dsCheck

dsCheck evaluates off-target effects of long double-stranded RNAs in RNAi experiments by simulating Dicer-mediated cleavage into siRNA candidates and performing sensitive homology searches to identify and rank potential unintended target genes.

Key Features:

• Estimation of Off-Target Effects: Estimates off-target effects caused by long dsRNAs by modeling potential siRNAs generated from the input sequence.
• Simulation of Dicer Processing: Simulates Dicer cleavage of long dsRNA into short-interfering RNA (siRNA) cocktails to reflect possible processed products.
• Homology Search Algorithm: Uses a homology search algorithm that examines individual 19 nucleotide (nt) substrings from dsRNA sequences to identify significant similarity to non-target genes.
• Potential Off-Target Gene Listing and Ranking: Generates and ranks a list of potential off-target gene candidates by likelihood of siRNA-mediated interaction.
• Verification of Designed dsRNAs: Verifies specificity of existing dsRNA sequences by identifying potential unintended targets.
• Design of Off-Target-Minimized dsRNAs: Enables design of new dsRNA sequences with minimized predicted off-target effects.

Scientific Applications:

• RNAi-based Functional Genomics: Supports assessment of gene knockdown specificity in RNAi experiments to improve interpretation of functional genomics studies.
• dsRNA Design and Validation: Assists in verifying and designing dsRNA reagents with reduced off-target potential for experimental use.
• Molecular Biology, Genetics, and Biotechnology: Facilitates selection and validation of gene-silencing reagents across molecular biology, genetics, and biotechnology applications.

Methodology:

Input nucleotide sequences are processed by simulating Dicer-mediated cleavage to generate siRNA candidates; these candidates are subjected to a sensitive homology search of individual 19 nt substrings using the tool's algorithm, and resulting potential off-target interactions are ranked and listed by likelihood.