Figure 2
The distribution of Drexel gRNAs across the HIV-1 LTR. (A) The first 20 nucleotides of a gRNA bind to its complementary target sequence with variable tolerance to mismatches at different positions. Positions distal from the PAM have a higher tolerance to mismatches than proximal positions as indicated by the penalty score. The position-specific penalty score associated with mismatches between a gRNA and its target site was previously defined by Hsu et al. and others19,60. (B) The chart contains the sequence of the top 10 Drexel gRNAs (D-LTR) predicted to have broad-spectrum activity against diverse HIV-1 LTRs and their location within the HIV-1 HXB2 reference genome. The PAM indicates the direction of gRNA targeting. *Temple LTR-A, B, C, and D gRNA sequences (now referred to as T-LTR-237050, LTR-158980, LTR-158121 and LTR-119555) were obtained from Hu et al. for comparison24. Shuffle-LTR-268210 was used as a negative control. (C) The LTR schematic depicts the location of the Drexel gRNAs and the comparison gRNAs used in reference to the HXB2 LTR in relation to its structural features and common transcription factor binding sites.
