RNA Lassos

SomaGenics’ proprietary Lasso has two functional moieties. The antisense sequence is easily customizable and is sensitive to single nucleotide mismatches. The universal hairpin ribozyme moiety serves two functions: first, it acts to generate the mature Lasso from longer RNAs by self-processing, allowing production by in vitro transcription; and second, it substantially improves the performance of the probe through circularization and other mechanisms.

Lasso schematics
The RNA Lasso Hybridization Probe

Current detection methods that require nucleic acid hybridization have a trade-off between sensitivity and specificity.

Lasso Probes

Specific detection of HCV genotypes with SomaGenics' Lasso probes. Note absence of cross-reaction.

  • Long probes (≥60 nucleotides) provide good efficacy of hybridization but have poor sequence specificity.
  • Short probes (<25 nucleotides) provide higher sequence-specificity but lower efficacy of hybridization than long probes.

The compromise between efficacy and specificity is never ideal and is in large part responsible for the significant variability in output that plagues the use of microarray and other hybridization-based assays.  While the diagnostics industry has focused on improvements in probe immobilization and data analysis, there is a need for improvements in probe design that addresses the specificity-sensitivity tradeoff.   SomaGenics has developed the RNA lasso detection platform to fulfill this need.


Advantages of SomaGenics' Lasso Technology

Lassos are an ideal combination of efficiency, sensitivity and specificity

  • Match or exceed the hybridization kinetics of long polynucleotide probes
  • Match or exceed the sequence-specificity of short oligonucleotide probes
  • Match or exceed the sensitivity (signal-to-noise ratio) of ordinary probes
  • Form strong complexes with long RNA targets that are more stable than ordinary RNA-RNA and RNA-DNA duplexes
    • Stable under PAGE with 8M urea
    • Can efficiently hybridize with structured ssRNA and dsDNA targets
  • Circular structure enhances the sequence-specificity and efficiency of hybridization
  • DNA and RNA target capture and enrichment for selective deep sequencing

References

  1. Dallas, A., Balatskaya, S.V., Kuo, T-C., Vlassov, A.V., Kaspar, R.L., Kisich, K., Kazakov, S.A., Johnston, B.H. (2008) Hairpin ribozyme-antisense RNA derivatives act as molecular Lassos. Nucleic Acids Res. 36(21):6752-66; Epub Oct 25, 2008. PMID 18953032
  2. S. A. Kazakov, S. V. Balatskaya, and B. H. Johnston (2006)  Ligation of the hairpin ribozyme in cis induced by freezing and dehydration. RNA 12: 446-456. PMID 16495237
  3. S. A Kazakov and B. H. Johnston (2008) Development of gene profile-responsive antisense agents.  In Gene Profiles in Drug Design, B. A Lidbury and S. Mahalingam, eds., CRC Press, Boca Rotan, FL.