Publications

New CADMAD Publications

  1. Accurate, model-based tuning of synthetic gene expression using introns in S. cerevisiae (2014)
    Ido Yofe, Zohar Zafrir, Rachel Blau, Maya Schuldiner, Tamir Tuller, Ehud Shapiro and Ben-Yehezkel T PLoS Genet Jun 26;10(6):e1004407
  2. Mapping the translation initiation landscape of an S. cerevisiae gene using fluorescent proteins (2013)
    Ben-Yehezkel T, Hadas Zur, Tzipy Marx, Ehud Shapiro, Tamir Tuller Genomics Volume 102, Issue 4, October 2013, Pages 419–429
  3. Synthesis and cell free cloning of DNA using programmable microfluidics (2014)
    ​Ben Yehezkel T, Arnaud Rival, Ofir Raz, Rafael Cohen, Tzipy Marx, Miguel Camara, Stephan Heeb Jean-Frederic Dubern, Birgit Koch, Natalio Krasnogor, Cyril Delatre and Ehud Shapiro Nature Methods (in final minor revision, available upon request)
  4. Systematic study of synthetic coding sequence features in S. cerevisiae exposes gene-expression determinants (2014)
    ​Ben-Yehezkel T*, Shimshi Atar*, Tzipy Marx, Rafael Cohen, Alon Diament, Alex Dana, Anna Feldman, Ehud Shapiro, Tamir Tuller , EMBO Mol Sys Bio (in final minor revision, available upon request)
  5. Heuristic for maximizing DNA reuse in synthetic DNA library assembly (2014)
    ​Jonathan Blakes*, Ofir Raz*, Uriel Feige, Jaume Bacardit, Paweł Widera, Ben-Yehezkel T, Ehud Shapiro, Natalio Krasnogor ACS Synth Biol 2014 Aug 14;3(8):529-42.

 

The technology of DNA Machinery has been under development at Prof. Shapiro's lab at the Weizmann Institute of Science over the past seven years.  It includes the following major components:

  1. Automated and efficient method for de novo DNA synthesis and error correction

    A key challenge in composing long DNA molecules is that the synthetic oligo building blocks are error-prone, resulting in sequence errors in the composed DNA. Shapiro and his team have developed a system and method for the automated composition and error correction of long DNA molecules and their libraries, described in patent application WO/2007/148337 and in the report "Recursive construction of perfect DNA molecules from imperfect oligonucleotides" (Molecular Systems Biology 4:191, 2008).
    This publication is available at Nature.com and also included as Appendix A bellow.
     

  2. Automated DNA editing platform

    DNA modification and editing are common tasks in biotechnology and biological research. DNA modifications of all types are performed by a plethora of labor-intensive methods such as site directed mutagenesis, homologous recombination, by the use of restriction and ligation enzymes and other methods. If several modifications are required then the modifications are typically done one at a time in a serial manner. Shapiro's team has developed a new method for DNA editing that allows easy composition and manipulation of DNA as a piece of text. The method uses one core operation, called Y, which joins two DNA fragments into one, to implement all basic text editing operations on DNA molecules, including insert, delete, replace, cut & paste and copy & paste.  It uses a computer algorithm to plan an optimal, parallel edit protocol that is executed by an automated laboratory platform they have developed.  By maximizing the use of existing DNA fragment such as plasmids, genomic DNA or PCR products the method provides a highly efficient and fast method to generate DNA candidates and large scale combinatorial DNA libraries.  The method is described in the manuscript “Why not edit DNA the way we edit text?”, as well as in a pending patent application the article is included as Appendix B bellow.
     

  3. Lab automation platform

    A high-level lab automation programming language was developed over the past five years at Prof. Shapiro's lab.   A lab automation platform incorporating this language is installed and is heavily used in leading labs at the Weizmann Institute of Science as well as at Teva, and additional installations are on their way. The platform allows flexible and efficient programming of laboratory robots with diverse integrated laboratory equipment. The platform supports effective robot programming by lab members, as well as the automated execution of computer-generated protocols. The manuscript “A laboratory automation platform programming language”, describing the language and its applications to date, is available upon request.
    A short movie presenting our lab automation.
     

  4. Single-molecule PCR for DNA error correction

    An in vitro alternative for in vivo DNA cloning must be integrated into DNA synthesis to improve throughput. A new smPCR-based procedure developed at Shapiro's lab can be employed as a general substitute to in vivo cloning, thereby allowing DNA synthesis and error-correction completely in vitro.  The method is described in the paper "De novo DNA synthesis using single-molecule PCR", to appear in Nucleic Acid Research, included here as Appendix cialis générique en pharmacie C.
     

  5. DNAps architecture

    The DNA processing platform is an integrated in silico/in vitro system of computational software modules and an automated laboratory. The system consists of computers, a laboratory liquid handling robot equipped with automated storage system, an automated PCR platform, a real-time PCR, a capillary electrophoresis machine, a colony picker, incubators and optionally an oligo synthesizer. To perform a DNA editing task, DNAps is provided with the set of relevant available DNA molecules, as well as the sequences of the desired target molecules. The system then finds an optimal protocol to construct the target sequences while maximizing the use of DNA fragments from the input molecules. This protocol is then translated into a robotic program that executes the protocol on the lab automation platform, producing, validating and, if needed, error-correcting the target molecules.