Assembling DNA fragments by USER fusion

Narayana Annaluru, Héloïse Muller, Sivaprakash Ramalingam, Karthikeyan Kandavelou, Viktoriya London, Sarah M. Richardson, Jessica S. Dymond, Eric M. Cooper, Joel S. Bader, Jef D. Boeke, Srinivasan Chandrasegaran

    Research output: Chapter in Book/Report/Conference proceedingChapter


    Recent advances in DNA synthesis technology make it possible to design and synthesize DNA fragments of several kb in size. However, the process of assembling the smaller DNA fragments into a larger DNA segment is still a cumbersome process. In this chapter, we describe the use of the uracil specific excision reaction (USER)-mediated approach for rapid and efficient assembly of multiple DNA fragments both in vitro and in vivo (using Escherichia coli). For USER fusion in vitro assembly, each of the individual building blocks (BBs), 0.75 kb in size (that are to be assembled), was amplified using the appropriate forward and reverse primers containing a single uracil (U) and DNA polymerase. The overlaps between adjoining BBs were 8-13 base pairs. An equimolar of the amplified BBs were mixed together and treated by USER enzymes to generate complementary 3'single-strand overhangs between adjoining BBs, which were then ligated and amplified simultaneously to generate the larger 3-kb segments. The assembled fragments were then cloned into plasmid vectors and sequenced to confirm their identity. For USER fusion in vivo assembly in E. coli, USER treatment of the BBs was performed in the presence of a synthetic plasmid, which had 8-13 base pair overlaps at the 5'-end of the 5' BB and at the 3'-end of the 3' BB in the mixture. The USER treated product was then transformed directly into E. coli to efficiently and correctly reconstitute the recombinant plasmid containing the desired target insert. The latter approach was also used to rapidly assemble three different target genes into a vector to form a new synthetic plasmid construct.

    Original languageEnglish (US)
    Title of host publicationGene Synthesis
    Subtitle of host publicationMethods and Protocols
    EditorsJean Peccoud
    Number of pages19
    StatePublished - 2012

    Publication series

    NameMethods in Molecular Biology
    ISSN (Print)1064-3745


    • DNA assembly
    • Endo VIII
    • Synthetic yeast
    • UDG
    • USER enzymes
    • Uracil excision

    ASJC Scopus subject areas

    • Molecular Biology
    • Genetics

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  • Cite this

    Annaluru, N., Muller, H., Ramalingam, S., Kandavelou, K., London, V., Richardson, S. M., Dymond, J. S., Cooper, E. M., Bader, J. S., Boeke, J. D., & Chandrasegaran, S. (2012). Assembling DNA fragments by USER fusion. In J. Peccoud (Ed.), Gene Synthesis: Methods and Protocols (pp. 77-95). (Methods in Molecular Biology; Vol. 852).