Brief reports

Analysis by siRNA_profile program displays novel thermodynamic characteristics of highly functional siRNA molecules

Pirkko Muhonen¹ , Ranga N Parthasarathy² , Anthony J Janckila² , Kalman G Büki¹ and H Kalervo Väänänen¹

¹  Institute of Biomedicine, Department of Anatomy, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland

²  Veterans Affairs Medical Center, and University of Louisville, Louisville, KY, USA

author email corresponding author email

Source Code for Biology and Medicine 2008, 3:8doi:10.1186/1751-0473-3-8

Published:	21 May 2008

Abstract

Objective

Here we report the improved results of a new siRNA design program and analysis tool called siRNA_profile that reveals an additional criterion for bioinformatic search of highly functional siRNA sequences.

Methods

We retrospectively analysed over 2400 siRNA sequences from 34 genes and with known efficacies to categorize factors that differentiate highly, moderately and non-functional siRNA sequences in more detail. We tested the biological relevance of siRNA_profile in CHO cells stably expressing human TRACP.

Results

The highly functional siRNA molecules exhibited lower overall stabilities than non-functional siRNAs after taking into consideration all the nucleotides from 5'-terminus to the 3'-terminus along the siRNA molecule, in addition to the 5'-section of the antisense strand and the region between 9–14 nucleotides as previously has been acknowledged. Comparison of the siRNA_profile program to five other programs resulted in a wide range of selected siRNA sequences with diverse gene silencing capacities, even when the target was only 197 nucleotides long. Six siRNA design programs selected 24 different siRNA sequences, and only 6 of them were selected by two or more programs. The other 18 sequences were individually selected by these six programs.

Conclusion

Low general stability of dsRNA plays a significant role in the RNAi pathway and is a recommended criterion to consider, in addition to 5'-instability, internal instability, nucleotide preferences and target mRNA position, when designing highly efficient siRNAs.