BridgeRNADesigner

A command line interface for designing bridge RNAs for bridge editing. Accompanies the papers "Bridge RNAs direct modular and programmable recombination of target and donor DNA", Durrant & Perry et al. (2024), and "Megabase-scale human genome rearrangement with programmable bridge recombinases", Perry et al. (2025).

Dependencies

• Tested on python 3.8
• Tested on Linux and Mac

Installation

pip install bridgernadesigner

Usage

Command to design a bridge RNA for a given target and donor sequence, and a bridge RNA scaffold.

brna-design --target ATCAGGCCTACGTC --donor ACAGTATCTTGTAT --scaffold ISCro4_enhanced

Example output:

>BridgeRNA_tgt_ATCAGGCCTACGTC_dnr_ACAGTATCTTGTAT_scaffold_ISCro4_enhanced
AGTGCAGGGAGAACCGGCCAGTTCTCTCTGCCATGCGGTCCGCATGCCGTATCAGGCCTTGGGCTAATAACCCGTGACGTAGATTGGCAGCGGACCGCGCCGTTCTCCACAAGTGACAAACCGGACAGTATCATGGACCGGTTTTCCCGGTAATCCGCATTCACAAGGCTGGTCTCACTTGTGGAGAACG
>BridgeRNA_tgt_ATCAGGCCTACGTC_dnr_ACAGTATCTTGTAT_scaffold_ISCro4_enhanced_split_tbl
AGTGCAGGGAGAACCGGCCAGTTCTCTCTGCCATGCGGTCCGCATGCCGTATCAGGCCTTGGGCTAATAACCCGTGACGTAGATTGGCAGCGGACCGC
>BridgeRNA_tgt_ATCAGGCCTACGTC_dnr_ACAGTATCTTGTAT_scaffold_ISCro4_enhanced_split_dbl
CGTTCTCCACAAGTGACAAACCGGACAGTATCATGGACCGGTTTTCCCGGTAATCCGCATTCACAAGGCTGGTCTCACTTGTGGAGAACG

This should run very quickly on a Mac or Linux machine. There is also an option to output the sequence in Stockholm format with multiple tracks.

brna-design --target ATCAGGCCTACGTC --donor ACAGTATCTTGTAT --scaffold ISCro4_enhanced -of stockholm

# STOCKHOLM 1.0
BridgeRNA_tgt_ATCAGGCCTACGTC_dnr_ACAGTATCTTGTAT_scaffold_ISCro4_enhanced     AGTGCAGGGAGAACCGGCCAGTTCTCTCTGCCATGCGGTCCGCATGCCGTATCAGGCCTTGGGCTAATAACCCGTGACGTAGATTGGCAGCGGACCGCGCCGTTCTCCACAAGTGACAAACCGGACAGTATCATGGACCGGTTTTCCCGGTAATCCGCATTCACAAGGCTGGTCTCACTTGTGGAGAACG
#=GC bRNA_template                                                           AGTGCAGGGAGAACCGGCCAGTTCTCTCTGCCATGCGGTCCGCATGCCGTNNNNNNNNNTGGGCTAATAACCCGTNNNNNNNNNTGGCAGCGGACCGCGCCGTTCTCCACAAGTGACAAACCGGNNNNNNNNATGGACCGGTTTTCCCGGTAATCCGCNNTCNNNNNNNTGGTCTCACTTGTGGAGAACG
#=GC guides                                                                  ..................................................LLLLLLLCC................RRRRRCCHH........................................lllllllc..........................rr..rrrcchh.....................
//

In the #=GC guides track, the L character indicates the programmable nucleotides of the LTG, the R character indicates the programmable nucleotides of the RTG, the C character indicates the guide nucleotides of the target core, the H character indicates the position of the programmable handshake guide nucleotides, the l character indicates the programmable nucleotides of the LDG, the r character indicates the programmable nucleotides of the RDG, the c character indicates the guide nucleotides of the donor core, and the h character indicates the position of the programmable handshake guide nucleotides.

Citation

Please cite the linked publications above if you use any aspect of this code in your work.