Glossary

siRNA

Small interfering RNA. Short double-stranded RNA molecules that can silence gene expression through the RNA interference (RNAi) pathway.

Off-target

Unintended binding of siRNA to mRNA sequences other than the intended target, which can cause unwanted gene silencing.

Thermodynamics

The study of energy changes in RNA folding and hybridization, crucial for predicting siRNA stability and effectiveness.

Thermodynamic Asymmetry

The stability difference between the 5’ and 3’ ends of an siRNA duplex. Proper asymmetry (less stable 5’ end on guide strand) promotes correct guide strand selection into RISC. Based on research by Khvorova et al. (2003) and others showing this is critical for siRNA functionality.

Asymmetry Score

A numerical measure (0-1) of thermodynamic asymmetry in siRNA duplexes. Higher scores indicate better asymmetry for guide strand incorporation into RISC. Calculated from the free energy difference between duplex ends.

Paired Fraction

The fraction of nucleotides in the siRNA guide strand that are paired with the passenger strand in the predicted secondary structure. Values of 0.5-0.7 are optimal for effective RISC loading.

MFE

Minimum Free Energy. The free energy of the most stable RNA secondary structure. Optimal values for siRNA are -2 to -8 kcal/mol for effective RISC processing.

Duplex Stability

The total free energy change (ΔG) for siRNA duplex formation, measured in kcal/mol. Optimal range is -15 to -25 kcal/mol for balanced stability and RISC loading.

Delta DG End

The difference in stability between the 3’ and 5’ ends of the siRNA duplex (ΔG₃’ - ΔG₅’). Positive values (+2 to +6 kcal/mol) indicate proper asymmetry for guide strand selection.

RISC

RNA-Induced Silencing Complex. The protein complex that incorporates siRNA and uses it to cleave complementary mRNA.

Guide strand

The strand of siRNA that is incorporated into RISC and guides target recognition.

Passenger strand

The strand of siRNA that is typically degraded during RISC loading.

Seed region

Nucleotides 2-8 of the siRNA guide strand, critical for target recognition.

ORF

Open Reading Frame. A sequence of DNA or RNA that can be translated into protein.

GC content

The percentage of guanine and cytosine nucleotides in a sequence, affecting stability.

Tm

Melting temperature. The temperature at which half of RNA duplexes dissociate.

Vienna RNA

Software package for RNA secondary structure prediction and thermodynamic analysis.

NCBI

National Center for Biotechnology Information. Database of genetic sequences.

Ensembl

Genome database project providing gene annotations and comparative genomics.

Nextflow

Workflow management system for computational pipelines.

BLAST

Basic Local Alignment Search Tool for sequence similarity searches.