PlatinumCRISPr sgRNA

PlatinumCRISPr evaluates base-pairing and sequence composition parameters for optimal design of highly efficient sgRNAs for Cas9 genome editing.

Key Features:

• Structure-optimized sgRNA selection: Evaluates correct folding of sgRNAs and Cas9 structural information to predict sgRNA activity.
• Multi-parameter evaluation: Assesses base-pairing and sequence composition parameters including secondary structure of the sgRNA, sequence context of the seed region, GC context, and detrimental motifs.
• Cross-dataset validation: Compares over 10 data sets to identify major constraints in sgRNA design and variation among prediction tools.

Scientific Applications:

• Gene knockout generation: Selects sgRNAs to efficiently generate gene deletions, as demonstrated in Drosophila Ythdc1 and Ythdf.
• Homologous recombination: Improves efficiency of gene replacements by optimizing Cas9 cleavage activity.
• m6A research: Targets genes that bind to N6 methylated adenosines (m6A) in mRNA.

Methodology:

In vitro assays were used to determine intrinsic molecular parameters for maximal sgRNA activity, followed by comparison of over 10 data sets to identify design constraints.