Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript.

Nawwaf Kharma (1) , Luc Varin (1) , Aida Abu-Baker (2) , Jonathan Ouellet (3) , Sabrine Najeh (3) , Mohammad-Reza Ehdaeivand (1) , Gabriel Belmonte (1) , Anas Ambri (1) , Guy Rouleau (2) , Jonathan Perreault (3)

1 Concordia University [Montreal]
2 Montreal Neurological Hospital
3 INRS-IAF - Institut Armand Frappier

We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemented procedure, which takes into consideration multiple objectives leading to a multi-objective ranking of the computer-generated ribozymes. Many ribozymes were assayed and validated, including four ribozymes targeting the transcript of a disease-causing gene (a mutant version of PABPN1). These four ribozymes were successfully tested in vitro and in vivo, for their ability to cleave the targeted transcript. The wet-lab positive results of the test are presented here demonstrating the real-world potential of both hammerhead ribozymes and RiboSoft. RiboSoft is freely available at the website http://ribosoft.fungalgenomics.ca/ribosoft/.

Domains: Life Sciences [q-bio]; Life Sciences [q-bio]; Genetics

Nawwaf Kharma, Luc Varin, Aida Abu-Baker, Jonathan Ouellet, Sabrine Najeh, et al.. Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript.. Nucleic Acids Research, 2016, 44 (4), pp.e39. ⟨10.1093/nar/gkv1111⟩. ⟨pasteur-01351212⟩