Thermodynamic criteria for high hit rate antisense oligonucleotide design.

Antisense oligonucleotides are used for therapeutic applications and in functional genomic studies. In practice, however, many of the oligonucleotides complementary to an mRNA have little or no antisense activity. Theoretical strategies to improve the 'hit rate' in antisense screens will reduce the cost of discovery and may lead to identification of antisense oligonucleotides with increased potency. Statistical analysis performed on data collected from more than 1000 experiments with phosphorothioate-modified oligonucleotides revealed that the oligo-probes, which form stable duplexes with RNA (DeltaG(o)37 < or = -30 kcal/mol) and have small self-interaction potential, are more frequently efficient than molecules that form less stable oligonucleotide-RNA hybrids or more stable self-structures. To achieve optimal statistical preference, the values for self-interaction should be (DeltaG(o)37) > or = -8 kcal/mol for inter-oligonucleotide pairing and (DeltaG(o)37) > or = -1.1 kcal/mol for intra-molecular pairing. Selection of oligonucleotides with these thermodynamic values in the analyzed experiments would have increased the 'hit rate' by as much as 6-fold.

[1]  A D Tsodikov,et al.  Thermodynamic calculations and statistical correlations for oligo-probes design. , 2003, Nucleic acids research.

[2]  C. Lawrence,et al.  Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. , 2001, Nucleic acids research.

[3]  G Sczakiel,et al.  Computer-aided calculation of the local folding potential of target RNA and its use for ribozyme design. , 1997, Methods in molecular biology.

[4]  N. Sugimoto,et al.  Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. , 1995, Biochemistry.

[5]  J. SantaLucia,et al.  Thermodynamics and NMR of internal G.T mismatches in DNA. , 1997, Biochemistry.

[6]  G Sczakiel,et al.  Theoretical and experimental approaches to design effective antisense oligonucleotides. , 2000, Frontiers in bioscience : a journal and virtual library.

[7]  J. SantaLucia,et al.  Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.

[8]  D. Turner,et al.  Predicting oligonucleotide affinity to nucleic acid targets. , 1999, RNA.

[9]  G Sczakiel,et al.  A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability. , 1999, Nucleic acids research.

[10]  Volker Patzel,et al.  RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts , 2000, Nucleic Acids Res..

[11]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[12]  D. Turner,et al.  Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.

[13]  Olga V. Matveeva,et al.  ODNBase-a web database for antisense oligonucleotide effectiveness studies , 2000, Bioinform..

[14]  Volker Patzel,et al.  Theoretical design of antisense genes with statistically increased efficacy , 2000, Nucleic Acids Res..

[15]  Harold R Garner,et al.  Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts. , 2003, Nucleic acids research.