From Gene Editing to Pathway Design: How AI is Transforming Synthetic Biology

by Andrii Buvailo, PhD          Biopharma insight

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It is hard to overestimate the potential of biotechnology to address some of the most pressing challenges of the 21st century. These challenges include feeding a growing global population, improving healthcare and access to therapies, and mitigating the impacts of climate change.

Considering the “data-rich” nature of biological experimentation and heavy reliance on such data, no wonder why artificial intelligence (AI) is playing a crucial role in advancing synthetic biology by facilitating the design, construction, and optimization of biological systems. Some of the key ways AI is used to advance synthetic biology include:

 

CRISPR-based gene editing

Artificial intelligence plays a significant role in enhancing gene editing using CRISPR-Cas9 technology. CRISPR-Cas9 is a powerful gene-editing tool that allows researchers to make precise edits in the genome by adding, deleting, or altering sections of the DNA sequence. However, one of the challenges in CRISPR-Cas9 technology is the prediction and minimization of off-target effects, which are unintended modifications in DNA sequences that are similar to the intended target site.

AI can help address this issue by analyzing vast amounts of genomic data to predict potential off-target effects and their likelihood, thus guiding researchers towards more accurate and efficient gene editing. Machine learning algorithms can be trained on large datasets of genomic sequences and CRISPR-Cas9 cutting profiles to predict off-target effects based on the similarities between the target and off-target sequences, as well as other factors like chromatin accessibility.

Moreover, AI can assist in identifying optimal target sites for CRISPR-Cas9 editing by analyzing the genomic context, functional annotations, and potential off-target sites. This enables researchers to select target sites with minimal off-target risks and higher editing efficiency.

Another aspect where AI can contribute to CRISPR-Cas9 technology is the optimization of guide RNA (gRNA) design. The gRNA is a crucial component in the CRISPR-Cas9 system, responsible for guiding the Cas9 nuclease to the target DNA sequence. AI algorithms can be employed to analyze sequence features, predict gRNA binding efficiency, and suggest optimal gRNA sequences for a specific target, improving the overall gene editing efficiency and specificity.

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