Attachment site, not linker length, bounds tethered base editor windows
- 1School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
Abstract
Base editors act on the DNA strand displaced within an R-loop, and the set of positions they convert, the activity window, has been engineered for a decade on the assumption that linker length and attachment geometry determine it. We built a geometric model that predicts where a tethered deaminase acts from linker statistics, steric exclusion, and R-loop geometry alone; fitted three parameters to two previously reported profiles, held them fixed, and scored predictions against 50 architectures from seven studies, with each substrate coordinate withheld. Varying the contour length by a factor of 16 does not shift the predicted window at all, whereas changing the attachment site does: across 185 buildable single-linker designs at thirteen attachment sites, the predicted peak never leaves protospacer positions 3 to 12, positions 1, 2 and 13 to 20 are reached by no design, and transfer to Cas12a fails by five to six nucleotides in a way that localizes to the fusion junction rather than to reach, sterics or substrate. Tether geometry, therefore, bounds where a fused deaminase can act without predicting where it does so, making attachment site rather than linker length the effective design variable.
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BibTeX
@misc{ali2026attachment,
title = {{Attachment site, not linker length, bounds tethered base editor windows}},
author = {A. A. Mahaboob Ali and E. J. R. Nelson},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.16.751980},
url = {https://www.biorxiv.org/content/10.64898/2026.09.16.751980v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Attachment site, not linker length, bounds tethered base editor windows
AU - A. A. Mahaboob Ali
AU - E. J. R. Nelson
PY - 2026
DA - 2026/09/16
PB - bioRxiv
DO - 10.64898/2026.09.16.751980
UR - https://www.biorxiv.org/content/10.64898/2026.09.16.751980v1
AB - Base editors act on the DNA strand displaced within an R-loop, and the set of positions they convert, the activity window, has been engineered for a decade on the assumption that linker length and attachment geometry determine it. We built a geometric model that predicts where a tethered deaminase acts from linker statistics, steric exclusion, and R-loop geometry alone; fitted three parameters to two previously reported profiles, held them fixed, and scored predictions against 50 architectures from seven studies, with each substrate coordinate withheld. Varying the contour length by a factor of 16 does not shift the predicted window at all, whereas changing the attachment site does: across 185 buildable single-linker designs at thirteen attachment sites, the predicted peak never leaves protospacer positions 3 to 12, positions 1, 2 and 13 to 20 are reached by no design, and transfer to Cas12a fails by five to six nucleotides in a way that localizes to the fusion junction rather than to reach, sterics or substrate. Tether geometry, therefore, bounds where a fused deaminase can act without predicting where it does so, making attachment site rather than linker length the effective design variable.
ER -