TY - JOUR
T1 - pyBrick-DNA
T2 - A Python-Based Environment for Automated Genetic Component Assembly
AU - Cavero Rozas, Gladys M.
AU - Cisneros Mandujano, Jose M.
AU - Ferreyra Chombo, Yomali A.
AU - Moreno Rencoret, Daniela V.
AU - Ortiz Mora, Yerko M.
AU - Gutiérrez Pescarmona, Martín E.
AU - Donayre Torres, Alberto J.
N1 - Publisher Copyright:
© Mary Ann Liebert, Inc.
PY - 2023/12/1
Y1 - 2023/12/1
N2 - 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.
AB - 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.
KW - CRISPR
KW - GenBank
KW - automation tool
KW - genetic assembly
KW - genetic components
KW - synthetic biology
UR - http://www.scopus.com/inward/record.url?scp=85179074357&partnerID=8YFLogxK
U2 - 10.1089/cmb.2023.0008
DO - 10.1089/cmb.2023.0008
M3 - Article
C2 - 38010519
AN - SCOPUS:85179074357
SN - 1066-5277
VL - 30
SP - 1315
EP - 1321
JO - Journal of Computational Biology
JF - Journal of Computational Biology
IS - 12
ER -