plasmid addgene plasmid id 242429  (Addgene inc)

Journal: Nature Communications

Article Title: Precision multiplexed base editing in human cells using Cas12a-derived base editors

doi: 10.1038/s41467-025-59653-x

Figure Lengend Snippet: A The ability of Cas12a to process gRNA arrays without accessory factors allows for the efficient delivery of many gRNAs into a single cell. Truncated gRNAs can be used to prevent deamination of neighboring bases. Created in BioRender. Schweitzer, A. (2025) https://BioRender.com/z2a6bsw . B Comparison of two published dLbCas12a-derived CBE and ( C ), one published dLbCas12a-derived ABE system for MBE in HEK293 cells. Heatmaps show normalized mean %T/%G values from three independent replicates ( n = 3). Normalization was performed by subtracting the mean %T/%G values of the nt-ctrl condition from the mean %T/%G values of the experimental condition. Only positions 7–12 for CBEs and positions 8–12 of ABEs are shown, as those correspond to the editing window of the used systems. sg: single guide, dg: double guide, tg: triple guide. Source data are provided as a Source Data file.

Article Snippet: For co-transfection experiments, HEK293 cells were transfected with 340 ng gRNA expression plasmid and 500 ng base editor plasmid (Addgene IDs 171697, 171698, 138504, 138506, 114081, and 114082, Supplementary Data ).

Techniques: Comparison, Derivative Assay

Journal: Nature Communications

Article Title: Precision multiplexed base editing in human cells using Cas12a-derived base editors

doi: 10.1038/s41467-025-59653-x

Figure Lengend Snippet: A Schematic of the architecture of the three gRNA expression plasmids used in this study. SV40: Simian Virus 40 termination signal. B Schematic of gRNA array architectures used in this study. The standard array consists of the DR and guide sequences and does not include any additional sequence elements. The SynSep array includes an AAAT sequence upstream of each DR sequence, and the VarSep arrays include variable 4 nt sequences upstream of each DR sequence (see Supplementary Data ). C Comparison of different array architectures for BEACON2-mediated multiplex editing of 14 RUNX1 target sites. D Editing frequencies of gRNAs across arrays shown in ( C ), normalized to their efficiency when expressed using the standard array architecture. E BEACON2-mediated multiplex editing of 3–16 target sites, across six genes located on five chromosomes. F , Comparison of a Pol-III promoter (hU6) and two Pol-II promoters (CMV and EFs1a) for the expression of the standard gRNA array shown in ( D ). All data are the mean ± SD of three independent replicates ( n = 3). C – F show normalized mean %T values at the highest edited C for each gRNA as determined based on the single gRNA condition. Normalization was performed by subtracting the mean %T of the non-targeting (nt-ctrl) condition from the mean %T of the experimental condition. Source data are provided as a Source Data file.

Article Snippet: For co-transfection experiments, HEK293 cells were transfected with 340 ng gRNA expression plasmid and 500 ng base editor plasmid (Addgene IDs 171697, 171698, 138504, 138506, 114081, and 114082, Supplementary Data ).

Techniques: Expressing, Virus, Sequencing, Comparison, Multiplex Assay

Journal: Nature Communications

Article Title: Precision multiplexed base editing in human cells using Cas12a-derived base editors

doi: 10.1038/s41467-025-59653-x

Figure Lengend Snippet: A Total number of mutations found in three edited clones and one clone transfected with a non-targeting (nt-ctrl) gRNA. B Total number of detected single-nucleotide variants (SNVs) by base-change for three edited clones and one clone transfected with an nt-ctrl gRNA. C Summary of allele frequencies observed at the 16 targeted sites after editing with the 16x gRNA array (Fig. ), showing combined outcomes based on the number of edited Cs. Data represents three cell clones isolated from the edited population. D Total number of edited target sites per clone. E Overlap of C > T/G > A SNVs detected in our analysis and predicted off-target sites by Cas-OFFinder.

Article Snippet: For co-transfection experiments, HEK293 cells were transfected with 340 ng gRNA expression plasmid and 500 ng base editor plasmid (Addgene IDs 171697, 171698, 138504, 138506, 114081, and 114082, Supplementary Data ).

Techniques: Clone Assay, Transfection, Isolation

Journal: Nature Communications

Article Title: Precision multiplexed base editing in human cells using Cas12a-derived base editors

doi: 10.1038/s41467-025-59653-x

Figure Lengend Snippet: A Editing outcomes mediated by BEACON1 and BEACON2 when used with a triple gRNA array targeting RUNX1 . B Editing outcomes mediated by BEACON1 and BEACON2 at 16 target sites in HeLa cells transfected with a CMV promoter-driven 16x gRNA array and the respective BE system. Editing outcomes in HEK293-B2 cells mediated by BEACON2 transfected with the same 16 × gRNA array as presented in Fig. . A , B show normalized mean %T values at the highest edited C for each gRNA as determined based on the single gRNA condition. Normalization was performed by subtracting the mean %T of the non-targeting (nt-ctrl) condition from the mean %T of the experimental condition. Source data are provided as a Source Data file.

Article Snippet: For co-transfection experiments, HEK293 cells were transfected with 340 ng gRNA expression plasmid and 500 ng base editor plasmid (Addgene IDs 171697, 171698, 138504, 138506, 114081, and 114082, Supplementary Data ).

Techniques: Transfection