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Image Search Results


( A ) Computational pipeline to identify vrRNA targeting rules. Four possible non-contiguous recognition patterns where vrRNA’s GGY/NN motifs recognizes NN (0 nt skip), xNN (1 nt skip), xxNN (2 nt skip), or xxxNN (3 nt skip) were tested. ( B ) NN match frequency distributions for each skip rule. Each alignment to the E. coli pan-genome is scored by the percentage of matching vrRNA NN positions (rightward shift indicates higher match quality). (C) VIPR targeting mechanism. Every NN position of vrRNA base-pairs with the target using the 1 nt skip rule. The orange base corresponds to the “skip base”. (D) In vitro competitive binding assay with SUSP1 VIPR (Vipr-vrRNA ribonucleoprotein) using different skip rule substrates (fluorescein-labeled; FAM) and salmon sperm competitor DNA. The competitor to substrate ratio is 0, 1, 2, and 10 fold excess by weight. (E) VIPR mediated green fluorescent protein (GFP) repression assay. Empt vector (EV) was used as negative control. (F) GFP repression assay results with reprogrammed vrRNAs.

Journal: bioRxiv

Article Title: A Noncontiguous Code for RNA-Guided DNA Recognition Preceded CRISPR

doi: 10.64898/2026.04.26.720920

Figure Lengend Snippet: ( A ) Computational pipeline to identify vrRNA targeting rules. Four possible non-contiguous recognition patterns where vrRNA’s GGY/NN motifs recognizes NN (0 nt skip), xNN (1 nt skip), xxNN (2 nt skip), or xxxNN (3 nt skip) were tested. ( B ) NN match frequency distributions for each skip rule. Each alignment to the E. coli pan-genome is scored by the percentage of matching vrRNA NN positions (rightward shift indicates higher match quality). (C) VIPR targeting mechanism. Every NN position of vrRNA base-pairs with the target using the 1 nt skip rule. The orange base corresponds to the “skip base”. (D) In vitro competitive binding assay with SUSP1 VIPR (Vipr-vrRNA ribonucleoprotein) using different skip rule substrates (fluorescein-labeled; FAM) and salmon sperm competitor DNA. The competitor to substrate ratio is 0, 1, 2, and 10 fold excess by weight. (E) VIPR mediated green fluorescent protein (GFP) repression assay. Empt vector (EV) was used as negative control. (F) GFP repression assay results with reprogrammed vrRNAs.

Article Snippet: 1 μΜ of purified SUSP1 VIPR RNP was incubated with 1 μΜ of FAM-labeled target dsDNA and purified salmon sperm competitor DNA (10mg/mL, Invitrogen) in 50mM HEPES (pH 6.8), 100mM KCl, 5mM MgCL 2 , 0.1% glycerol (v/v), and 1mM TCEP.

Techniques: In Vitro, Competitive Binding Assay, Labeling, Plasmid Preparation, Negative Control

Diagrams of the different skip rule patterns tested (top). Fluorescein (FAM) channel imaging of 12% native PAGE gel depicting SUSP1 VIPR RNP binding to different skip rule patterned DNA target in a competitive binding assay. Salmon sperm DNA was supplied as a competitor substrate at a ratio of 0, 1, 2, and 10 fold excess by weight compared to the FAM labeled substrate.

Journal: bioRxiv

Article Title: A Noncontiguous Code for RNA-Guided DNA Recognition Preceded CRISPR

doi: 10.64898/2026.04.26.720920

Figure Lengend Snippet: Diagrams of the different skip rule patterns tested (top). Fluorescein (FAM) channel imaging of 12% native PAGE gel depicting SUSP1 VIPR RNP binding to different skip rule patterned DNA target in a competitive binding assay. Salmon sperm DNA was supplied as a competitor substrate at a ratio of 0, 1, 2, and 10 fold excess by weight compared to the FAM labeled substrate.

Article Snippet: 1 μΜ of purified SUSP1 VIPR RNP was incubated with 1 μΜ of FAM-labeled target dsDNA and purified salmon sperm competitor DNA (10mg/mL, Invitrogen) in 50mM HEPES (pH 6.8), 100mM KCl, 5mM MgCL 2 , 0.1% glycerol (v/v), and 1mM TCEP.

Techniques: Imaging, Clear Native PAGE, Binding Assay, Competitive Binding Assay, Labeling