bridgernadesigner 0.0.1

Software package to design bridge RNAs as described by Durrant & Perry et al. 2024

BridgeRNADesigner

A command line interface for designing Bridge RNAs for Bridge Editing. Accompanies the paper "Bridge RNAs direct modular and programmable recombination of target and donor DNA" by Durrant & Perry et al. 2024.

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.

brna-design --target ATCGGGCCTACGCA --donor ACAGTATCTTGTAT

Example output:

# STOCKHOLM 1.0
BridgeRNA_tgt_ATCGGGCCTACGCA_dnr_ACAGTATCTTGTAT     AGTGCAGAGAAAATCGGCCAGTTTTCTCTGCCTGCAGTCCGCATGCCGTATCGGGCCTTGGGTTCTAACCTGTTGCGTAGATTTATGCAGCGGACTGCCTTTCTCCCAAAGTGATAAACCGGACAGTATCATGGACCGGTTTTCCCGGTAATCCGTATTTACAAGGCTGGTTTCACT
#=GC bRNA_template                                  AGTGCAGAGAAAATCGGCCAGTTTTCTCTGCCTGCAGTCCGCATGCCGTNNNNNNNNNTGGGTTCTAACCTGTNNNNNNNNNTTATGCAGCGGACTGCCTTTCTCCCAAAGTGATAAACCGGNNNNNNNNATGGACCGGTTTTCCCGGTAATCCGTNNTTNNNNNNNTGGTTTCACT
#=GC guides                                         .................................................LLLLLLLCC...............RRRRRCCHH........................................lllllllc..........................rr..rrrcchh..........
#=GC SS                                             ((.(((((((((((......)))))))))))))(((((((((.(((.............<(((.<>.)))>...............))))))))))))...........((((...<(((..........<.(((((((.....)))))...))....>.........)))>.))))
//

This should run very quickly on a Mac or Linux machine. The code can also automatically generate annealing oligos in FASTA format:

brna-design --target ATCGGGCCTACGCA --donor ACAGTATCTTGTAT -of fasta --include-annealing-oligos

Output:

>BridgeRNA_tgt_ATCGGGCCTACGCA_dnr_ACAGTATCTTGTAT
AGTGCAGAGAAAATCGGCCAGTTTTCTCTGCCTGCAGTCCGCATGCCGTATCGGGCCTTGGGTTCTAACCTGTTGCGTAGATTTATGCAGCGGACTGCCTTTCTCCCAAAGTGATAAACCGGACAGTATCATGGACCGGTTTTCCCGGTAATCCGTATTTACAAGGCTGGTTTCACT
>BridgeRNA_tgt_ATCGGGCCTACGCA_dnr_ACAGTATCTTGTAT_oligo_anneal_fiveprime_stem_loop_top
TAGCAGTGCAGAGAAAATCGGCCAGTTTTCTCTGCCTGCAGTCCGCATG
>BridgeRNA_tgt_ATCGGGCCTACGCA_dnr_ACAGTATCTTGTAT_oligo_anneal_fiveprime_stem_loop_btm
ACGGCATGCGGACTGCAGGCAGAGAAAACTGGCCGATTTTCTCTGCACT
>BridgeRNA_tgt_ATCGGGCCTACGCA_dnr_ACAGTATCTTGTAT_oligo_anneal_tbl_top
CCGTATCGGGCCTTGGGTTCTAACCTGTTGCGTAGATTTATGCAGCGGACTGCCTTTCTC
>BridgeRNA_tgt_ATCGGGCCTACGCA_dnr_ACAGTATCTTGTAT_oligo_anneal_tbl_btm
TTGGGAGAAAGGCAGTCCGCTGCATAAATCTACGCAACAGGTTAGAACCCAAGGCCCGAT
>BridgeRNA_tgt_ATCGGGCCTACGCA_dnr_ACAGTATCTTGTAT_oligo_anneal_dbl_top
CCAAAGTGATAAACCGGACAGTATCATGGACCGGTTTTCCCGGTAATCCGTATTTACAAGGCTGGTTTCACT
>BridgeRNA_tgt_ATCGGGCCTACGCA_dnr_ACAGTATCTTGTAT_oligo_anneal_dbl_btm
GGCCAGTGAAACCAGCCTTGTAAATACGGATTACCGGGAAAACCGGTCCATGATACTGTCCGGTTTATCACT

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 our paper if you use any aspect of this code in your work.