Fig. 1

Lox biology and Lox barcode cassette. a Lox DNA sequences. Lox sites are composed of two 13 bp palindromic Cre binding sites and an 8 bp core (original LoxP sequence shown). Asymmetric cleavage sites in the core are indicated by arrows. b Cre mediated site-specific excision and inversion of a sequence with a minimum of 82 bp between two Lox sites on the same chromosome [38]. If Lox sites are oriented in the same direction, productive recombination excises the sequence, while if they are oriented in opposite direction the sequence is inverted (i.e., the reverse complement). c An alternating Lox cassette with 13 elements of size 7 bp. To illustrate how barcodes are generated, two excision and one inversion event are shown that create from the initial cassette a size-stable barcode with three random elements. Pairs of interacting Lox sites are indicated by a, b, and c. Elements affected by recombination have colored background. The barcode with three elements is size-stable as Lox sites oriented in the same direction (arrows) are closer than the minimal Lox interaction distance of 82 bp, precluding further excision. d Four concatenated alternating Lox cassettes of length 13 elements each with poorly-interacting Lox site variants [41] result in a code diversity greater than 10¹²