwin
Journal:  ACS Synth Biol       Date:  2015-04-16       Impact factor: 5.110

2.  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

3.  Construction of biologically functional bacterial plasmids in vitro.

Authors:  S N Cohen; A C Chang; H W Boyer; R B Helling
Journal:  Proc Natl Acad Sci U S A       Date:  1973-11       Impact factor: 11.205

4.  Programming cells by multiplex genome engineering and accelerated evolution.

Authors:  Harris H Wang; Farren J Isaacs; Peter A Carr; Zachary Z Sun; George Xu; Craig R Forest; George M Church
Journal:  Nature       Date:  2009-07-26       Impact factor: 49.962

5.  Bottom-up genome assembly using the Bacillus subtilis genome vector.

Authors:  Mitsuhiro Itaya; Kyoko Fujita; Azusa Kuroki; Kenji Tsuge
Journal:  Nat Methods       Date:  2007-12-09       Impact factor: 28.547

6.  iBrick: a new standard for iterative assembly of biological parts with homing endonucleases.

Authors:  Jia-Kun Liu; Wei-Hua Chen; Shuang-Xi Ren; Guo-Ping Zhao; Jin Wang
Journal:  PLoS One       Date:  2014-10-20       Impact factor: 3.240

7.  The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes.

Authors:  Rafael Silva-Rocha; Esteban Martínez-García; Belén Calles; Max Chavarría; Alejandro Arce-Rodríguez; Aitor de Las Heras; A David Páez-Espino; Gonzalo Durante-Rodríguez; Juhyun Kim; Pablo I Nikel; Raúl Platero; Víctor de Lorenzo
Journal:  Nucleic Acids Res       Date:  2012-11-23       Impact factor: 16.971

8.  2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts.

Authors:  Mariana Leguia; Jennifer An Brophy; Douglas Densmore; Angel Asante; J Christopher Anderson
Journal:  J Biol Eng       Date:  2013-01-10       Impact factor: 4.355

9.  DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways.

Authors:  Zengyi Shao; Hua Zhao; Huimin Zhao
Journal:  Nucleic Acids Res       Date:  2008-12-12       Impact factor: 16.971

10.  USER friendly DNA engineering and cloning method by uracil excision.

Authors:  Jurate Bitinaite; Michelle Rubino; Kamini Hingorani Varma; Ira Schildkraut; Romualdas Vaisvila; Rita Vaiskunaite
Journal:  Nucleic Acids Res       Date:  2007-03-06       Impact factor: 16.971

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  57 in total

1.  Introducing a class of standardized and interchangeable parts utilizing programmed ribosomal frameshifts for synthetic biology applications.

Authors:  Harland E Brandon; Jenna R Friedt; Graeme D Glaister; Suneet K Kharey; Dustin D Smith; Zak K Stinson; Hans-Joachim Wieden
Journal:  Translation (Austin)       Date:  2015-11-03

2.  Protocols for C-Brick DNA Standard Assembly Using Cpf1.

Authors:  Shi-Yuan Li; Guo-Ping Zhao; Jin Wang
Journal:  J Vis Exp       Date:  2017-06-15       Impact factor: 1.355

3.  Computer-Aided Planning for the Verification of Large Batches of DNA Constructs.

Authors:  Valentin Zulkower
Journal:  Methods Mol Biol       Date:  2021

4.  Design of Heteronuclear Metalloenzymes.

Authors:  A Bhagi-Damodaran; P Hosseinzadeh; E Mirts; J Reed; I D Petrik; Y Lu
Journal:  Methods Enzymol       Date:  2016-07-26       Impact factor: 1.600

5.  Balancing gene expression without library construction via a reusable sRNA pool.

Authors:  Amar Ghodasara; Christopher A Voigt
Journal:  Nucleic Acids Res       Date:  2017-07-27       Impact factor: 16.971

6.  Combinatorial assembly platform enabling engineering of genetically stable metabolic pathways in cyanobacteria.

Authors:  George M Taylor; Andrew Hitchcock; John T Heap
Journal:  Nucleic Acids Res       Date:  2021-12-02       Impact factor: 16.971

7.  Functional Studies of Genetic Variants Associated with Human Diseases in Notch Signaling-Related Genes Using Drosophila.

Authors:  Sheng-An Yang; Jose L Salazar; David Li-Kroeger; Shinya Yamamoto
Journal:  Methods Mol Biol       Date:  2022

8.  Rapid 40 kb Genome Construction from 52 Parts through Data-optimized Assembly Design.

Authors:  John M Pryor; Vladimir Potapov; Katharina Bilotti; Nilisha Pokhrel; Gregory J S Lohman
Journal:  ACS Synth Biol       Date:  2022-05-25       Impact factor: 5.249

Review 9.  Bioproduction of riboflavin: a bright yellow history.

Authors:  José Luis Revuelta; Rodrigo Ledesma-Amaro; Patricia Lozano-Martinez; David Díaz-Fernández; Rubén M Buey; Alberto Jiménez
Journal:  J Ind Microbiol Biotechnol       Date:  2016-09-30       Impact factor: 3.346

Review 10.  Harnessing plant metabolic diversity.

Authors:  Charlie Owen; Nicola J Patron; Ancheng Huang; Anne Osbourn
Journal:  Curr Opin Chem Biol       Date:  2017-05-17       Impact factor: 8.972

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