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siAbasic: a comprehensive database for potent siRNA-6Ø sequences without off-target effects.
Jongyeun Park1, Seung Hyun Ahn1, Kwang Moon Cho1
1Department of Life Sciences, Korea University, Seoul, Korea.
Database : the Journal of Biological Databases and Curation
|October 16, 2018
Summary
Small interfering RNA (siRNA) modifications eliminate off-target gene silencing. A new database, siAbasic, identifies potent siRNA sequences with improved on-target efficiency for research and clinical use.
Area of Science:
- Molecular Biology
- Bioinformatics
- RNA Interference
Background:
- Small interfering RNA (siRNA) is crucial for gene silencing but often causes unintended off-target effects due to microRNA (miRNA)-like activity.
- Modifying siRNA by introducing an abasic nucleotide at position 6 (siRNA-6Ø) can eliminate off-target repression by destabilizing transitional nucleation.
- However, the on-target efficiency of siRNA-6Ø varies, necessitating a deeper understanding of the principles governing its effectiveness.
Purpose of the Study:
- To identify the key principles that determine the on-target efficiency of siRNA-6Ø.
- To develop a bioinformatics tool for predicting potent siRNA-6Ø sequences with minimal off-target effects.
- To provide a resource for selecting effective siRNA-6Ø sequences for experimental and clinical applications.
Main Methods:
- Analysis of miRNA-target interactions using Ago HITS-CLIP data to correlate transitional nucleation stability with RNA interference target affinity.
- Interrogation of siRNA screening efficiency, experimental data, and conserved miRNA sequences to determine the optimal free energy range for transitional nucleation (ΔG[2:5]) in siRNA-6Ø.
- Development of the 'siAbasic' database incorporating factors like location, GC content, nucleotide stretches, SNPs, and repetitive elements to predict potent siRNA-6Ø sequences.
Main Results:
- The stability of transitional nucleation (positions 2-6) in siRNA-6Ø is critical for on-target activity.
- An optimal free energy range for transitional nucleation (positions 2-5) of -6 to -3.5 kcal/mol is required for effective on-target activity in siRNA-6Ø.
- The 'siAbasic' database successfully identifies potent siRNA-6Ø sequences for over 95% of human and mouse genes, with experimental validation confirming their therapeutic potential.
Conclusions:
- siRNA-6Ø modifications effectively eliminate off-target effects while maintaining high on-target activity.
- The siAbasic database provides a valuable resource for selecting potent and specific siRNA-6Ø sequences, crucial for advancing RNA interference-based therapeutics.
- This work establishes a framework for designing highly efficient and specific siRNA sequences for both research and clinical applications.
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