Quantitative CRISPRi Design

Spacer sequence:  Please input N20 sequence, must use A, T (or U), C, G.

Temperature (K):   Please input temperature (K), make sure it is in the interval of [293.15, 323.15].

Submit

Quantitative CRISPR interference was designed to evaluate the binding activity of mismatched sgRNAs. This model is based on our previously published paper:

Feng, Huibao, et al. "Guide-target mismatch effects on dCas9–sgRNA binding activity in living bacterial cells." Nucleic Acids Research 49.3 (2021): 1263-1277.

Additionally, we have integrated the latest nucleic acid thermodynamic data into the model:

Xiang, Tongjun, et al. "Thermodynamic Parameters Contributions of Single Internal Mismatches In RNA/DNA Hybrid Duplexes." bioRxiv (2022): 2022-11.

For the source code, please refer to our GitHub site:

GitHub Repository

To implement this model, two inputs are required:

1. N20 sequence: The sequence (from 5’ to 3’) of the N20 sequence.
2. Temperature: The temperature in degrees Kelvin.