pyBrick-DNA: A Python-Based Environment for Automated Genetic Component Assembly

Gladys M. Cavero Rozas, Jose M. Cisneros Mandujano, Yomali A. Ferreyra Chombo, Daniela V. Moreno Rencoret, Yerko M. Ortiz Mora, Martín E. Gutiérrez Pescarmona, Alberto J. Donayre Torres

Research output: Contribution to journalArticlepeer-review

Abstract

Genetic component assembly is key in the simulation and implementation of genetic circuits. Automating this process, thus accelerating prototyping, is a necessity. We present pyBrick-DNA, a software written in Python, that assembles components for the construction of genetic circuits. pyBrick-DNA (colab.pyBrick.com) is a user-friendly environment where scientists can select genetic sequences or input custom sequences to build genetic assemblies. All components are modularly fused to generate a ready-to-go single DNA fragment. It includes Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and plant gene-editing components. Hence, pyBrick-DNA can generate a functional CRISPR construct composed of a single-guided RNA integrated with Cas9, promoters, and terminator elements. The outcome is a DNA sequence, along with a graphical representation, composed of user-selected genetic parts, ready to be synthesized and cloned in vivo. Moreover, the sequence can be exported as a GenBank file allowing its use with other synthetic biology tools.

Original languageEnglish
Pages (from-to)1315-1321
Number of pages7
JournalJournal of Computational Biology
Volume30
Issue number12
DOIs
StatePublished - 1 Dec 2023

Keywords

  • CRISPR
  • GenBank
  • automation tool
  • genetic assembly
  • genetic components
  • synthetic biology

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