Nearest-neighbor effects modulate loxP spacer DNA chemical shifts and guide oligonucleotide design for NMR studies

Cre recombinase catalyzes site-specific DNA recombination at pseudo-palindromic loxP sites through two rounds of strand cleavage, exchange, and religation. Cre is a potential gene editing tool of interest due its lack of requirements for external energy sources or host factors, as well as the fact that it does not generate potentially cytotoxic double-stranded DNA breaks. However, broader applications of Cre in editing noncanonical target sequences requires a deeper understanding of the DNA features that enable target site selection and efficient recombination. Although Cre recombines loxP DNA in a specific and ordered fashion, it makes few direct contacts to the loxP spacer, the region where recombination occurs. Furthermore, little is known about the structural and dynamic features of the loxP spacer that make it a suitable target for Cre. To enable NMR spectroscopic studies of the spacer, we have aimed to identify a fragment of the 34-bp loxP site that retains the structural features of the spacer while minimizing the spectral crowding and line-broadening seen in longer oligonucleotides. We report sequential backbone resonance assignments for loxP oligonucleotides of varying lengths and evaluate chemical shift differences, Δδ, between the oligos. Analysis of flanking sequence effects and mutations on spacer chemical shifts indicates that nearest-neighbor and next-nearest-neighbor effects dominate the chemical environment experienced by the spacer. We have identified a 16-bp oligonucleotide that adequately preserves the structural environment of the spacer, setting the stage for NMR-based structure determination and dynamics investigations.